Trajectory analysis¶
This example shows how to compute interactions for a trajectory performed using NAMD software for a small protein tyrosine phosphatase LMW-PTP in a complex with inhibitor MES (PDB: 5KQM) and visualize the results using Matplotlib library and VMD program.
In the tutorial, we will use already prepared files for simulation (PDB and DCD file).
Parse trajectory¶
We start by parsing PDB and DCD files, which contain LMW-PTP protein structure (available as tutorial files). PDB file contains the coordinates of protein structure with water and counter ions. DCD file is a binary file that contains a short simulation computed in NAMD package (20 frames). The commands shown below are explained in Trajectory Analysis tutorial.
In [1]: PDBfile = '5kqm_all_sci.pdb'
In [2]: DCDfile = 'NAMD_D2_co100.dcd'
In [3]: atoms = parsePDB(PDBfile)
In [4]: dcd = Trajectory(DCDfile)
In [5]: dcd.link(atoms)
In [6]: dcd.setCoords(atoms)
@> 19321 atoms and 1 coordinate set(s) were parsed in 0.17s.
To compute hydrogen bonds for each frame of the simulation use
calcHydrogenBondsTrajectory() function:
In [7]: calcHydrogenBondsTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG101 P NH1_1516 <---> ASP98 P OD1_1463 2.0 33.1
@> HSE72 P NE2_1042 <---> ASN15 P OD1_165 2.6 34.8
@> GLN143 P NE2_2192 <---> GLU139 P OE2_2126 2.7 9.2
@> HSE66 P NE2_957 <---> GLU139 P OE1_2125 2.7 6.4
@> ARG40 P N_561 <---> LYS6 P O_37 2.7 17.1
@> ARG58 P N_813 <---> ASP56 P OD1_788 2.7 30.0
@> ALA45 P N_634 <---> ARG75 P O_1097 2.8 35.1
@> ASN53 P ND2_747 <---> GLU50 P OE1_708 2.8 18.2
@> ALA74 P N_1064 <---> ASN53 P O_751 2.8 21.3
@> ASP56 P N_780 <---> ILE16 P O_189 2.8 27.0
@> LYS110 P NZ_1667 <---> THR84 P O_1240 2.8 38.2
@> LEU116 P N_1758 <---> CYS90 P O_1342 2.8 15.0
@> SER103 P N_1546 <---> LEU99 P O_1485 2.8 29.1
@> ASN134 P N_2045 <---> ASP137 P OD2_2091 2.8 22.6
@> PHE152 P N_2321 <---> CYS148 P O_2275 2.8 8.3
@> ASN95 P N_1398 <---> ASP92 P OD1_1368 2.8 12.6
@> LYS6 P N_16 <---> ASN38 P O_536 2.8 25.0
@> ILE77 P N_1115 <---> ALA45 P O_643 2.8 12.2
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.8 27.7
@> LEU99 P N_1467 <---> ASN95 P O_1411 2.8 15.5
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.8 9.6
@> GLY52 P N_731 <---> ALA74 P O_1073 2.8 6.6
@> ASP32 P N_435 <---> LYS28 P O_385 2.8 8.8
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.8 17.7
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 21.7
@> ARG27 P N_340 <---> GLU23 P O_293 2.8 15.4
@> TYR142 P N_2159 <---> PHE138 P O_2113 2.9 14.2
@> GLY133 P N_2038 <---> PRO130 P O_1995 2.9 25.4
@> PHE26 P N_320 <---> ALA22 P O_278 2.9 4.9
@> ASN15 P ND2_166 <---> SER19 P OG_232 2.9 32.1
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.9 19.7
@> ARG75 P NH2_1093 <---> ASP42 P OD2_610 2.9 23.5
@> ARG97 P N_1431 <---> GLU93 P O_1386 2.9 22.2
@> ARG65 P NH2_941 <---> GLU139 P OE1_2125 2.9 32.3
@> VAL25 P N_304 <---> ILE21 P O_268 2.9 8.2
@> LEU153 P N_2341 <---> CYS149 P O_2286 2.9 12.5
@> SER7 P N_38 <---> ASP86 P OD2_1270 2.9 39.9
@> ASP86 P N_1261 <---> SER7 P OG_45 2.9 34.7
@> ARG58 P NH2_832 <---> TYR131 P O_2016 2.9 33.1
@> THR46 P N_644 <---> CYS12 P O_130 2.9 36.1
@> GLN144 P N_2197 <---> THR140 P O_2142 2.9 23.3
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.9 12.4
@> LEU89 P N_1313 <---> LEU9 P O_83 2.9 29.5
@> THR31 P N_421 <---> ARG27 P O_363 2.9 24.1
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.9 24.6
..
..
@> ARG40 P NH1_577 <---> THR84 P OG1_1233 2.9 8.4
@> ALA44 P N_624 <---> PHE10 P O_103 2.9 33.2
@> GLU154 P N_2360 <---> ARG150 P O_2310 3.0 22.6
@> VAL8 P N_49 <---> ARG40 P O_584 3.0 25.0
@> SER19 P N_225 <---> CYS12 P SG_127 3.3 8.0
@> PHE82 P N_1197 <---> LYS79 P O_1169 3.4 37.7
@> ASP81 P N_1185 <---> THR78 P OG1_1140 3.5 39.5
@> LYS102 P NZ_1540 <---> ASP98 P OD2_1464 3.5 26.1
@> ARG147 P NH2_2260 <---> GLN124 P OE1_1892 3.5 33.9
@> VAL106 P N_1588 <---> SER103 P O_1556 3.5 34.2
@> Number of detected hydrogen bonds: 124.
@> Frame: 1
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> LYS112 P NZ_1699 <---> GLU114 P OE1_1735 2.5 20.8
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.5 15.6
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.5 36.5
@> THR78 P OG1_1140 <---> ASP81 P OD2_1194 2.6 25.2
@> SER7 P OG_45 <---> ASP86 P OD2_1270 2.6 32.3
@> LYS102 P NZ_1540 <---> ASP98 P OD2_1464 2.6 18.6
@> LYS112 P NZ_1699 <---> HSE157 P OT1_2423 2.6 17.8
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 2.6 17.6
@> SER118 P OG_1791 <---> LEU115 P O_1757 2.7 25.6
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.7 6.4
@> GLN124 P N_1881 <---> ASP120 P OD1_1824 2.7 17.2
@> ARG147 P NH1_2257 <---> GLN124 P OE1_1892 2.7 11.8
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.7 14.6
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.7 23.9
@> TYR87 P OH_1286 <---> HSE157 P OT1_2423 2.7 11.6
@> SER43 P OG_620 <---> GLU23 P OE1_290 2.7 15.2
@> LYS28 P NZ_380 <---> ASP32 P OD1_443 2.7 3.6
@> LYS110 P NZ_1667 <---> ASP86 P OD1_1269 2.7 25.2
@> THR140 P OG1_2135 <---> SER136 P O_2081 2.7 5.2
@> LEU116 P N_1758 <---> CYS90 P O_1342 2.7 24.4
@> THR5 P OG1_8 <---> ASN38 P O_536 2.7 38.6
@> LYS64 P N_900 <---> GLN60 P O_860 2.7 26.8
@> ARG147 P NH1_2257 <---> ASP120 P OD2_1825 2.7 15.2
@> ARG27 P N_340 <---> GLU23 P O_293 2.7 21.9
@> TYR119 P OH_1808 <---> GLU114 P OE1_1735 2.7 15.9
@> ARG18 P NH1_217 <---> ILE127 P O_1954 2.8 16.0
@> SER103 P N_1546 <---> LEU99 P O_1485 2.8 13.6
@> LYS102 P N_1524 <---> ASP98 P O_1466 2.8 15.9
@> ARG58 P NH1_829 <---> GLY133 P O_2044 2.8 31.9
@> ARG75 P NH2_1093 <---> ASP42 P OD2_610 2.8 13.0
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.8 13.2
..
..
@> ILE127 P N_1936 <---> MET91 P O_1359 3.3 29.4
@> ASN104 P N_1557 <---> ASN100 P O_1499 3.4 12.6
@> GLN105 P N_1571 <---> ARG101 P O_1523 3.4 38.7
@> ARG147 P N_2241 <---> GLN143 P O_2196 3.4 10.9
@> ASP56 P N_780 <---> ILE16 P O_189 3.4 25.5
@> ASN95 P N_1398 <---> ASP92 P OD1_1368 3.5 32.5
@> HSE72 P NE2_1042 <---> ASN15 P OD1_165 3.5 7.1
@> VAL106 P N_1588 <---> LYS102 P O_1545 3.5 29.8
@> ILE21 P N_250 <---> CYS17 P O_200 3.5 34.9
@> LEU96 P N_1412 <---> ASP92 P O_1371 3.5 8.7
@> Number of detected hydrogen bonds: 123.
@> Frame: 2
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.5 4.9
@> THR31 P OG1_427 <---> ARG27 P O_363 2.5 5.5
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.6 8.2
@> LYS112 P NZ_1699 <---> HSE157 P OT1_2423 2.6 19.0
@> ARG75 P NH2_1093 <---> ASP42 P OD2_610 2.6 25.0
@> TYR119 P OH_1808 <---> GLU114 P OE2_1736 2.6 10.3
@> LYS102 P NZ_1540 <---> ASP98 P OD2_1464 2.6 7.9
@> TYR87 P OH_1286 <---> HSE157 P OT1_2423 2.7 14.1
@> LYS64 P N_900 <---> GLN60 P O_860 2.7 4.9
@> SER43 P OG_620 <---> GLU23 P OE1_290 2.7 8.6
@> THR78 P OG1_1140 <---> ASP81 P OD2_1194 2.7 6.5
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.7 25.0
@> SER118 P OG_1791 <---> LEU115 P O_1757 2.7 26.9
@> LYS28 P NZ_380 <---> ASP32 P OD2_444 2.7 13.9
@> THR84 P OG1_1233 <---> GLU80 P O_1184 2.7 13.4
@> LEU89 P N_1313 <---> LEU9 P O_83 2.8 11.8
@> ARG147 P NH1_2257 <---> GLN124 P OE1_1892 2.8 15.1
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.8 18.0
@> ILE35 P N_478 <---> VAL30 P O_420 2.8 20.7
@> PHE26 P N_320 <---> ALA22 P O_278 2.8 21.8
@> VAL11 P N_104 <---> LEU89 P O_1331 2.8 10.3
@> VAL25 P N_304 <---> ILE21 P O_268 2.8 9.2
@> SER7 P OG_45 <---> ASP86 P OD2_1270 2.8 29.4
@> HSE72 P NE2_1042 <---> ASN15 P OD1_165 2.8 37.1
@> ASN34 P N_464 <---> THR31 P O_434 2.8 19.7
@> LYS110 P N_1651 <---> PHE82 P O_1216 2.8 9.2
@> LYS110 P NZ_1667 <---> ASP86 P OD1_1269 2.8 13.5
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.8 8.0
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.8 14.9
@> VAL8 P N_49 <---> ARG40 P O_584 2.8 19.4
@> ARG18 P NH1_217 <---> ILE127 P O_1954 2.8 7.0
@> LYS155 P N_2375 <---> ALA151 P O_2320 2.8 15.1
@> HSE66 P NE2_957 <---> GLU139 P OE1_2125 2.8 28.9
@> ARG147 P NH1_2257 <---> ASP120 P OD2_1825 2.8 31.7
@> ARG97 P N_1431 <---> GLU93 P O_1386 2.8 15.2
@> LYS123 P N_1859 <---> ASP120 P OD1_1824 2.8 34.0
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.8 10.3
@> ASP86 P N_1261 <---> SER7 P OG_45 2.8 22.0
@> ARG65 P N_922 <---> SER61 P O_871 2.8 24.4
@> ILE127 P N_1936 <---> MET91 P O_1359 2.8 4.1
@> LYS112 P NZ_1699 <---> HSE157 P ND1_2414 2.9 14.0
@> GLY67 P N_963 <---> MET63 P O_899 2.9 38.6
@> SER103 P N_1546 <---> LEU99 P O_1485 2.9 17.1
@> LYS112 P NZ_1699 <---> GLU114 P OE2_1736 2.9 18.1
@> ARG75 P NE_1087 <---> ASP42 P OD2_610 2.9 38.3
@> ALA44 P N_624 <---> PHE10 P O_103 2.9 30.1
@> ILE68 P N_970 <---> MET63 P O_899 2.9 12.9
@> ARG58 P N_813 <---> ASP56 P OD1_788 2.9 21.1
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.9 26.3
@> ALA45 P N_634 <---> ARG75 P O_1097 2.9 27.7
..
..
@> HSE66 P N_946 <---> CYS62 P O_882 2.9 17.6
@> ASP32 P N_435 <---> LYS28 P O_385 3.0 20.4
@> VAL146 P N_2225 <---> TYR142 P O_2179 3.0 20.7
@> VAL106 P N_1588 <---> LYS102 P O_1545 3.0 10.6
@> ARG40 P N_561 <---> LYS6 P O_37 3.4 33.1
@> HSE157 P N_2407 <---> TYR119 P OH_1808 3.4 27.6
@> ARG65 P NH1_938 <---> GLU139 P OE1_2125 3.4 32.0
@> GLU114 P N_1724 <---> ILE88 P O_1312 3.5 13.0
@> ASP92 P N_1360 <---> ASN95 P OD1_1406 3.5 35.4
@> ASN15 P ND2_166 <---> SER43 P OG_620 3.5 33.3
@> Number of detected hydrogen bonds: 113.
..
..
@> Frame: 20
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG97 P NE_1444 <---> GLU93 P OE1_1383 2.5 12.5
@> SER19 P OG_232 <---> ASN15 P OD1_165 2.6 31.5
@> ARG27 P NH1_356 <---> GLU23 P OE1_290 2.6 19.1
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.6 21.5
@> GLN122 P NE2_1854 <---> ASP120 P OD2_1825 2.6 39.7
@> SER118 P OG_1791 <---> GLU114 P OE2_1736 2.6 24.5
@> ARG65 P NH1_938 <---> GLU139 P OE1_2125 2.7 6.1
@> ARG65 P NH2_941 <---> ASP135 P OD1_2067 2.7 15.6
@> SER43 P OG_620 <---> GLU23 P OE2_291 2.7 13.9
@> ARG75 P NE_1087 <---> ASP42 P OD1_609 2.7 26.5
@> ARG150 P NE_2300 <---> GLU154 P OE2_2372 2.7 4.9
@> VAL106 P N_1588 <---> LYS102 P O_1545 2.7 16.2
@> LYS28 P N_364 <---> ALA24 P O_303 2.7 38.8
@> HSE157 P NE2_2418 <---> PHE152 P O_2340 2.7 28.5
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.7 19.3
@> ARG97 P NH2_1450 <---> GLU93 P OE2_1384 2.7 15.8
@> ARG75 P NH2_1093 <---> ASP42 P OD1_609 2.7 30.5
@> ALA45 P N_634 <---> ARG75 P O_1097 2.7 22.3
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 2.7 19.2
@> THR31 P OG1_427 <---> ARG27 P O_363 2.7 13.1
@> ARG150 P NH2_2306 <---> GLU154 P OE1_2371 2.7 8.5
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.7 14.8
@> GLY67 P N_963 <---> MET63 P O_899 2.7 25.3
@> LEU89 P N_1313 <---> LEU9 P O_83 2.8 18.4
@> ARG101 P NH1_1516 <---> ASP98 P OD2_1464 2.8 11.5
@> ILE77 P N_1115 <---> ALA45 P O_643 2.8 39.9
@> LYS110 P N_1651 <---> PHE82 P O_1216 2.8 32.3
@> LEU29 P N_386 <---> VAL25 P O_319 2.8 5.4
@> ASN100 P N_1486 <---> LEU96 P O_1430 2.8 6.7
@> LYS102 P N_1524 <---> ASP98 P O_1466 2.8 4.9
@> THR78 P OG1_1140 <---> ASP81 P OD2_1194 2.8 10.5
@> VAL8 P N_49 <---> ARG40 P O_584 2.8 16.8
@> GLU154 P N_2360 <---> ARG150 P O_2310 2.8 15.1
@> LYS110 P NZ_1667 <---> ASP86 P OD2_1270 2.8 32.5
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.8 3.3
@> ILE35 P N_478 <---> VAL30 P O_420 2.8 7.9
@> ARG58 P NH1_829 <---> GLY133 P O_2044 2.8 34.3
@> GLN105 P N_1571 <---> ARG101 P O_1523 2.8 29.9
@> SER7 P N_38 <---> ASP86 P OD1_1269 2.8 10.5
@> ARG101 P NH2_1519 <---> ASP98 P OD1_1463 2.8 17.5
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 20.5
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.8 16.0
@> SER103 P OG_1553 <---> LEU99 P O_1485 2.9 21.4
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.9 6.7
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.9 7.9
..
..
@> ALA151 P N_2311 <---> ARG147 P O_2264 3.3 28.5
@> ILE88 P N_1294 <---> LYS112 P O_1704 3.3 8.1
@> CYS12 P N_120 <---> ALA44 P O_633 3.4 24.0
@> GLN124 P NE2_1893 <---> ILE126 P O_1935 3.4 3.3
@> ARG97 P N_1431 <---> GLU93 P O_1386 3.4 28.8
@> SER61 P N_861 <---> TYR57 P O_812 3.4 29.6
@> GLN122 P NE2_1854 <---> ASP120 P OD1_1824 3.5 17.2
@> Number of detected hydrogen bonds: 114.
Similarly, it can be done with other interaction types. Salt bridges
(residues with opposite changes) with calcSaltBridgesTrajectory():
In [8]: calcSaltBridgesTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating salt bridges.
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 2.8
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.9
@> ASP32 P OD1_443_444 <---> LYS28 P NZ_380 3.0
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 3.1
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.7
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 3.8
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.9
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 4.1
@> GLU114 P OE1_1735_1736 <---> LYS112 P NZ_1699 4.1
@> ASP120 P OD1_1824_1825 <---> ARG147 P NH1_2257_2260 4.2
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 4.2
@> HSE157 P NE2_2418 <---> GLU114 P OE1_1735_1736 4.4
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 4.6
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.6
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 5.0
@> Number of detected salt bridges: 16.
@> Frame: 1
@> Calculating salt bridges.
@> ASP32 P OD1_443_444 <---> LYS28 P NZ_380 2.6
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.6
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 2.8
@> GLU114 P OE1_1735_1736 <---> LYS112 P NZ_1699 3.1
@> HSE157 P NE2_2418 <---> GLU114 P OE1_1735_1736 3.2
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 3.3
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.4
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 3.4
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.5
@> ASP120 P OD1_1824_1825 <---> ARG147 P NH1_2257_2260 3.8
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.8
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 3.8
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 4.0
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.5
@> Number of detected salt bridges: 14.
@> Frame: 2
@> Calculating salt bridges.
@> GLU114 P OE1_1735_1736 <---> LYS112 P NZ_1699 2.6
@> ASP32 P OD1_443_444 <---> LYS28 P NZ_380 2.6
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 2.7
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.9
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.1
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.6
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 3.6
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 3.7
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 3.7
@> ASP120 P OD1_1824_1825 <---> ARG147 P NH1_2257_2260 3.8
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.9
@> HSE157 P NE2_2418 <---> GLU114 P OE1_1735_1736 4.2
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.3
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 4.6
@> ASP86 P OD1_1269_1270 <---> LYS6 P NZ_32 5.0
@> Number of detected salt bridges: 15.
..
..
@> Frame: 18
@> Calculating salt bridges.
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.6
@> ASP32 P OD1_443_444 <---> LYS28 P NZ_380 2.7
@> ASP135 P OD1_2067_2068 <---> ARG65 P NH1_938_941 2.8
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.0
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 3.4
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.6
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.6
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 4.2
@> ARG97 P NH1_1447_1450 <---> GLU93 P OE1_1383_1384 4.5
@> ARG150 P NH1_2303_2306 <---> GLU154 P OE1_2371_2372 4.5
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.5
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 4.7
@> Number of detected salt bridges: 13.
@> Frame: 19
@> Calculating salt bridges.
@> ASP135 P OD1_2067_2068 <---> ARG65 P NH1_938_941 2.7
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.9
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.1
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.3
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 3.7
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.7
@> ARG97 P NH1_1447_1450 <---> GLU93 P OE1_1383_1384 3.7
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 3.9
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 4.0
@> ARG150 P NH1_2303_2306 <---> GLU154 P OE1_2371_2372 4.2
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.6
@> Number of detected salt bridges: 12.
@> Frame: 20
@> Calculating salt bridges.
@> ASP135 P OD1_2067_2068 <---> ARG65 P NH1_938_941 2.5
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.7
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 2.8
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 3.4
@> ARG97 P NH1_1447_1450 <---> GLU93 P OE1_1383_1384 3.5
@> ARG150 P NH1_2303_2306 <---> GLU154 P OE1_2371_2372 3.7
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.7
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 4.0
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 4.0
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.4
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 4.7
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 4.8
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 5.0
@> Number of detected salt bridges: 14.
Repulsive Ionic Bonding using calcRepulsiveIonicBondingTrajectory() for residues with
the same charges:
In [9]: calcRepulsiveIonicBondingTrajectory(atoms, dcd, distA=7)
@> Frame: 0
@> Calculating repulsive ionic bonding.
@> LYS102 P NZ_1540 <---> ARG101 P NH1_1516_1519 4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Frame: 1
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 2
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 3
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 4
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 5
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 6
@> Calculating repulsive ionic bonding.
@> LYS102 P NZ_1540 <---> ARG101 P NH1_1516_1519 4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Frame: 7
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 8
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 9
@> Calculating repulsive ionic bonding.
@> LYS102 P NZ_1540 <---> ARG101 P NH1_1516_1519 4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Frame: 10
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
..
..
@> Frame: 20
@> Calculating repulsive ionic bonding.
@> ARG147 P NH1_2257_2260 <---> LYS123 P NZ_1875 4.5
@> Number of detected Repulsive Ionic Bonding interactions: 1.
Pi-Stacking interactions using calcPiStackingTrajectory():
In [10]: calcPiStackingTrajectory(atoms, dcd, distA=5)
@> Frame: 0
@> Calculating Pi stacking interactions.
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 3.9 162.1
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> TYR119 P 1802_1803_1805_1807_1810_1812 4.4 3.0
@> PHE26 P 327_328_330_332_334_336 <---> TRP39 P 549_550_551_553_555_557 4.8 75.5
@> TYR132 P 2024_2025_2027_2029_2032_2034 <---> TYR131 P 2003_2004_2006_2008_2011_2013 4.9 91.4
@> Number of detected Pi stacking interactions: 4.
@> Frame: 1
@> Calculating Pi stacking interactions.
@> PHE26 P 327_328_330_332_334_336 <---> TRP39 P 549_550_551_553_555_557 4.8 71.0
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 4.8 138.9
@> Number of detected Pi stacking interactions: 2.
@> Frame: 2
@> Calculating Pi stacking interactions.
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 3.6 174.2
@> Number of detected Pi stacking interactions: 1.
@> Frame: 3
@> Calculating Pi stacking interactions.
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 4.1 143.3
@> Number of detected Pi stacking interactions: 1.
@> Frame: 4
@> Calculating Pi stacking interactions.
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 4.3 137.5
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> PHE152 P 2328_2329_2331_2333_2335_2337 5.0 73.7
@> Number of detected Pi stacking interactions: 2.
..
..
@> Frame: 19
@> Calculating Pi stacking interactions.
@> TYR132 P 2024_2025_2027_2029_2032_2034 <---> TYR131 P 2003_2004_2006_2008_2011_2013 4.6 62.2
@> TYR119 P 1802_1803_1805_1807_1810_1812 <---> PHE152 P 2328_2329_2331_2333_2335_2337 4.9 60.8
@> Number of detected Pi stacking interactions: 2.
@> Frame: 20
@> Calculating Pi stacking interactions.
@> TYR119 P 1802_1803_1805_1807_1810_1812 <---> PHE152 P 2328_2329_2331_2333_2335_2337 4.7 125.5
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 4.8 165.0
@> TYR132 P 2024_2025_2027_2029_2032_2034 <---> TYR131 P 2003_2004_2006_2008_2011_2013 4.9 116.3
@> Number of detected Pi stacking interactions: 3.
Pi-Cation interactions using calcPiCationTrajectory():
In [11]: calcPiCationTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.5
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.8
@> Number of detected cation-pi interactions: 3.
@> Frame: 1
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 3.5
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.9
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 4.9
@> TYR131 P 2003_2004_2006_2008_2011_2013 <---> ARG58 P NH1_829_832 4.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 2
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 2.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.1
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.5
@> Number of detected cation-pi interactions: 3.
@> Frame: 3
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 2.6
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.6
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 3.8
@> Number of detected cation-pi interactions: 3.
@> Frame: 4
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.8
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS155 P NZ_2391 4.8
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.9
@> Number of detected cation-pi interactions: 4.
..
..
@> Frame: 19
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.9
@> Number of detected cation-pi interactions: 1.
@> Frame: 20
@> Calculating cation-Pi interactions.
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.0
@> Number of detected cation-pi interactions: 1.
Hydrophobic interactions using calcHydrophohicTrajectory():
In [12]: calcHydrophohicTrajectory(atoms, dcd)
@> Frame: 0
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@> ALA156 P CB_240114s <---> TYR87 P OH_1286 3.0 22.0
@> ALA24 P CB_29814s <---> MET63 P CE_894 3.3 5.2
@> ILE68 P CG2_97614s <---> MET63 P CE_894 3.3 52.4
@> TYR142 P CZ_217114s <---> VAL146 P CG2_2235 3.5 49.7
@> PHE10 P CD1_9214s <---> ALA22 P CB_273 3.5 31.2
@> LYS6 P CD_2614s <---> TRP39 P CZ2_555 3.5 68.7
@> PHE26 P CE2_33614s <---> VAL30 P CG1_411 3.6 21.1
@> ILE88 P CD_130714s <---> ALA111 P CB_1677 3.6 21.2
@> VAL11 P CG2_11414s <---> ILE88 P CG2_1300 3.6 9.3
@> VAL41 P CG2_59514s <---> PHE26 P CD2_334 3.6 16.6
@> PHE152 P CE1_233114s <---> ALA156 P CB_2401 3.7 17.5
@> LYS79 P CG_115514s <---> VAL106 P CG2_1598 3.7 25.1
@> LEU99 P CD2_148014s <---> ILE77 P CD_1128 3.7 12.0
@> PHE82 P CD1_120514s <---> ILE88 P CD_1307 3.7 17.6
@> LEU116 P CD2_177114s <---> ILE127 P CD_1949 3.7 17.4
@> VAL8 P CG1_5514s <---> PHE26 P CE2_336 3.7 12.1
@> LEU96 P CD1_142114s <---> ILE113 P CG2_1711 3.7 17.0
@> LEU9 P CD2_7814s <---> ILE77 P CD_1128 3.7 15.4
@> LEU89 P CD1_132214s <---> VAL8 P CG2_59 3.8 15.9
@> ILE126 P CD_193014s <---> LEU125 P CD1_1907 3.8 54.2
@> VAL141 P CG1_214914s <---> ILE127 P CG2_1942 3.9 11.5
@> MET91 P SD_135314s <---> ILE127 P CD_1949 3.9 35.9
@> ALA44 P CB_62814s <---> LEU9 P CD1_74 3.9 15.1
@> VAL25 P CG2_31414s <---> TYR142 P CE1_2169 3.9 12.0
@> ILE21 P CG2_25614s <---> MET63 P SD_893 4.0 20.8
@> LEU153 P CD1_235014s <---> TRP39 P NE1_547 4.0 9.4
@> PHE85 P CZ_125314s <---> LEU9 P CD1_74 4.0 32.1
@> ILE35 P CD_49114s <---> TRP39 P NE1_547 4.0 26.0
@> LEU29 P CD1_39514s <---> VAL25 P CG1_310 4.1 19.7
@> ALA74 P CB_106814s <---> ILE16 P CG2_177 4.1 6.7
@> ARG75 P CG_108114s <---> ALA44 P CB_628 4.1 36.2
@> ARG18 P CG_20814s <---> VAL141 P CG1_2149 4.1 20.3
@> LYS102 P CD_153414s <---> ILE77 P CG2_1121 4.1 17.5
@> TYR119 P CE1_180514s <---> LEU89 P CD2_1326 4.1 11.6
@> ARG40 P CG_56814s <---> PHE85 P CE2_1257 4.3 60.9
@> LYS28 P CG_37114s <---> ILE68 P CD_983 4.3 21.8
@> PHE138 P CD2_210814s <---> ILE21 P CD_263 4.3 6.6
@> TYR131 P CE1_200614s <---> ILE16 P CD_184 4.3 8.9
@> ARG58 P CG_82014s <---> PHE138 P CE1_2104 4.5 59.4
@> Number of detected hydrophobic interactions: 39.
@> Frame: 1
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@> MET63 P SD_89314s <---> TYR142 P CD1_2167 3.3 26.8
@> ALA24 P CB_29814s <---> MET63 P CE_894 3.4 7.1
@> VAL8 P CG2_5914s <---> PHE10 P CZ_96 3.4 27.8
@> LEU96 P CD1_142114s <---> ILE113 P CG2_1711 3.4 13.3
@> LEU116 P CD1_176714s <---> PHE10 P CE1_94 3.5 13.5
@> PHE82 P CZ_120914s <---> ILE77 P CD_1128 3.6 20.4
@> ILE68 P CD_98314s <---> TYR142 P OH_2172 3.6 27.4
@> PHE26 P CE2_33614s <---> VAL30 P CG1_411 3.6 28.1
@> ALA156 P CB_240114s <---> PHE152 P CD1_2329 3.6 24.5
@> VAL11 P CG2_11414s <---> ILE88 P CG2_1300 3.6 8.6
@> LYS102 P CD_153414s <---> ILE77 P CG2_1121 3.7 18.2
@> LEU99 P CD2_148014s <---> ILE77 P CD_1128 3.7 8.0
@> LEU153 P CD1_235014s <---> VAL30 P CG1_411 3.7 14.5
@> LEU9 P CD2_7814s <---> ILE77 P CD_1128 3.7 16.0
@> TRP39 P CD1_54514s <---> VAL30 P CG1_411 3.7 14.9
@> PHE138 P CD2_210814s <---> ILE21 P CD_263 3.8 15.8
@> TYR119 P OH_180814s <---> ALA156 P CB_2401 3.8 18.6
@> VAL146 P CG2_223514s <---> TYR142 P CZ_2171 3.8 40.5
@> VAL25 P CG2_31414s <---> TYR142 P CD1_2167 3.8 14.3
@> MET91 P CE_135414s <---> LEU116 P CD2_1771 3.8 19.1
@> ILE35 P CD_49114s <---> LEU153 P CD1_2350 3.9 17.2
@> VAL41 P CG2_59514s <---> PHE26 P CD2_334 3.9 21.9
@> ILE127 P CD_194914s <---> LEU116 P CD2_1771 3.9 11.7
@> LEU29 P CD1_39514s <---> VAL25 P CG1_310 3.9 25.1
@> ALA22 P CB_27314s <---> LEU116 P CD2_1771 4.0 7.3
@> ALA111 P CB_167714s <---> ILE88 P CD_1307 4.0 14.9
@> ARG75 P CG_108114s <---> ALA44 P CB_628 4.0 36.8
@> ILE126 P CD_193014s <---> LEU125 P CG_1905 4.0 53.2
@> VAL106 P CG2_159814s <---> PHE82 P CD2_1211 4.0 13.1
@> PHE85 P CZ_125314s <---> LEU9 P CD1_74 4.1 28.5
@> ARG40 P CG_56814s <---> PHE85 P CE2_1257 4.1 50.3
@> TYR87 P CD1_128114s <---> LEU89 P CD2_1326 4.2 14.7
@> LYS28 P CG_37114s <---> ILE68 P CG2_976 4.2 15.9
@> LYS79 P CG_115514s <---> VAL106 P CG2_1598 4.2 20.4
@> ARG18 P CG_20814s <---> VAL141 P CG1_2149 4.3 10.9
@> ARG58 P CG_82014s <---> PHE138 P CD1_2102 4.3 48.8
@> ALA74 P CB_106814s <---> ILE16 P CG2_177 4.4 4.3
@> ARG150 P CG_229414s <---> LEU29 P CD2_399 4.5 22.3
@> Number of detected hydrophobic interactions: 38.
..
..
@> Frame: 20
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@> LEU96 P CD1_142114s <---> ILE113 P CG2_1711 3.3 21.1
@> ILE88 P CD_130714s <---> PHE82 P CD2_1211 3.4 25.2
@> VAL11 P CG2_11414s <---> LEU99 P CD1_1476 3.4 11.5
@> MET63 P SD_89314s <---> TYR142 P CE1_2169 3.4 37.7
@> TRP39 P NE1_54714s <---> LEU153 P CD1_2350 3.4 19.2
@> ALA111 P CB_167714s <---> ILE88 P CD_1307 3.5 23.0
@> ILE35 P CD_49114s <---> LEU153 P CD1_2350 3.5 16.4
@> VAL30 P CG1_41114s <---> LEU153 P CD2_2354 3.5 9.8
@> LEU9 P CD2_7814s <---> ILE77 P CD_1128 3.5 17.0
@> PHE10 P CE1_9414s <---> LEU89 P CD1_1322 3.5 25.4
@> TYR119 P CE1_180514s <---> LEU89 P CD2_1326 3.6 18.5
@> ALA24 P CB_29814s <---> MET63 P CE_894 3.6 13.8
@> PHE26 P CZ_33214s <---> LEU153 P CD1_2350 3.6 27.1
@> VAL8 P CG2_5914s <---> LEU89 P CD1_1322 3.6 13.0
@> ALA22 P CB_27314s <---> PHE10 P CD1_92 3.6 29.5
@> MET91 P CE_135414s <---> ALA22 P CB_273 3.7 9.1
@> VAL41 P CG2_59514s <---> PHE26 P CD2_334 3.7 17.5
@> LEU116 P CD2_177114s <---> MET91 P SD_1353 3.7 21.9
@> ALA44 P CB_62814s <---> VAL11 P CG1_110 3.7 34.2
@> LYS6 P CD_2614s <---> TRP39 P CH2_557 3.7 44.8
@> VAL146 P CG2_223514s <---> TYR142 P CE2_2176 3.8 39.4
@> PHE85 P CE1_125114s <---> LEU9 P CD1_74 3.8 31.6
@> ILE21 P CG2_25614s <---> VAL25 P CG2_314 3.8 25.0
@> VAL141 P CG1_214914s <---> ILE21 P CD_263 3.9 13.0
@> ILE68 P CG1_98014s <---> MET63 P CE_894 3.9 37.2
@> PHE152 P CZ_233314s <---> LEU89 P CD1_1322 3.9 18.0
@> ARG18 P CG_20814s <---> VAL141 P CG1_2149 4.0 26.2
@> ARG75 P CG_108114s <---> ALA44 P CB_628 4.2 27.4
@> ILE127 P CD_194914s <---> LEU116 P CD2_1771 4.3 7.9
@> LYS79 P CG_115514s <---> VAL106 P CG2_1598 4.3 15.6
@> LEU29 P CG_39314s <---> VAL25 P CG1_310 4.3 21.7
@> ILE126 P CG1_192714s <---> LEU125 P CG_1905 4.4 55.6
@> Number of detected hydrophobic interactions: 32.
In this particular example you will not have disulfide bonds, but you can
compute it using calcDisulfideBondsTrajectory():
In [13]: calcDisulfideBondsTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 1
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 2
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 3
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 4
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
..
..
Compute all availabe types of interactions¶
First, we instantiate a InteractionsTrajectory instance, which stores all the
information about interactions for protein structure for multiple frames.
With InteractionsTrajectory.calcProteinInteractionsTrajectory(), we can compute all
types of interactions such as hydrogen bonds, salt bridges, repulsive ionic bonding,
Pi-cation, Pi-stacking, and hydrophobic) at once. Be aware that those
computations may take a while, depending on the size of the system and the number
of frames that are stored by the DCD file. Therefore, we recommend saving the
results as a filename file. filename file, here
calcProteinInteractionsTrajectory.pkl, can be reloaded and used with all available
functions and methods.
In [14]: interactionsTrajectory = InteractionsTrajectory('trajectory')
In [15]: interactionsTrajectory.calcProteinInteractionsTrajectory(atoms, dcd,
....: filename='calcProteinInteractionsTrajectory')
....:
@> Frame: 0
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG101 P NH1_1516 <---> ASP98 P OD1_1463 2.0 33.1
@> HSE72 P NE2_1042 <---> ASN15 P OD1_165 2.6 34.8
@> GLN143 P NE2_2192 <---> GLU139 P OE2_2126 2.7 9.2
@> HSE66 P NE2_957 <---> GLU139 P OE1_2125 2.7 6.4
@> ARG40 P N_561 <---> LYS6 P O_37 2.7 17.1
@> ARG58 P N_813 <---> ASP56 P OD1_788 2.7 30.0
@> ALA45 P N_634 <---> ARG75 P O_1097 2.8 35.1
@> ASN53 P ND2_747 <---> GLU50 P OE1_708 2.8 18.2
@> ALA74 P N_1064 <---> ASN53 P O_751 2.8 21.3
@> ASP56 P N_780 <---> ILE16 P O_189 2.8 27.0
@> LYS110 P NZ_1667 <---> THR84 P O_1240 2.8 38.2
@> LEU116 P N_1758 <---> CYS90 P O_1342 2.8 15.0
@> SER103 P N_1546 <---> LEU99 P O_1485 2.8 29.1
@> ASN134 P N_2045 <---> ASP137 P OD2_2091 2.8 22.6
@> PHE152 P N_2321 <---> CYS148 P O_2275 2.8 8.3
@> ASN95 P N_1398 <---> ASP92 P OD1_1368 2.8 12.6
@> LYS6 P N_16 <---> ASN38 P O_536 2.8 25.0
@> ILE77 P N_1115 <---> ALA45 P O_643 2.8 12.2
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.8 27.7
@> LEU99 P N_1467 <---> ASN95 P O_1411 2.8 15.5
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.8 9.6
@> GLY52 P N_731 <---> ALA74 P O_1073 2.8 6.6
@> ASP32 P N_435 <---> LYS28 P O_385 2.8 8.8
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.8 17.7
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 21.7
@> ARG27 P N_340 <---> GLU23 P O_293 2.8 15.4
@> TYR142 P N_2159 <---> PHE138 P O_2113 2.9 14.2
@> GLY133 P N_2038 <---> PRO130 P O_1995 2.9 25.4
@> PHE26 P N_320 <---> ALA22 P O_278 2.9 4.9
@> ASN15 P ND2_166 <---> SER19 P OG_232 2.9 32.1
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.9 19.7
@> ARG75 P NH2_1093 <---> ASP42 P OD2_610 2.9 23.5
@> ARG97 P N_1431 <---> GLU93 P O_1386 2.9 22.2
@> ARG65 P NH2_941 <---> GLU139 P OE1_2125 2.9 32.3
@> VAL25 P N_304 <---> ILE21 P O_268 2.9 8.2
@> LEU153 P N_2341 <---> CYS149 P O_2286 2.9 12.5
@> SER7 P N_38 <---> ASP86 P OD2_1270 2.9 39.9
@> ASP86 P N_1261 <---> SER7 P OG_45 2.9 34.7
@> ARG58 P NH2_832 <---> TYR131 P O_2016 2.9 33.1
@> THR46 P N_644 <---> CYS12 P O_130 2.9 36.1
@> GLN144 P N_2197 <---> THR140 P O_2142 2.9 23.3
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.9 12.4
@> LEU89 P N_1313 <---> LEU9 P O_83 2.9 29.5
@> THR31 P N_421 <---> ARG27 P O_363 2.9 24.1
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.9 24.6
@> CYS148 P N_2265 <---> GLN144 P O_2213 2.9 9.3
@> GLU23 P N_279 <---> SER19 P O_235 2.9 15.4
@> ILE68 P N_970 <---> MET63 P O_899 2.9 13.0
@> PHE10 P N_84 <---> ASP42 P O_612 2.9 22.8
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.9 10.1
@> SER61 P N_861 <---> TYR57 P O_812 2.9 35.1
@> CYS145 P N_2214 <---> VAL141 P O_2158 2.9 15.9
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.9 31.5
@> LYS64 P N_900 <---> GLN60 P O_860 2.9 22.9
@> LEU9 P N_65 <---> TYR87 P O_1293 2.9 16.4
@> ASN38 P N_523 <---> ILE35 P O_496 2.9 29.1
@> VAL11 P N_104 <---> LEU89 P O_1331 2.9 29.7
@> ASN100 P N_1486 <---> LEU96 P O_1430 2.9 10.3
..
..
@> Number of detected hydrogen bonds: 124.
@> Calculating salt bridges.
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 2.8
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.9
@> ASP32 P OD1_443_444 <---> LYS28 P NZ_380 3.0
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 3.1
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.7
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 3.8
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.9
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 4.1
@> GLU114 P OE1_1735_1736 <---> LYS112 P NZ_1699 4.1
@> ASP120 P OD1_1824_1825 <---> ARG147 P NH1_2257_2260 4.2
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 4.2
@> HSE157 P NE2_2418 <---> GLU114 P OE1_1735_1736 4.4
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 4.6
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.6
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 5.0
@> Number of detected salt bridges: 16.
@> Calculating repulsive ionic bonding.
@> LYS102 P NZ_1540 <---> ARG101 P NH1_1516_1519 4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Calculating Pi stacking interactions.
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 3.9 162.1
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> TYR119 P 1802_1803_1805_1807_1810_1812 4.4 3.0
@> PHE26 P 327_328_330_332_334_336 <---> TRP39 P 549_550_551_553_555_557 4.8 75.5
@> TYR132 P 2024_2025_2027_2029_2032_2034 <---> TYR131 P 2003_2004_2006_2008_2011_2013 4.9 91.4
@> Number of detected Pi stacking interactions: 4.
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.5
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.8
@> Number of detected cation-pi interactions: 3.
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@> ALA156 P CB_240114s <---> TYR87 P OH_1286 3.0 22.0
@> ALA24 P CB_29814s <---> MET63 P CE_894 3.3 5.2
@> ILE68 P CG2_97614s <---> MET63 P CE_894 3.3 52.4
@> TYR142 P CZ_217114s <---> VAL146 P CG2_2235 3.5 49.7
@> PHE10 P CD1_9214s <---> ALA22 P CB_273 3.5 31.2
@> LYS6 P CD_2614s <---> TRP39 P CZ2_555 3.5 68.7
@> PHE26 P CE2_33614s <---> VAL30 P CG1_411 3.6 21.1
@> ILE88 P CD_130714s <---> ALA111 P CB_1677 3.6 21.2
@> VAL11 P CG2_11414s <---> ILE88 P CG2_1300 3.6 9.3
@> VAL41 P CG2_59514s <---> PHE26 P CD2_334 3.6 16.6
@> PHE152 P CE1_233114s <---> ALA156 P CB_2401 3.7 17.5
@> LYS79 P CG_115514s <---> VAL106 P CG2_1598 3.7 25.1
@> LEU99 P CD2_148014s <---> ILE77 P CD_1128 3.7 12.0
@> PHE82 P CD1_120514s <---> ILE88 P CD_1307 3.7 17.6
@> LEU116 P CD2_177114s <---> ILE127 P CD_1949 3.7 17.4
@> VAL8 P CG1_5514s <---> PHE26 P CE2_336 3.7 12.1
@> LEU96 P CD1_142114s <---> ILE113 P CG2_1711 3.7 17.0
@> LEU9 P CD2_7814s <---> ILE77 P CD_1128 3.7 15.4
@> LEU89 P CD1_132214s <---> VAL8 P CG2_59 3.8 15.9
@> ILE126 P CD_193014s <---> LEU125 P CD1_1907 3.8 54.2
@> VAL141 P CG1_214914s <---> ILE127 P CG2_1942 3.9 11.5
@> MET91 P SD_135314s <---> ILE127 P CD_1949 3.9 35.9
@> ALA44 P CB_62814s <---> LEU9 P CD1_74 3.9 15.1
@> VAL25 P CG2_31414s <---> TYR142 P CE1_2169 3.9 12.0
@> ILE21 P CG2_25614s <---> MET63 P SD_893 4.0 20.8
@> LEU153 P CD1_235014s <---> TRP39 P NE1_547 4.0 9.4
@> PHE85 P CZ_125314s <---> LEU9 P CD1_74 4.0 32.1
@> ILE35 P CD_49114s <---> TRP39 P NE1_547 4.0 26.0
@> LEU29 P CD1_39514s <---> VAL25 P CG1_310 4.1 19.7
@> ALA74 P CB_106814s <---> ILE16 P CG2_177 4.1 6.7
@> ARG75 P CG_108114s <---> ALA44 P CB_628 4.1 36.2
@> ARG18 P CG_20814s <---> VAL141 P CG1_2149 4.1 20.3
@> LYS102 P CD_153414s <---> ILE77 P CG2_1121 4.1 17.5
@> TYR119 P CE1_180514s <---> LEU89 P CD2_1326 4.1 11.6
@> ARG40 P CG_56814s <---> PHE85 P CE2_1257 4.3 60.9
@> LYS28 P CG_37114s <---> ILE68 P CD_983 4.3 21.8
@> PHE138 P CD2_210814s <---> ILE21 P CD_263 4.3 6.6
@> TYR131 P CE1_200614s <---> ILE16 P CD_184 4.3 8.9
@> ARG58 P CG_82014s <---> PHE138 P CE1_2104 4.5 59.4
@> Number of detected hydrophobic interactions: 39.
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
..
..
@> Frame: 20
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG97 P NE_1444 <---> GLU93 P OE1_1383 2.5 12.5
@> SER19 P OG_232 <---> ASN15 P OD1_165 2.6 31.5
@> ARG27 P NH1_356 <---> GLU23 P OE1_290 2.6 19.1
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.6 21.5
@> GLN122 P NE2_1854 <---> ASP120 P OD2_1825 2.6 39.7
@> SER118 P OG_1791 <---> GLU114 P OE2_1736 2.6 24.5
@> ARG65 P NH1_938 <---> GLU139 P OE1_2125 2.7 6.1
@> ARG65 P NH2_941 <---> ASP135 P OD1_2067 2.7 15.6
@> SER43 P OG_620 <---> GLU23 P OE2_291 2.7 13.9
@> ARG75 P NE_1087 <---> ASP42 P OD1_609 2.7 26.5
@> ARG150 P NE_2300 <---> GLU154 P OE2_2372 2.7 4.9
@> VAL106 P N_1588 <---> LYS102 P O_1545 2.7 16.2
@> LYS28 P N_364 <---> ALA24 P O_303 2.7 38.8
@> HSE157 P NE2_2418 <---> PHE152 P O_2340 2.7 28.5
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.7 19.3
@> ARG97 P NH2_1450 <---> GLU93 P OE2_1384 2.7 15.8
@> ARG75 P NH2_1093 <---> ASP42 P OD1_609 2.7 30.5
@> ALA45 P N_634 <---> ARG75 P O_1097 2.7 22.3
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 2.7 19.2
@> THR31 P OG1_427 <---> ARG27 P O_363 2.7 13.1
@> ARG150 P NH2_2306 <---> GLU154 P OE1_2371 2.7 8.5
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.7 14.8
@> GLY67 P N_963 <---> MET63 P O_899 2.7 25.3
@> LEU89 P N_1313 <---> LEU9 P O_83 2.8 18.4
@> ARG101 P NH1_1516 <---> ASP98 P OD2_1464 2.8 11.5
@> ILE77 P N_1115 <---> ALA45 P O_643 2.8 39.9
@> LYS110 P N_1651 <---> PHE82 P O_1216 2.8 32.3
@> LEU29 P N_386 <---> VAL25 P O_319 2.8 5.4
@> ASN100 P N_1486 <---> LEU96 P O_1430 2.8 6.7
@> LYS102 P N_1524 <---> ASP98 P O_1466 2.8 4.9
@> THR78 P OG1_1140 <---> ASP81 P OD2_1194 2.8 10.5
@> VAL8 P N_49 <---> ARG40 P O_584 2.8 16.8
@> GLU154 P N_2360 <---> ARG150 P O_2310 2.8 15.1
@> LYS110 P NZ_1667 <---> ASP86 P OD2_1270 2.8 32.5
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.8 3.3
@> ILE35 P N_478 <---> VAL30 P O_420 2.8 7.9
@> ARG58 P NH1_829 <---> GLY133 P O_2044 2.8 34.3
@> GLN105 P N_1571 <---> ARG101 P O_1523 2.8 29.9
@> SER7 P N_38 <---> ASP86 P OD1_1269 2.8 10.5
@> ARG101 P NH2_1519 <---> ASP98 P OD1_1463 2.8 17.5
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 20.5
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.8 16.0
@> SER103 P OG_1553 <---> LEU99 P O_1485 2.9 21.4
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.9 6.7
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.9 7.9
@> ARG18 P NH1_217 <---> ILE127 P O_1954 2.9 13.0
@> LYS155 P NZ_2391 <---> TYR119 P O_1815 2.9 27.9
@> ARG150 P N_2287 <---> VAL146 P O_2240 2.9 39.3
@> ARG65 P NH1_938 <---> ASP135 P OD2_2068 2.9 39.2
@> VAL30 P N_405 <---> PHE26 P O_339 2.9 2.0
@> VAL11 P N_104 <---> LEU89 P O_1331 2.9 19.9
@> GLN144 P N_2197 <---> THR140 P O_2142 2.9 16.4
@> LEU116 P N_1758 <---> CYS90 P O_1342 2.9 22.2
@> SER103 P N_1546 <---> LEU99 P O_1485 2.9 35.6
@> ASP56 P N_780 <---> ILE16 P O_189 2.9 5.0
@> GLU139 P N_2114 <---> ASP135 P O_2070 2.9 33.1
@> PHE10 P N_84 <---> ASP42 P O_612 2.9 11.4
@> LYS155 P N_2375 <---> ALA151 P O_2320 2.9 39.0
@> PHE26 P N_320 <---> ALA22 P O_278 2.9 21.1
@> THR140 P N_2129 <---> SER136 P O_2081 3.0 36.4
@> ALA74 P N_1064 <---> ASN53 P O_751 3.0 20.8
@> LYS6 P N_16 <---> ASN38 P O_536 3.0 12.1
@> ARG65 P N_922 <---> SER61 P O_871 3.0 15.7
@> LEU9 P N_65 <---> TYR87 P O_1293 3.0 6.8
..
..
@> Number of detected hydrogen bonds: 114.
@> Calculating salt bridges.
@> ASP135 P OD1_2067_2068 <---> ARG65 P NH1_938_941 2.5
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.7
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 2.8
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 3.4
@> ARG97 P NH1_1447_1450 <---> GLU93 P OE1_1383_1384 3.5
@> ARG150 P NH1_2303_2306 <---> GLU154 P OE1_2371_2372 3.7
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.7
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 4.0
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 4.0
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.4
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 4.7
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 4.8
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 5.0
@> Number of detected salt bridges: 14.
@> Calculating repulsive ionic bonding.
@> ARG147 P NH1_2257_2260 <---> LYS123 P NZ_1875 4.5
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Calculating Pi stacking interactions.
@> TYR119 P 1802_1803_1805_1807_1810_1812 <---> PHE152 P 2328_2329_2331_2333_2335_2337 4.7 125.5
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 4.8 165.0
@> TYR132 P 2024_2025_2027_2029_2032_2034 <---> TYR131 P 2003_2004_2006_2008_2011_2013 4.9 116.3
@> Number of detected Pi stacking interactions: 3.
@> Calculating cation-Pi interactions.
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.0
@> Number of detected cation-pi interactions: 1.
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@> LEU96 P CD1_142114s <---> ILE113 P CG2_1711 3.3 21.1
@> ILE88 P CD_130714s <---> PHE82 P CD2_1211 3.4 25.2
@> VAL11 P CG2_11414s <---> LEU99 P CD1_1476 3.4 11.5
@> MET63 P SD_89314s <---> TYR142 P CE1_2169 3.4 37.7
@> TRP39 P NE1_54714s <---> LEU153 P CD1_2350 3.4 19.2
@> ALA111 P CB_167714s <---> ILE88 P CD_1307 3.5 23.0
@> ILE35 P CD_49114s <---> LEU153 P CD1_2350 3.5 16.4
@> VAL30 P CG1_41114s <---> LEU153 P CD2_2354 3.5 9.8
@> LEU9 P CD2_7814s <---> ILE77 P CD_1128 3.5 17.0
@> PHE10 P CE1_9414s <---> LEU89 P CD1_1322 3.5 25.4
@> TYR119 P CE1_180514s <---> LEU89 P CD2_1326 3.6 18.5
@> ALA24 P CB_29814s <---> MET63 P CE_894 3.6 13.8
@> PHE26 P CZ_33214s <---> LEU153 P CD1_2350 3.6 27.1
@> VAL8 P CG2_5914s <---> LEU89 P CD1_1322 3.6 13.0
@> ALA22 P CB_27314s <---> PHE10 P CD1_92 3.6 29.5
@> MET91 P CE_135414s <---> ALA22 P CB_273 3.7 9.1
@> VAL41 P CG2_59514s <---> PHE26 P CD2_334 3.7 17.5
@> LEU116 P CD2_177114s <---> MET91 P SD_1353 3.7 21.9
@> ALA44 P CB_62814s <---> VAL11 P CG1_110 3.7 34.2
@> LYS6 P CD_2614s <---> TRP39 P CH2_557 3.7 44.8
@> VAL146 P CG2_223514s <---> TYR142 P CE2_2176 3.8 39.4
@> PHE85 P CE1_125114s <---> LEU9 P CD1_74 3.8 31.6
@> ILE21 P CG2_25614s <---> VAL25 P CG2_314 3.8 25.0
@> VAL141 P CG1_214914s <---> ILE21 P CD_263 3.9 13.0
@> ILE68 P CG1_98014s <---> MET63 P CE_894 3.9 37.2
@> PHE152 P CZ_233314s <---> LEU89 P CD1_1322 3.9 18.0
@> ARG18 P CG_20814s <---> VAL141 P CG1_2149 4.0 26.2
@> ARG75 P CG_108114s <---> ALA44 P CB_628 4.2 27.4
@> ILE127 P CD_194914s <---> LEU116 P CD2_1771 4.3 7.9
@> LYS79 P CG_115514s <---> VAL106 P CG2_1598 4.3 15.6
@> LEU29 P CG_39314s <---> VAL25 P CG1_310 4.3 21.7
@> ILE126 P CG1_192714s <---> LEU125 P CG_1905 4.4 55.6
@> Number of detected hydrophobic interactions: 32.
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> File with interactions saved.
The results are displayed on the screen and they can be fetch by
using InteractionsTrajectory.getInteractions() method.
In [16]: interactionsTrajectory.getInteractions()
[[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.5997, 34.752],
['GLN143', 'NE2_2192', 'P', 'GLU139', 'OE2_2126', 'P', 2.7287, 9.1822],
['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7314, 6.3592],
['ARG40', 'N_561', 'P', 'LYS6', 'O_37', 'P', 2.7479, 17.1499],
['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.7499, 29.9737],
['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.7609, 35.0983],
['ASN53', 'ND2_747', 'P', 'GLU50', 'OE1_708', 'P', 2.7702, 18.2336],
['ALA74', 'N_1064', 'P', 'ASN53', 'O_751', 'P', 2.7782, 21.3375],
['ASP56', 'N_780', 'P', 'ILE16', 'O_189', 'P', 2.7793, 27.0481],
['LYS110', 'NZ_1667', 'P', 'THR84', 'O_1240', 'P', 2.7977, 38.2213],
['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.8072, 15.0239],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
['ASN134', 'N_2045', 'P', 'ASP137', 'OD2_2091', 'P', 2.8132, 22.562],
['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8141, 8.2562],
['ASN95', 'N_1398', 'P', 'ASP92', 'OD1_1368', 'P', 2.8148, 12.5701],
['LYS6', 'N_16', 'P', 'ASN38', 'O_536', 'P', 2.8178, 25.0306],
['ILE77', 'N_1115', 'P', 'ALA45', 'O_643', 'P', 2.8179, 12.1856],
['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.8204, 27.6617],
['LEU99', 'N_1467', 'P', 'ASN95', 'O_1411', 'P', 2.8205, 15.4867],
['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.8247, 9.5914],
['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.832, 6.6442],
['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.8357, 8.8318],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8429, 17.7147],
['GLN143', 'N_2180', 'P', 'GLU139', 'O_2128', 'P', 2.8445, 21.6714],
['ARG27', 'N_340', 'P', 'GLU23', 'O_293', 'P', 2.8446, 15.4167],
['TYR142', 'N_2159', 'P', 'PHE138', 'O_2113', 'P', 2.8515, 14.2061],
['GLY133', 'N_2038', 'P', 'PRO130', 'O_1995', 'P', 2.854, 25.4301],
['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.8541, 4.8732],
['ASN15', 'ND2_166', 'P', 'SER19', 'OG_232', 'P', 2.8592, 32.1244],
['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.8632, 19.6664],
['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.8649, 23.5083],
['ARG97', 'N_1431', 'P', 'GLU93', 'O_1386', 'P', 2.8654, 22.24],
['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.8655, 32.3239],
['VAL25', 'N_304', 'P', 'ILE21', 'O_268', 'P', 2.8666, 8.2255],
['LEU153', 'N_2341', 'P', 'CYS149', 'O_2286', 'P', 2.8707, 12.4931],
['SER7', 'N_38', 'P', 'ASP86', 'OD2_1270', 'P', 2.8732, 39.8839],
['ASP86', 'N_1261', 'P', 'SER7', 'OG_45', 'P', 2.8753, 34.7426],
..
[['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE1_1735', 'P', 2.5487, 20.8176],
['THR78', 'N_1134', 'P', 'ASP81', 'OD2_1194', 'P', 2.5494, 15.6392],
['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.5496, 36.5043],
['THR78', 'OG1_1140', 'P', 'ASP81', 'OD2_1194', 'P', 2.5756, 25.1514],
['SER7', 'OG_45', 'P', 'ASP86', 'OD2_1270', 'P', 2.5904, 32.2995],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.5963, 18.6089],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.6334, 17.8203],
['ARG75', 'NH2_1093', 'P', 'ASP81', 'OD1_1193', 'P', 2.6367, 17.6426],
['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.6547, 25.6442],
['ARG58', 'NE_826', 'P', 'ASP56', 'OD1_788', 'P', 2.6611, 6.4459],
['GLN124', 'N_1881', 'P', 'ASP120', 'OD1_1824', 'P', 2.6666, 17.1571],
['ARG147', 'NH1_2257', 'P', 'GLN124', 'OE1_1892', 'P', 2.6875, 11.8479],
['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 2.6879, 14.5803],
['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.6889, 23.9375],
['TYR87', 'OH_1286', 'P', 'HSE157', 'OT1_2423', 'P', 2.6945, 11.5603],
['SER43', 'OG_620', 'P', 'GLU23', 'OE1_290', 'P', 2.6978, 15.166],
['LYS28', 'NZ_380', 'P', 'ASP32', 'OD1_443', 'P', 2.7003, 3.632],
['LYS110', 'NZ_1667', 'P', 'ASP86', 'OD1_1269', 'P', 2.7025, 25.1511],
['THR140', 'OG1_2135', 'P', 'SER136', 'O_2081', 'P', 2.71, 5.2209],
['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.7125, 24.3959],
['THR5', 'OG1_8', 'P', 'ASN38', 'O_536', 'P', 2.7162, 38.6072],
['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.7222, 26.7806],
['ARG147', 'NH1_2257', 'P', 'ASP120', 'OD2_1825', 'P', 2.731, 15.2446],
['ARG27', 'N_340', 'P', 'GLU23', 'O_293', 'P', 2.7341, 21.9432],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE1_1735', 'P', 2.735, 15.8502],
['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.7501, 16.0113],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.7535, 13.6202],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7626, 15.9446],
['ARG58', 'NH1_829', 'P', 'GLY133', 'O_2044', 'P', 2.7673, 31.8828],
['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.7744, 13.0389],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7935, 13.2257],
['GLU23', 'N_279', 'P', 'SER19', 'O_235', 'P', 2.8067, 10.8775],
['SER7', 'N_38', 'P', 'ASP86', 'OD2_1270', 'P', 2.813, 38.9132],
['VAL11', 'N_104', 'P', 'LEU89', 'O_1331', 'P', 2.8182, 13.801],
['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.8212, 18.2267],
['LEU9', 'N_65', 'P', 'TYR87', 'O_1293', 'P', 2.8249, 34.2551],
['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.8308, 14.8745],
['ILE68', 'N_970', 'P', 'MET63', 'O_899', 'P', 2.8328, 9.2758],
..
[['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 2.5097, 4.9218],
['THR31', 'OG1_427', 'P', 'ARG27', 'O_363', 'P', 2.5496, 5.4538],
['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.5525, 8.1856],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.5902, 19.0335],
['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.6114, 24.975],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6441, 10.2991],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6466, 7.8982],
['TYR87', 'OH_1286', 'P', 'HSE157', 'OT1_2423', 'P', 2.6516, 14.0793],
['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.6643, 4.9246],
['SER43', 'OG_620', 'P', 'GLU23', 'OE1_290', 'P', 2.7024, 8.6062],
['THR78', 'OG1_1140', 'P', 'ASP81', 'OD2_1194', 'P', 2.7158, 6.5273],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7184, 24.9984],
['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.7238, 26.9156],
['LYS28', 'NZ_380', 'P', 'ASP32', 'OD2_444', 'P', 2.7274, 13.9298],
['THR84', 'OG1_1233', 'P', 'GLU80', 'O_1184', 'P', 2.7314, 13.4406],
['LEU89', 'N_1313', 'P', 'LEU9', 'O_83', 'P', 2.7581, 11.8493],
['ARG147', 'NH1_2257', 'P', 'GLN124', 'OE1_1892', 'P', 2.7633, 15.0984],
['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.765, 17.97],
['ILE35', 'N_478', 'P', 'VAL30', 'O_420', 'P', 2.7659, 20.7163],
['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.7663, 21.7712],
['VAL11', 'N_104', 'P', 'LEU89', 'O_1331', 'P', 2.767, 10.3325],
['VAL25', 'N_304', 'P', 'ILE21', 'O_268', 'P', 2.7679, 9.2024],
['SER7', 'OG_45', 'P', 'ASP86', 'OD2_1270', 'P', 2.7682, 29.4143],
['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.7756, 37.1399],
['ASN34', 'N_464', 'P', 'THR31', 'O_434', 'P', 2.7794, 19.6803],
['LYS110', 'N_1651', 'P', 'PHE82', 'O_1216', 'P', 2.7863, 9.1814],
['LYS110', 'NZ_1667', 'P', 'ASP86', 'OD1_1269', 'P', 2.7932, 13.508],
['ARG58', 'NE_826', 'P', 'ASP56', 'OD1_788', 'P', 2.8021, 8.0221],
['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.8066, 14.9419],
['VAL8', 'N_49', 'P', 'ARG40', 'O_584', 'P', 2.8114, 19.4027],
['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.8173, 6.9549],
['LYS155', 'N_2375', 'P', 'ALA151', 'O_2320', 'P', 2.8212, 15.1026],
['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.8239, 28.9105],
['ARG147', 'NH1_2257', 'P', 'ASP120', 'OD2_1825', 'P', 2.8257, 31.6579],
['ARG97', 'N_1431', 'P', 'GLU93', 'O_1386', 'P', 2.8291, 15.1587],
['LYS123', 'N_1859', 'P', 'ASP120', 'OD1_1824', 'P', 2.8292, 34.0011],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8381, 10.253],
['ASP86', 'N_1261', 'P', 'SER7', 'OG_45', 'P', 2.8406, 22.034],
['ARG65', 'N_922', 'P', 'SER61', 'O_871', 'P', 2.8423, 24.4142],
['ILE127', 'N_1936', 'P', 'MET91', 'O_1359', 'P', 2.8469, 4.126],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'ND1_2414', 'P', 2.8616, 14.018],
['GLY67', 'N_963', 'P', 'MET63', 'O_899', 'P', 2.8626, 38.6183],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8761, 17.0562],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.8761, 18.0626],
['ARG75', 'NE_1087', 'P', 'ASP42', 'OD2_610', 'P', 2.8795, 38.3078],
['ALA44', 'N_624', 'P', 'PHE10', 'O_103', 'P', 2.8798, 30.1431],
['ILE68', 'N_970', 'P', 'MET63', 'O_899', 'P', 2.8902, 12.9079],
['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.903, 21.0711],
['THR78', 'N_1134', 'P', 'ASP81', 'OD2_1194', 'P', 2.9152, 26.3475],
['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.9235, 27.7222],
..
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.5321, 12.1754],
['SER7', 'OG_45', 'P', 'ASP86', 'OD2_1270', 'P', 2.5681, 8.2326],
['SER43', 'OG_620', 'P', 'GLU23', 'OE1_290', 'P', 2.5908, 6.4741],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.5911, 17.069],
['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.6234, 15.5609],
['THR78', 'OG1_1140', 'P', 'ASP81', 'OD2_1194', 'P', 2.6239, 11.6022],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6274, 12.9418],
['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.6388, 5.0129],
['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.6571, 20.4048],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6666, 5.0368],
['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.677, 21.8922],
['ARG18', 'NH2_220', 'P', 'ASP92', 'OD2_1369', 'P', 2.6813, 31.3689],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.6844, 12.4337],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7018, 15.5273],
['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.7094, 34.9749],
['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7146, 21.3402],
['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.719, 23.3583],
['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.7207, 8.4795],
['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.7283, 14.8893],
['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 2.7353, 26.7201],
['THR31', 'OG1_427', 'P', 'ARG27', 'O_363', 'P', 2.7466, 22.4844],
['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.7489, 16.6396],
['ARG58', 'NH1_829', 'P', 'TYR132', 'O_2037', 'P', 2.7511, 23.6002],
['ARG147', 'NH1_2257', 'P', 'ASP120', 'OD1_1824', 'P', 2.7592, 19.3384],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7625, 21.1367],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7703, 4.1752],
['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.7726, 18.0115],
['ARG65', 'NH1_938', 'P', 'GLU139', 'OE1_2125', 'P', 2.7749, 18.9952],
['GLY133', 'N_2038', 'P', 'ASP137', 'OD2_2091', 'P', 2.7764, 32.7458],
['ARG75', 'NH2_1093', 'P', 'ASP81', 'OD1_1193', 'P', 2.7783, 16.8911],
['TYR87', 'OH_1286', 'P', 'HSE157', 'OT2_2424', 'P', 2.7928, 9.9286],
['ILE35', 'N_478', 'P', 'VAL30', 'O_420', 'P', 2.7945, 6.0583],
['LYS28', 'NZ_380', 'P', 'ASP32', 'OD2_444', 'P', 2.7993, 35.4827],
['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8, 5.5477],
['LYS110', 'NZ_1667', 'P', 'ASP86', 'OD1_1269', 'P', 2.8021, 14.2767],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.813, 11.6498],
['GLN60', 'N_844', 'P', 'ASP56', 'O_791', 'P', 2.8156, 25.2584],
['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.8209, 30.082],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8375, 24.3092],
['ARG150', 'N_2287', 'P', 'VAL146', 'O_2240', 'P', 2.8394, 21.6561],
..
..
[['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.2931, 21.0747],
['ILE88', 'CD_1307', 'P', 'PHE82', 'CD2_1211', 'P', 3.3689, 25.2319],
['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.3771, 11.4804],
['MET63', 'SD_893', 'P', 'TYR142', 'CE1_2169', 'P', 3.3896, 37.7382],
['TRP39', 'NE1_547', 'P', 'LEU153', 'CD1_2350', 'P', 3.4345, 19.2142],
['ALA111', 'CB_1677', 'P', 'ILE88', 'CD_1307', 'P', 3.4669, 22.9943],
['ILE35', 'CD_491', 'P', 'LEU153', 'CD1_2350', 'P', 3.4868, 16.4472],
['VAL30', 'CG1_411', 'P', 'LEU153', 'CD2_2354', 'P', 3.4938, 9.7531],
['LEU9', 'CD2_78', 'P', 'ILE77', 'CD_1128', 'P', 3.5133, 16.9544],
['PHE10', 'CE1_94', 'P', 'LEU89', 'CD1_1322', 'P', 3.5468, 25.3848],
['TYR119', 'CE1_1805', 'P', 'LEU89', 'CD2_1326', 'P', 3.554, 18.5297],
['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.5859, 13.7697],
['PHE26', 'CZ_332', 'P', 'LEU153', 'CD1_2350', 'P', 3.6118, 27.1048],
['VAL8', 'CG2_59', 'P', 'LEU89', 'CD1_1322', 'P', 3.6199, 12.9537],
['ALA22', 'CB_273', 'P', 'PHE10', 'CD1_92', 'P', 3.6246, 29.4846],
['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 3.6628, 9.0978],
['VAL41', 'CG2_595', 'P', 'PHE26', 'CD2_334', 'P', 3.6792, 17.4783],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6984, 21.9302],
['ALA44', 'CB_628', 'P', 'VAL11', 'CG1_110', 'P', 3.7022, 34.2417],
['LYS6', 'CD_26', 'P', 'TRP39', 'CH2_557', 'P', 3.7135, 44.8],
['VAL146', 'CG2_2235', 'P', 'TYR142', 'CE2_2176', 'P', 3.7622, 39.414],
['PHE85', 'CE1_1251', 'P', 'LEU9', 'CD1_74', 'P', 3.8118, 31.6126],
['ILE21', 'CG2_256', 'P', 'VAL25', 'CG2_314', 'P', 3.825, 25.047],
['VAL141', 'CG1_2149', 'P', 'ILE21', 'CD_263', 'P', 3.8615, 13.036],
['ILE68', 'CG1_980', 'P', 'MET63', 'CE_894', 'P', 3.8698, 37.1931],
['PHE152', 'CZ_2333', 'P', 'LEU89', 'CD1_1322', 'P', 3.9131, 17.9674],
['ARG18', 'CG_208', 'P', 'VAL141', 'CG1_2149', 'P', 3.9881, 26.173],
['ARG75', 'CG_1081', 'P', 'ALA44', 'CB_628', 'P', 4.1878, 27.3996],
['ILE127', 'CD_1949', 'P', 'LEU116', 'CD2_1771', 'P', 4.2643, 7.8575],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2738, 15.6412],
['LEU29', 'CG_393', 'P', 'VAL25', 'CG1_310', 'P', 4.3325, 21.7286],
['ILE126', 'CG1_1927', 'P', 'LEU125', 'CG_1905', 'P', 4.4374, 55.6364]]],
[[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[]]]
Moreover, we can display the evolution of each interaction type during the simulation. There are the following types of plots: hydrogen bonds (blue), salt bridges (yellow), hydrophobic interactions (silver), Pi-stacking (green), Pi-cation (orange), repulsive ionic bonding (red), disulfide bonds(black).
In [17]: interactionsTrajectory.getTimeInteractions()
If the structure is stable, we will not observe a lot of changes in protein structure.
Similar to the single PDB analysis, we have an access to each interaction
type by using: InteractionsTrajectory.getHydrogenBonds() method, etc.
In [18]: interactionsTrajectory.getHydrogenBonds()
[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.5997, 34.752],
['GLN143', 'NE2_2192', 'P', 'GLU139', 'OE2_2126', 'P', 2.7287, 9.1822],
['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7314, 6.3592],
['ARG40', 'N_561', 'P', 'LYS6', 'O_37', 'P', 2.7479, 17.1499],
['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.7499, 29.9737],
['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.7609, 35.0983],
['ASN53', 'ND2_747', 'P', 'GLU50', 'OE1_708', 'P', 2.7702, 18.2336],
['ALA74', 'N_1064', 'P', 'ASN53', 'O_751', 'P', 2.7782, 21.3375],
['ASP56', 'N_780', 'P', 'ILE16', 'O_189', 'P', 2.7793, 27.0481],
['LYS110', 'NZ_1667', 'P', 'THR84', 'O_1240', 'P', 2.7977, 38.2213],
['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.8072, 15.0239],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
['ASN134', 'N_2045', 'P', 'ASP137', 'OD2_2091', 'P', 2.8132, 22.562],
['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8141, 8.2562],
['ASN95', 'N_1398', 'P', 'ASP92', 'OD1_1368', 'P', 2.8148, 12.5701],
['LYS6', 'N_16', 'P', 'ASN38', 'O_536', 'P', 2.8178, 25.0306],
['ILE77', 'N_1115', 'P', 'ALA45', 'O_643', 'P', 2.8179, 12.1856],
['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.8204, 27.6617],
['LEU99', 'N_1467', 'P', 'ASN95', 'O_1411', 'P', 2.8205, 15.4867],
['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.8247, 9.5914],
['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.832, 6.6442],
['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.8357, 8.8318],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8429, 17.7147],
['GLN143', 'N_2180', 'P', 'GLU139', 'O_2128', 'P', 2.8445, 21.6714],
['ARG27', 'N_340', 'P', 'GLU23', 'O_293', 'P', 2.8446, 15.4167],
['TYR142', 'N_2159', 'P', 'PHE138', 'O_2113', 'P', 2.8515, 14.2061],
['GLY133', 'N_2038', 'P', 'PRO130', 'O_1995', 'P', 2.854, 25.4301],
['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.8541, 4.8732],
['ASN15', 'ND2_166', 'P', 'SER19', 'OG_232', 'P', 2.8592, 32.1244],
['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.8632, 19.6664],
['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.8649, 23.5083],
['ARG97', 'N_1431', 'P', 'GLU93', 'O_1386', 'P', 2.8654, 22.24],
['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.8655, 32.3239],
['VAL25', 'N_304', 'P', 'ILE21', 'O_268', 'P', 2.8666, 8.2255],
['LEU153', 'N_2341', 'P', 'CYS149', 'O_2286', 'P', 2.8707, 12.4931],
['SER7', 'N_38', 'P', 'ASP86', 'OD2_1270', 'P', 2.8732, 39.8839],
['ASP86', 'N_1261', 'P', 'SER7', 'OG_45', 'P', 2.8753, 34.7426],
['ARG58', 'NH2_832', 'P', 'TYR131', 'O_2016', 'P', 2.8815, 33.1098],
['THR46', 'N_644', 'P', 'CYS12', 'O_130', 'P', 2.883, 36.1279],
['GLN144', 'N_2197', 'P', 'THR140', 'O_2142', 'P', 2.8836, 23.2545],
['THR78', 'N_1134', 'P', 'ASP81', 'OD2_1194', 'P', 2.8869, 12.4465],
['LEU89', 'N_1313', 'P', 'LEU9', 'O_83', 'P', 2.8946, 29.5105],
['THR31', 'N_421', 'P', 'ARG27', 'O_363', 'P', 2.896, 24.1287],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8975, 24.576],
['CYS148', 'N_2265', 'P', 'GLN144', 'O_2213', 'P', 2.8976, 9.3165],
['GLU23', 'N_279', 'P', 'SER19', 'O_235', 'P', 2.8979, 15.4146],
['ILE68', 'N_970', 'P', 'MET63', 'O_899', 'P', 2.8986, 12.9903],
['PHE10', 'N_84', 'P', 'ASP42', 'O_612', 'P', 2.9026, 22.751],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.912, 10.1158],
['SER61', 'N_861', 'P', 'TYR57', 'O_812', 'P', 2.9132, 35.1196],
['CYS145', 'N_2214', 'P', 'VAL141', 'O_2158', 'P', 2.9144, 15.8507],
['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.9199, 31.5487],
['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.9211, 22.8783],
['LEU9', 'N_65', 'P', 'TYR87', 'O_1293', 'P', 2.9229, 16.439],
['ASN38', 'N_523', 'P', 'ILE35', 'O_496', 'P', 2.9255, 29.091],
['VAL11', 'N_104', 'P', 'LEU89', 'O_1331', 'P', 2.9316, 29.7192],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.933, 10.3321],
['GLN124', 'N_1881', 'P', 'ASP120', 'OD2_1825', 'P', 2.9333, 27.4547],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9361, 9.2855],
['GLN76', 'NE2_1110', 'P', 'THR46', 'O_657', 'P', 2.9381, 31.3836],
['ARG40', 'NH1_577', 'P', 'THR84', 'OG1_1233', 'P', 2.9482, 8.3748],
['ALA44', 'N_624', 'P', 'PHE10', 'O_103', 'P', 2.9499, 33.1771],
['GLU154', 'N_2360', 'P', 'ARG150', 'O_2310', 'P', 2.956, 22.5898],
['VAL8', 'N_49', 'P', 'ARG40', 'O_584', 'P', 2.9631, 25.0079],
['MET63', 'N_883', 'P', 'GLY59', 'O_843', 'P', 2.9733, 18.2731],
['GLN60', 'N_844', 'P', 'ASP56', 'O_791', 'P', 2.9795, 35.5229],
['ILE35', 'N_478', 'P', 'VAL30', 'O_420', 'P', 2.9811, 23.5092],
['VAL146', 'N_2225', 'P', 'TYR142', 'O_2179', 'P', 2.9914, 31.4798],
['ARG58', 'NH1_829', 'P', 'TYR131', 'O_2016', 'P', 2.9942, 38.0937],
['ASN53', 'N_738', 'P', 'GLU50', 'O_711', 'P', 2.995, 28.587],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9952, 32.2712],
['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.9957, 25.9507],
['ARG75', 'N_1074', 'P', 'ASN15', 'OD1_165', 'P', 3.0026, 25.0853],
['GLN144', 'NE2_2209', 'P', 'ILE126', 'O_1935', 'P', 3.0038, 18.2744],
['ASN34', 'N_464', 'P', 'THR31', 'O_434', 'P', 3.0041, 18.2465],
['ASN15', 'ND2_166', 'P', 'SER43', 'OG_620', 'P', 3.0129, 25.6996],
['ARG58', 'NE_826', 'P', 'ASP56', 'OD1_788', 'P', 3.017, 22.2284],
['ARG27', 'NH1_356', 'P', 'GLU23', 'OE2_291', 'P', 3.0175, 36.9342],
['ILE127', 'N_1936', 'P', 'MET91', 'O_1359', 'P', 3.018, 17.5601],
['TYR119', 'OH_1808', 'P', 'HSE157', 'N_2407', 'P', 3.0224, 28.0923],
['HSE157', 'N_2407', 'P', 'TYR119', 'OH_1808', 'P', 3.0224, 19.1804],
['GLU139', 'N_2114', 'P', 'ASP135', 'O_2070', 'P', 3.0245, 27.9246],
['LEU29', 'N_386', 'P', 'VAL25', 'O_319', 'P', 3.0299, 19.1089],
['SER47', 'N_658', 'P', 'LEU13', 'O_149', 'P', 3.0386, 28.8029],
['VAL30', 'N_405', 'P', 'PHE26', 'O_339', 'P', 3.0394, 17.6883],
['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 3.0464, 19.6807],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.051, 21.4045],
['LYS155', 'N_2375', 'P', 'ALA151', 'O_2320', 'P', 3.0555, 21.3244],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.059, 24.1606],
['ASP120', 'N_1816', 'P', 'GLY117', 'O_1783', 'P', 3.0623, 12.666],
['CYS62', 'N_872', 'P', 'ARG58', 'O_836', 'P', 3.0651, 20.443],
['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 3.0679, 4.2778],
['ALA24', 'N_294', 'P', 'PRO20', 'O_249', 'P', 3.0751, 29.9487],
['ARG150', 'N_2287', 'P', 'VAL146', 'O_2240', 'P', 3.078, 12.7022],
['LYS28', 'N_364', 'P', 'ALA24', 'O_303', 'P', 3.0783, 19.9504],
['VAL141', 'N_2143', 'P', 'ASP137', 'O_2093', 'P', 3.081, 18.4811],
['ASP98', 'N_1455', 'P', 'SER94', 'O_1397', 'P', 3.0844, 19.56],
['LEU96', 'N_1412', 'P', 'ASP92', 'O_1371', 'P', 3.085, 36.3254],
['ALA22', 'N_269', 'P', 'ARG18', 'O_224', 'P', 3.088, 21.873],
['ALA151', 'N_2311', 'P', 'ARG147', 'O_2264', 'P', 3.0991, 15.5713],
['GLY67', 'N_963', 'P', 'LYS64', 'O_921', 'P', 3.122, 22.7833],
['ASP42', 'N_601', 'P', 'VAL8', 'O_64', 'P', 3.1331, 35.5671],
['ARG65', 'N_922', 'P', 'SER61', 'O_871', 'P', 3.1339, 23.3682],
['TRP39', 'N_537', 'P', 'SER36', 'O_507', 'P', 3.1343, 15.1775],
['LYS123', 'N_1859', 'P', 'ASP120', 'O_1827', 'P', 3.1375, 18.6589],
['MET91', 'N_1343', 'P', 'ASN95', 'OD1_1406', 'P', 3.1581, 39.0427],
['THR140', 'N_2129', 'P', 'SER136', 'O_2081', 'P', 3.1742, 30.2937],
['PHE85', 'N_1241', 'P', 'ASP81', 'O_1196', 'P', 3.1845, 20.2243],
['ASN15', 'N_157', 'P', 'CYS12', 'SG_127', 'P', 3.2043, 37.4576],
['ALA111', 'N_1673', 'P', 'PHE82', 'O_1216', 'P', 3.2054, 20.58],
['ARG147', 'N_2241', 'P', 'GLN143', 'O_2196', 'P', 3.2416, 12.0678],
['ARG75', 'NH2_1093', 'P', 'ASP81', 'OD1_1193', 'P', 3.2447, 29.3403],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 3.2687, 28.6743],
['ARG147', 'NH1_2257', 'P', 'GLN124', 'OE1_1892', 'P', 3.3008, 29.853],
['PHE138', 'N_2094', 'P', 'ASN134', 'O_2058', 'P', 3.3062, 31.0247],
['SER7', 'OG_45', 'P', 'THR84', 'O_1240', 'P', 3.3227, 35.5231],
['CYS12', 'N_120', 'P', 'ALA44', 'O_633', 'P', 3.3349, 36.1006],
..
..
In [19]: interactionsTrajectory.getSaltBridges()
[[['GLU139', 'OE1_2125_2126', 'P', 'HSE66', 'NE2_957', 'P', 2.8359],
['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.9163],
['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 3.037],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.0699],
['ARG27', 'NH1_356_359', 'P', 'GLU23', 'OE1_290_291', 'P', 3.7148],
['GLU139', 'OE1_2125_2126', 'P', 'ARG65', 'NH1_938_941', 'P', 3.7799],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.9359],
['ARG58', 'NH1_829_832', 'P', 'ASP56', 'OD1_788_789', 'P', 3.9486],
['ARG18', 'NH1_217_220', 'P', 'ASP92', 'OD1_1368_1369', 'P', 4.0693],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 4.0787],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.1543],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 4.1879],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.3835],
['ARG18', 'NH1_217_220', 'P', 'ASP129', 'OD1_1978_1979', 'P', 4.5608],
['ARG75', 'NH1_1090_1093', 'P', 'ASP42', 'OD1_609_610', 'P', 4.5612],
['GLU23', 'OE1_290_291', 'P', 'HSE72', 'NE2_1042', 'P', 4.99]],
[['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 2.5568],
['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.6325],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.8263],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 3.0552],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 3.2384],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.3269],
['ARG27', 'NH1_356_359', 'P', 'GLU23', 'OE1_290_291', 'P', 3.4115],
['GLU139', 'OE1_2125_2126', 'P', 'ARG65', 'NH1_938_941', 'P', 3.4427],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.5063],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8015],
['ARG58', 'NH1_829_832', 'P', 'ASP56', 'OD1_788_789', 'P', 3.8017],
['ARG18', 'NH1_217_220', 'P', 'ASP92', 'OD1_1368_1369', 'P', 3.8368],
['GLU139', 'OE1_2125_2126', 'P', 'HSE66', 'NE2_957', 'P', 3.9677],
['ARG75', 'NH1_1090_1093', 'P', 'ASP42', 'OD1_609_610', 'P', 4.5207]],
[['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5925],
['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 2.5955],
['GLU139', 'OE1_2125_2126', 'P', 'ARG65', 'NH1_938_941', 'P', 2.6677],
['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.945],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0796],
['ARG58', 'NH1_829_832', 'P', 'ASP56', 'OD1_788_789', 'P', 3.6],
['GLU139', 'OE1_2125_2126', 'P', 'HSE66', 'NE2_957', 'P', 3.6121],
['ARG18', 'NH1_217_220', 'P', 'ASP92', 'OD1_1368_1369', 'P', 3.6951],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.7353],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8213],
['ARG27', 'NH1_356_359', 'P', 'GLU23', 'OE1_290_291', 'P', 3.897],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.2197],
['ARG75', 'NH1_1090_1093', 'P', 'ASP42', 'OD1_609_610', 'P', 4.3401],
['ARG18', 'NH1_217_220', 'P', 'ASP129', 'OD1_1978_1979', 'P', 4.6103],
['ASP86', 'OD1_1269_1270', 'P', 'LYS6', 'NZ_32', 'P', 4.9726]],
[['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 2.5045],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8527],
['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.8842],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.2487],
..
..
In [20]: interactionsTrajectory.getHydrophobic()
[[['ALA156', 'CB_2401', 'P', 'TYR87', 'OH_1286', 'P', 3.0459, 21.959],
['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.3105, 5.1584],
['ILE68', 'CG2_976', 'P', 'MET63', 'CE_894', 'P', 3.3306, 52.4165],
['TYR142', 'CZ_2171', 'P', 'VAL146', 'CG2_2235', 'P', 3.4815, 49.7427],
['PHE10', 'CD1_92', 'P', 'ALA22', 'CB_273', 'P', 3.5334, 31.1973],
['LYS6', 'CD_26', 'P', 'TRP39', 'CZ2_555', 'P', 3.5427, 68.7284],
['PHE26', 'CE2_336', 'P', 'VAL30', 'CG1_411', 'P', 3.5603, 21.127],
['ILE88', 'CD_1307', 'P', 'ALA111', 'CB_1677', 'P', 3.5627, 21.2201],
['VAL11', 'CG2_114', 'P', 'ILE88', 'CG2_1300', 'P', 3.6386, 9.3289],
['VAL41', 'CG2_595', 'P', 'PHE26', 'CD2_334', 'P', 3.6448, 16.55],
['PHE152', 'CE1_2331', 'P', 'ALA156', 'CB_2401', 'P', 3.6594, 17.4765],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.6828, 25.1359],
['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6917, 11.9735],
['PHE82', 'CD1_1205', 'P', 'ILE88', 'CD_1307', 'P', 3.692, 17.6138],
['LEU116', 'CD2_1771', 'P', 'ILE127', 'CD_1949', 'P', 3.7057, 17.4094],
['VAL8', 'CG1_55', 'P', 'PHE26', 'CE2_336', 'P', 3.7106, 12.1392],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7263, 16.9718],
['LEU9', 'CD2_78', 'P', 'ILE77', 'CD_1128', 'P', 3.745, 15.4175],
['LEU89', 'CD1_1322', 'P', 'VAL8', 'CG2_59', 'P', 3.7672, 15.9262],
['ILE126', 'CD_1930', 'P', 'LEU125', 'CD1_1907', 'P', 3.7885, 54.1512],
['VAL141', 'CG1_2149', 'P', 'ILE127', 'CG2_1942', 'P', 3.8659, 11.4623],
['MET91', 'SD_1353', 'P', 'ILE127', 'CD_1949', 'P', 3.8864, 35.855],
['ALA44', 'CB_628', 'P', 'LEU9', 'CD1_74', 'P', 3.8992, 15.0915],
['VAL25', 'CG2_314', 'P', 'TYR142', 'CE1_2169', 'P', 3.92, 12.0265],
['ILE21', 'CG2_256', 'P', 'MET63', 'SD_893', 'P', 3.9614, 20.7701],
['LEU153', 'CD1_2350', 'P', 'TRP39', 'NE1_547', 'P', 3.967, 9.4118],
['PHE85', 'CZ_1253', 'P', 'LEU9', 'CD1_74', 'P', 4.0119, 32.0573],
['ILE35', 'CD_491', 'P', 'TRP39', 'NE1_547', 'P', 4.0172, 25.9805],
['LEU29', 'CD1_395', 'P', 'VAL25', 'CG1_310', 'P', 4.0642, 19.7098],
['ALA74', 'CB_1068', 'P', 'ILE16', 'CG2_177', 'P', 4.0772, 6.6731],
['ARG75', 'CG_1081', 'P', 'ALA44', 'CB_628', 'P', 4.0853, 36.2109],
['ARG18', 'CG_208', 'P', 'VAL141', 'CG1_2149', 'P', 4.104, 20.3057],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.1048, 17.4819],
['TYR119', 'CE1_1805', 'P', 'LEU89', 'CD2_1326', 'P', 4.1435, 11.5628],
['ARG40', 'CG_568', 'P', 'PHE85', 'CE2_1257', 'P', 4.2669, 60.8933],
['LYS28', 'CG_371', 'P', 'ILE68', 'CD_983', 'P', 4.2707, 21.8011],
['PHE138', 'CD2_2108', 'P', 'ILE21', 'CD_263', 'P', 4.3082, 6.5618],
['TYR131', 'CE1_2006', 'P', 'ILE16', 'CD_184', 'P', 4.3352, 8.9118],
['ARG58', 'CG_820', 'P', 'PHE138', 'CE1_2104', 'P', 4.4781, 59.4126]],
[['MET63', 'SD_893', 'P', 'TYR142', 'CD1_2167', 'P', 3.3036, 26.7569],
['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.3592, 7.0868],
['VAL8', 'CG2_59', 'P', 'PHE10', 'CZ_96', 'P', 3.3808, 27.8216],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.429, 13.2977],
['LEU116', 'CD1_1767', 'P', 'PHE10', 'CE1_94', 'P', 3.549, 13.546],
['PHE82', 'CZ_1209', 'P', 'ILE77', 'CD_1128', 'P', 3.5608, 20.4262],
['ILE68', 'CD_983', 'P', 'TYR142', 'OH_2172', 'P', 3.5692, 27.4475],
['PHE26', 'CE2_336', 'P', 'VAL30', 'CG1_411', 'P', 3.5789, 28.1292],
['ALA156', 'CB_2401', 'P', 'PHE152', 'CD1_2329', 'P', 3.6255, 24.4807],
['VAL11', 'CG2_114', 'P', 'ILE88', 'CG2_1300', 'P', 3.6421, 8.6093],
..
..
In [21]: interactionsTrajectory.getPiCation()
[[['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.6523],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.5323],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
4.828]],
[['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
3.4611],
['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.924],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.8561],
['TYR87',
'1280_1281_1283_1285_1288_1290',
'P',
'LYS112',
'NZ_1699',
'P',
4.9287],
['TYR131',
'2003_2004_2006_2008_2011_2013',
'P',
'ARG58',
'NH1_829_832',
'P',
4.9441]],
[['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
2.693],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.0971],
['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
4.4856]],
[['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
2.5938],
['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.5816],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 3.8296]],
[['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.9363],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.7618],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS155',
'NZ_2391',
'P',
4.8181],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
4.8867]],
[['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.2935],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
4.3158]],
[['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.8709],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.4195],
['PHE138',
'2101_2102_2104_2106_2108_2110',
'P',
'ARG58',
'NH1_829_832',
'P',
4.9708]],
..
..
In [22]: interactionsTrajectory.getPiStacking()
[[['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
3.8882,
162.1245],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'TYR119',
'1802_1803_1805_1807_1810_1812',
'P',
4.3605,
3.0063],
['PHE26',
'327_328_330_332_334_336',
'P',
'TRP39',
'549_550_551_553_555_557',
'P',
4.8394,
75.4587],
['TYR132',
'2024_2025_2027_2029_2032_2034',
'P',
'TYR131',
'2003_2004_2006_2008_2011_2013',
'P',
4.8732,
91.4358]],
[['PHE26',
'327_328_330_332_334_336',
'P',
'TRP39',
'549_550_551_553_555_557',
'P',
4.8046,
70.9506],
['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
4.8351,
138.8872]],
[['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
3.6419,
174.2245]],
[['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
4.1376,
143.3286]],
[['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
4.2999,
137.4965],
['TYR87',
'1280_1281_1283_1285_1288_1290',
'P',
'PHE152',
'2328_2329_2331_2333_2335_2337',
'P',
4.9646,
73.7093]],
[['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
4.2623,
158.0688],
..
..
Once we compute interactions, we can also select two that are interesting for
us by using selection or selection and selection2 if we want to
compare two chains of protein structure.
Here, we can display all interactions with residues with numbers between 100
and 106.
In [23]: interactionsTrajectory.getInteractions(selection='resid 100 to 106')
[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.933, 10.3321],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9361, 9.2855],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9952, 32.2712],
['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 3.0464, 19.6807],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 3.4548, 26.1223],
['VAL106', 'N_1588', 'P', 'SER103', 'O_1556', 'P', 3.4974, 34.2367]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.5963, 18.6089],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.7535, 13.6202],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7626, 15.9446],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.9067, 16.7879],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0125, 16.6445],
['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 3.0551, 13.8509],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 3.1649, 39.2608],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2195, 25.4359],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.3521, 12.6376],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.3904, 38.6896],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.46, 29.7639]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6466, 7.8982],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8761, 17.0562],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9269, 16.8394],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.984, 10.6183],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.101, 38.8603],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.2553, 38.5648]],
[['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.5911, 17.069],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6274, 12.9418],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7018, 15.5273],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8801, 16.6129],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9348, 25.5713],
['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 2.9562, 38.6882],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 3.1464, 36.9083],
['LYS102', 'NZ_1540', 'P', 'SER47', 'OG_665', 'P', 3.155, 33.2035],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.2314, 26.449]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6718, 15.3661],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.6858, 28.5654],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.7479, 25.7898],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7584, 9.5766],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.8029, 24.9678],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.9645, 18.3577],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.0085, 24.3135],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2018, 39.9842],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.2421, 26.211],
['ASN104', 'N_1557', 'P', 'ARG101', 'O_1523', 'P', 3.3623, 38.1443]],
[['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.6595, 13.3173],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.8351, 14.4292],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.8423, 25.7739],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.8761, 36.221],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.9016, 29.2602],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9501, 21.9519],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9534, 4.572],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.9715, 13.2817],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0385, 28.4861],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.0741, 22.6725],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.0961, 21.9463]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6673, 5.897],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.8621, 21.3715],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.9062, 37.2809],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.9467, 14.2625],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.0105, 15.1965],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.1835, 33.0481],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.2504, 29.8412],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.4557, 26.8981]],
[['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.6955, 15.9473],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7336, 13.04],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7844, 21.0059],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.7921, 34.0413],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.8616, 30.9582],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9622, 35.633],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9862, 9.5713],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.992, 28.725],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 3.0439, 38.4803],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2289, 6.3339],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.3376, 16.6525],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.3409, 32.703]],
[['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.6495, 18.2239],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.675, 14.3671],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.6999, 16.6616],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7186, 10.5368],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8422, 23.6928],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.8537, 21.8508],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8826, 12.651],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9711, 26.7601],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.1186, 14.3141],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.2655, 29.3262]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6587, 11.1386],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7047, 15.6631],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.791, 11.1184],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 2.801, 22.9498],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.9519, 31.5282],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.0148, 11.0913],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.3007, 38.2386],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.3317, 21.1],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.4041, 33.0264]],
[['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.5558, 15.1737],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.7324, 21.7444],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8949, 31.6832],
['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 2.9391, 22.8993],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 3.1202, 21.236],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.1673, 16.8727],
['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 3.1973, 19.7715],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.271, 31.13],
['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.3052, 14.7978]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.671, 37.3323],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.739, 34.0943],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.7588, 35.9299],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.8159, 18.3284],
['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 2.8621, 29.9939],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.8717, 34.7545],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9076, 6.0046],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.079, 29.8594],
['ASN104', 'N_1557', 'P', 'ARG101', 'O_1523', 'P', 3.4094, 37.1284],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.4107, 38.1571]],
[['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.6803, 15.1718],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7669, 25.5278],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.8242, 31.1474],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.0011, 28.4159],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.0907, 32.962],
['ASN104', 'N_1557', 'P', 'ARG101', 'O_1523', 'P', 3.0944, 31.0232],
['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 3.1066, 31.2941],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.153, 7.2531],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 3.1683, 35.5334]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.5916, 5.2678],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7483, 9.7499],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7533, 23.1952],
['GLN105', 'NE2_1583', 'P', 'ARG101', 'O_1523', 'P', 2.8947, 9.5954],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9874, 36.0359],
['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 2.9944, 17.1267],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0055, 24.8374],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0528, 29.1184],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.0686, 20.4109],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.1474, 24.7453]],
[['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.7044, 10.5924],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7509, 8.0677],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8112, 11.4161],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.8136, 16.1535],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.8215, 39.6551],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.8508, 18.2442],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9434, 34.3129],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.9806, 20.0253],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.1026, 29.4155]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.6685, 15.0847],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.757, 19.0853],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.7715, 5.5688],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.7976, 24.804],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.869, 19.5567],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.9269, 20.4698],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.1468, 8.581],
['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.2707, 39.8715],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2959, 34.2995]],
[['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.6797, 11.1273],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7404, 22.8181],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.8344, 21.332],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.8389, 18.5308],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8491, 12.329],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.9264, 7.5038],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 2.9504, 10.3511],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0236, 6.9167],
['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.106, 38.5309],
['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 3.2461, 4.2582]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.6103, 19.241],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.6343, 15.3945],
['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD2_1464', 'P', 2.6543, 10.2308],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7596, 12.1992],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.7949, 12.7041],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.9188, 34.6284],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9977, 39.8669],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.162, 37.02],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.1719, 26.513],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.2101, 36.7681]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7558, 29.536],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7988, 8.8578],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8421, 28.9541],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9436, 3.1426],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0155, 38.3833],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.0202, 2.421],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.2096, 28.1311],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 3.4213, 14.8714]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6129, 19.7326],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.6911, 19.978],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7089, 22.225],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.7963, 25.158],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8504, 16.7766],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8915, 21.1984],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0135, 31.6808],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.0372, 20.7935],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0379, 38.205],
['GLN105', 'NE2_1583', 'P', 'ARG101', 'O_1523', 'P', 3.2845, 28.1096],
['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.4421, 25.6483]],
[['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.6793, 16.1937],
['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD2_1464', 'P', 2.7584, 11.5432],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.775, 6.6534],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7754, 4.8907],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 2.8177, 29.9366],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.8304, 17.4803],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.856, 21.4102],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9243, 35.6267],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.0156, 9.3534]],
[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.0699],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.9359]],
[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.8263],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.5063]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0796]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8527],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.5055]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5251],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6639]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.784],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7415]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7833],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6905]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.118],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.7333]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9802],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3115]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1925],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3314]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1321],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.377]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5465],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.1424]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8662],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7765]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.4575],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7844]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7106],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2495]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9739],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3131]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0533],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.8328]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.2511],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6196]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.955],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.9277]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1188],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6654]],
[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.7506]],
[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2655]],
[],
[],
[],
[],
[],
[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2903]],
[],
[],
[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3093]],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.6828, 25.1359],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.1048, 17.4819]],
[['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 3.6601, 18.1513],
['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 4.0401, 13.1367],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2489, 20.4475]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.9579, 24.0447],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 3.993, 10.9852]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG1_1594', 'P', 3.7771, 25.8417],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.2695, 6.7328]],
[['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 3.7581, 24.2415],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.3995, 30.7521]],
[['LYS79', 'CD_1158', 'P', 'VAL106', 'CG2_1598', 'P', 3.9758, 19.5257],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.2315, 11.0609]],
[['VAL106', 'CG1_1594', 'P', 'PHE82', 'CG_1204', 'P', 3.8971, 17.973],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.0318, 20.1861]],
[['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 3.9504, 18.2026],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.0183, 24.7812],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.354, 18.5823]],
[['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.1345, 9.1889],
['LYS79', 'CD_1158', 'P', 'VAL106', 'CG2_1598', 'P', 4.1488, 19.0544]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.7492, 21.5977]],
[['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 3.7532, 20.5214],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.1843, 21.2188]],
[['LYS79', 'CD_1158', 'P', 'VAL106', 'CG2_1598', 'P', 4.1132, 33.2299],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.2545, 30.9532]],
[['VAL106', 'CG1_1594', 'P', 'PHE82', 'CG_1204', 'P', 4.2115, 22.6531],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.4451, 30.8638]],
[['LYS102', 'CD_1534', 'P', 'PHE82', 'CE2_1213', 'P', 4.1132, 21.6908],
['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 4.301, 14.4692]],
[['VAL106', 'CG1_1594', 'P', 'PHE82', 'CD1_1205', 'P', 3.769, 29.2683]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.7591, 26.6179]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG1_1594', 'P', 3.7466, 15.362],
['LYS102', 'CD_1534', 'P', 'PHE82', 'CZ_1209', 'P', 4.3692, 20.969]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.7838, 20.4368],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.2006, 12.5337]],
[['LYS102', 'CD_1534', 'P', 'PHE82', 'CZ_1209', 'P', 4.3001, 14.6918]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2078, 41.8606],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.3141, 10.5395]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2738, 15.6412]],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[]]
We can apply the same selection to any type of interaction, for example:
In [24]: interactionsTrajectory.getHydrophobic(selection='chain P and resid 90 to 100')
[[['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6917, 11.9735],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7263, 16.9718],
['MET91', 'SD_1353', 'P', 'ILE127', 'CD_1949', 'P', 3.8864, 35.855]],
[['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.429, 13.2977],
['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6871, 7.95],
['MET91', 'CE_1354', 'P', 'LEU116', 'CD2_1771', 'P', 3.8434, 19.1277]],
[['ILE88', 'CG2_1300', 'P', 'LEU99', 'CD1_1476', 'P', 3.5436, 9.3247],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.57, 23.3065],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6654, 17.4729]],
[['LEU99', 'CD1_1476', 'P', 'ILE88', 'CG2_1300', 'P', 3.5506, 10.5506],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.6132, 25.5246],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.6989, 21.7296]],
[['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.681, 13.3699],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.7838, 19.4208],
['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 3.8538, 35.0746],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CD_1718', 'P', 3.993, 32.6427],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.3995, 30.7521]],
[['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.4473, 9.6836],
['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 3.7931, 33.4972],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.8599, 15.7656],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG1_1715', 'P', 4.0839, 25.8005]],
[['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6656, 11.2061],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CD_1718', 'P', 3.7465, 13.9407],
['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 4.1873, 5.8643]],
[['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.577, 21.8565],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.7311, 16.6688],
['LEU99', 'CD1_1476', 'P', 'ILE77', 'CD_1128', 'P', 3.7918, 13.9645],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.0183, 24.7812]],
[['LEU99', 'CD1_1476', 'P', 'ILE88', 'CG2_1300', 'P', 3.493, 12.0525],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.8477, 17.8661],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.9465, 13.0407],
['ARG18', 'CG_208', 'P', 'MET91', 'CG_1350', 'P', 4.4773, 45.2545]],
[['MET91', 'SD_1353', 'P', 'ILE127', 'CD_1949', 'P', 3.6073, 35.8986],
['LEU99', 'CD1_1476', 'P', 'VAL11', 'CG1_110', 'P', 3.8196, 19.5026],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.8266, 8.1345]],
[['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.688, 16.5389],
['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.8303, 12.8658],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.9125, 20.3824],
['ARG18', 'CG_208', 'P', 'MET91', 'CG_1350', 'P', 4.3469, 47.3018]],
[['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.4146, 25.9366],
['LEU99', 'CD2_1480', 'P', 'PHE82', 'CZ_1209', 'P', 3.6458, 17.5698],
['ILE113', 'CG2_1711', 'P', 'LEU99', 'CD1_1476', 'P', 3.7998, 30.7151],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 4.0071, 18.0266],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.2545, 30.9532]],
[['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.5757, 19.6775],
['LEU99', 'CD2_1480', 'P', 'ILE88', 'CG2_1300', 'P', 3.8102, 10.1337],
['ILE113', 'CG2_1711', 'P', 'LEU96', 'CG_1419', 'P', 3.8694, 28.8723]],
[['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.5696, 9.6273],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.8426, 17.9602]],
[['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.511, 19.586],
['LEU99', 'CD1_1476', 'P', 'VAL11', 'CG2_114', 'P', 3.5732, 10.7329],
['MET91', 'CE_1354', 'P', 'LEU116', 'CD2_1771', 'P', 3.9678, 13.6217]],
[['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.6543, 13.7308],
['ILE113', 'CG2_1711', 'P', 'LEU96', 'CG_1419', 'P', 3.7456, 22.5419],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.8152, 17.9895]],
[['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.4849, 12.5888],
['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 3.5767, 9.5877],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7229, 15.3003],
['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 4.274, 35.6655]],
[['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6286, 22.7844],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.6984, 12.3956],
['ALA22', 'CB_273', 'P', 'MET91', 'CE_1354', 'P', 3.7795, 8.4161],
['LEU99', 'CD2_1480', 'P', 'ILE88', 'CG2_1300', 'P', 3.7921, 7.4352]],
[['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 3.4598, 42.01],
['LEU99', 'CD1_1476', 'P', 'ILE113', 'CG2_1711', 'P', 3.6609, 33.0336],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7378, 17.5379],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.7686, 14.0166]],
[['LEU99', 'CD1_1476', 'P', 'VAL11', 'CG2_114', 'P', 3.518, 18.8799],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.5399, 12.2359],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7165, 21.0434]],
[['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.2931, 21.0747],
['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.3771, 11.4804],
['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 3.6628, 9.0978],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6984, 21.9302]]]
In [25]: interactionsTrajectory.getHydrogenBonds(selection='chain P and resid 112 to 115')
[[['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8429, 17.7147],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8975, 24.576],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.912, 10.1158],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.051, 21.4045],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.059, 24.1606],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 3.2687, 28.6743]],
[['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE1_1735', 'P', 2.5487, 20.8176],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.6334, 17.8203],
['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.6547, 25.6442],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE1_1735', 'P', 2.735, 15.8502],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7935, 13.2257],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8946, 17.9316],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9523, 13.8795],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.0323, 8.8409],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.2094, 37.0837],
['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.2322, 23.7336],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE2_1736', 'P', 3.253, 23.8402]],
[['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.5902, 19.0335],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6441, 10.2991],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7184, 24.9984],
['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.7238, 26.9156],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8381, 10.253],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'ND1_2414', 'P', 2.8616, 14.018],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.8761, 18.0626],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0416, 27.2343],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.195, 38.6534],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.4603, 13.0317]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.5321, 12.1754],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6666, 5.0368],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.6844, 12.4337],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7625, 21.1367],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7703, 4.1752],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.813, 11.6498],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8375, 24.3092],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'ND1_2414', 'P', 2.8399, 24.5852],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.9985, 12.7544]],
[['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6438, 28.5062],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7748, 6.971],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8324, 30.6076],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8567, 3.076],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.8677, 22.3219],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9251, 9.0077],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0506, 7.4102],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.4475, 19.9922]],
[['TYR119', 'OH_1808', 'P', 'GLU114', 'OE1_1735', 'P', 2.6085, 18.3035],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.7054, 1.3697],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE1_1735', 'P', 2.7093, 27.1289],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8128, 18.817],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.0762, 12.1723],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.1037, 10.0101],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.1356, 19.0662],
['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.3017, 27.3282],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.3047, 11.3911]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.652, 10.3503],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.762, 14.1022],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7884, 21.6503],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.7994, 5.7305],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8628, 30.0771],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.9474, 28.4869],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.4304, 27.1097]],
[['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.7778, 28.0614],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.7868, 18.8919],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8504, 18.6098],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.9351, 15.9934],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.9391, 14.958]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.6858, 23.9752],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8512, 7.2231],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 2.9951, 23.9118],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.0881, 6.5417],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.1217, 14.0883],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.2069, 19.3312],
['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.2331, 32.7145]],
[['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.6385, 22.7134],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.6967, 1.035],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7267, 17.2895],
['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.8598, 29.0811],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9766, 16.8905],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.0616, 27.2229],
['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.4089, 25.9472]],
[['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.8001, 13.1653],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8336, 11.5184],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8683, 15.5308],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8949, 10.1824],
['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.9677, 16.3497],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.089, 17.9789]],
[['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7045, 11.8564],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8002, 5.9828],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8444, 31.549],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0718, 34.4381],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.3002, 12.0528]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.549, 18.6576],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.7292, 11.3872],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7951, 19.2119],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.861, 9.3445],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.8723, 5.3509],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.2056, 13.0868]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.7432, 12.0576],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8455, 10.8341],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8979, 18.8959],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.9513, 25.3055],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2646, 30.184]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.7509, 33.4365],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7569, 15.9129],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8989, 5.3091],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.0521, 14.9906],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2193, 17.7506]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.9107, 11.3311],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9279, 24.4459],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.9572, 22.8551],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.0531, 39.2571],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2647, 19.7898]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.7301, 6.4912],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.0067, 19.0131],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.0515, 32.6929],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.0654, 16.9354],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.2584, 28.3632]],
[['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.7161, 4.3692],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7665, 15.6553],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.833, 1.7101],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.9604, 20.771],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.1924, 36.5103],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.3101, 22.7426]],
[['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7306, 1.388],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7477, 25.8134],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.7669, 4.8657],
['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.7852, 20.1148]],
[['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8181, 19.759],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8698, 4.299],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.0671, 23.7084],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.1112, 27.1195],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.1262, 21.7619]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.6334, 24.4833],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8598, 7.853],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0172, 19.6851],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2603, 11.1927],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.3213, 8.0609]]]
In [26]: interactionsTrajectory.getSaltBridges(selection='chain P and resid 100 to 120')
[[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.0699],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.9359],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 4.0787],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.1543],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 4.1879],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.3835]],
[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.8263],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 3.0552],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 3.2384],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.3269],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.5063],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8015]],
[['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5925],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0796],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.7353],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8213],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.2197]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8527],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.2487],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 3.281],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 3.4289],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.5055],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.7295]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5251],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5476],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.8031],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.7693],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6639]],
[['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5445],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.784],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.9545],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.4269],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7415]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7833],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.7841],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.6393],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6905],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.9985]],
[['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.7718],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.118],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.7333],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.385]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9802],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.1049],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3115],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.4854]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1925],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.3668],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3314],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.6386]],
[['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.7461],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1321],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.377]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5465],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.7315],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.886],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.1424]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8662],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7765],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 4.9921]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.4575],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.6085],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.9194],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.3166],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7844]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7106],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.7026],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.794],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2495]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9739],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.397],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.5529],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.9267],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3131]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0533],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.7951],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.8215],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.9526],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.8328]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.2511],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6196],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.9186]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.955],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.9277]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1188],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6654],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.9234]],
[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.7506],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.4341]]]
In [27]: interactionsTrajectory.getRepulsiveIonicBonding(selection='chain P')
[[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2655]],
[],
[],
[],
[],
[],
[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2903]],
[],
[],
[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3093]],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[['ARG147', 'NH1_2257_2260', 'P', 'LYS123', 'NZ_1875', 'P', 4.4846]]]
Change selection criteria for interaction type¶
The interactionsTrajectory.calcProteinInteractionsTrajectory() method computes
interactions using default parameters for interactions. However, it can be
changed according to our needs. To do that, we need to recalculate the
selected types of interactions.
We can do it using the following functions: calcHydrogenBondsTrajectory(),
calcHydrogenBondsTrajectory(), calcSaltBridgesTrajectory(),
calcRepulsiveIonicBondingTrajectory(), calcPiStackingTrajectory(),
calcPiCationTrajectory(), calcHydrophohicTrajectory(), and use
InteractionsTrajectory.setNewHydrogenBondsTrajectory(),
InteractionsTrajectory.setNewSaltBridgesTrajectory(),
InteractionsTrajectory.setNewRepulsiveIonicBondingTrajectory(),
InteractionsTrajectory.setNewPiStackingTrajectory(),
InteractionsTrajectory.setNewPiCationTrajectory(),
InteractionsTrajectory.setNewHydrophohicTrajectory() method to replace it in the main
Instance.
For example:
Repulsive ionic bonding:
In [28]: newRIB = calcRepulsiveIonicBondingTrajectory(atoms, dcd, distA=8)
In [29]: interactionsTrajectory.setNewRepulsiveIonicBondingTrajectory(newRIB)
@> Frame: 0
@> Calculating repulsive ionic bonding.
@> ARG75 P NH1_1090_1093 <---> ARG40 P NH1_577_580 6.7
@> ASP81 P OD1_1193_1194 <---> GLU80 P OE1_1181_1182 7.0
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.6
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 1
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 4.5
@> ASP92 P OD1_1368_1369 <---> GLU93 P OE1_1383_1384 7.9
@> Number of detected Repulsive Ionic Bonding interactions: 2.
@> Frame: 2
@> Calculating repulsive ionic bonding.
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.8
@> ASP137 P OD1_2090_2091 <---> GLU128 P OE1_1966_1967 7.7
@> ASP81 P OD1_1193_1194 <---> GLU80 P OE1_1181_1182 7.9
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 3
@> Calculating repulsive ionic bonding.
@> GLU80 P OE1_1181_1182 <---> ASP81 P OD1_1193_1194 6.3
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.8
@> Number of detected Repulsive Ionic Bonding interactions: 2.
@> Frame: 4
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 6.0
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.8
@> ARG75 P NH1_1090_1093 <---> ARG40 P NH1_577_580 7.0
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 5
@> Calculating repulsive ionic bonding.
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.1
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.6
@> LYS79 P NZ_1164 <---> LYS102 P NZ_1540 7.8
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 6
@> Calculating repulsive ionic bonding.
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.1
@> LYS112 P NZ_1699 <---> LYS6 P NZ_32 6.4
@> LYS79 P NZ_1164 <---> LYS107 P NZ_1620 7.1
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 7
@> Calculating repulsive ionic bonding.
@> ARG147 P NH1_2257_2260 <---> LYS123 P NZ_1875 4.8
@> ASP42 P OD1_609_610 <---> GLU23 P OE1_290_291 5.9
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.4
@> ARG75 P NH1_1090_1093 <---> ARG40 P NH1_577_580 6.9
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 8
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 5.1
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.0
@> ASP81 P OD1_1193_1194 <---> GLU80 P OE1_1181_1182 7.2
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 9
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 4.3
@> GLU93 P OE1_1383_1384 <---> GLU128 P OE1_1966_1967 6.2
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.4
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 10
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 4.6
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 4.7
@> ASP92 P OD1_1368_1369 <---> GLU128 P OE1_1966_1967 6.4
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.4
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 11
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 5.3
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.6
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.7
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 12
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 5.9
@> ARG75 P NH1_1090_1093 <---> ARG40 P NH1_577_580 6.2
@> ARG150 P NH1_2303_2306 <---> ARG147 P NH1_2257_2260 7.2
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 13
@> Calculating repulsive ionic bonding.
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.6
@> ASP129 P OD1_1978_1979 <---> GLU128 P OE1_1966_1967 6.6
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 7.8
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.8
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 14
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 7.0
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.1
@> ASP81 P OD1_1193_1194 <---> GLU80 P OE1_1181_1182 7.2
@> ASP92 P OD1_1368_1369 <---> GLU128 P OE1_1966_1967 8.0
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 15
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 6.5
@> GLU154 P OE1_2371_2372 <---> ASP120 P OD1_1824_1825 6.5
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.6
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 16
@> Calculating repulsive ionic bonding.
@> ASP42 P OD1_609_610 <---> GLU23 P OE1_290_291 5.6
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 7.1
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.2
@> ASP129 P OD1_1978_1979 <---> GLU128 P OE1_1966_1967 7.2
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 17
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 4.9
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.5
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.4
@> GLU128 P OE1_1966_1967 <---> ASP129 P OD1_1978_1979 8.0
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 18
@> Calculating repulsive ionic bonding.
@> ASP42 P OD1_609_610 <---> GLU23 P OE1_290_291 5.7
@> ASP135 P OD1_2067_2068 <---> GLU139 P OE1_2125_2126 5.9
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.8
@> ASP92 P OD1_1368_1369 <---> GLU128 P OE1_1966_1967 6.8
@> GLU93 P OE1_1383_1384 <---> GLU128 P OE1_1966_1967 7.3
@> Number of detected Repulsive Ionic Bonding interactions: 5.
@> Frame: 19
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 5.3
@> GLU139 P OE1_2125_2126 <---> ASP135 P OD1_2067_2068 6.0
@> LYS79 P NZ_1164 <---> LYS107 P NZ_1620 6.1
@> ASP81 P OD1_1193_1194 <---> GLU80 P OE1_1181_1182 7.0
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 20
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 4.5
@> ASP135 P OD1_2067_2068 <---> GLU139 P OE1_2125_2126 5.5
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.1
@> LYS79 P NZ_1164 <---> LYS102 P NZ_1540 7.9
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Repulsive Ionic Bonding are replaced
Pi-cation interactions:
In [30]: newPiCation = calcPiCationTrajectory(atoms, dcd, distA=6)
In [31]: interactionsTrajectory.setNewPiCationTrajectory(newPiCation)
@> Frame: 0
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.5
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.8
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.0
@> TYR131 P 2003_2004_2006_2008_2011_2013 <---> ARG58 P NH1_829_832 5.1
@> Number of detected cation-pi interactions: 5.
@> Frame: 1
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 3.5
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.9
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 4.9
@> TYR131 P 2003_2004_2006_2008_2011_2013 <---> ARG58 P NH1_829_832 4.9
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.7
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 6.0
@> Number of detected cation-pi interactions: 7.
@> Frame: 2
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 2.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.1
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.5
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.6
@> Number of detected cation-pi interactions: 4.
@> Frame: 3
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 2.6
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.6
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 3.8
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.3
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.3
@> Number of detected cation-pi interactions: 5.
@> Frame: 4
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.8
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS155 P NZ_2391 4.8
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.9
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.3
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.4
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS6 P NZ_32 5.6
@> Number of detected cation-pi interactions: 7.
@> Frame: 5
@> Calculating cation-Pi interactions.
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.3
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.3
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 5.2
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.8
@> Number of detected cation-pi interactions: 4.
@> Frame: 6
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.4
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.0
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 5.0
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS6 P NZ_32 5.3
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.5
@> Number of detected cation-pi interactions: 6.
@> Frame: 7
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.2
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.9
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.7
@> Number of detected cation-pi interactions: 4.
@> Frame: 8
@> Calculating cation-Pi interactions.
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 3.8
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.5
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 5.4
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.6
@> Number of detected cation-pi interactions: 4.
@> Frame: 9
@> Calculating cation-Pi interactions.
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.4
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.8
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.2
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.4
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.5
@> PHE152 P 2328_2329_2331_2333_2335_2337 <---> LYS6 P NZ_32 5.8
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 5.8
@> Number of detected cation-pi interactions: 7.
@> Frame: 10
@> Calculating cation-Pi interactions.
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.8
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 4.9
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 5.0
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.2
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 5.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 11
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.1
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS155 P NZ_2391 4.4
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.8
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.4
HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 5.8
@>
@> Number of detected cation-pi interactions: 5.
@> Frame: 12
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.3
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.4
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.4
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.5
@> HSE72 P 1038_1039_1040_1042_1044 <---> ARG27 P NH1_356_359 5.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 13
@> Calculating cation-Pi interactions.
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.4
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.7
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.2
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 5.8
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS155 P NZ_2391 5.9
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 6.0
@> Number of detected cation-pi interactions: 6.
@> Frame: 14
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.6
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS6 P NZ_32 5.2
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.3
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 5.6
@> Number of detected cation-pi interactions: 4.
@> Frame: 15
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.4
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS6 P NZ_32 5.1
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 5.8
@> Number of detected cation-pi interactions: 4.
@> Frame: 16
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.8
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS6 P NZ_32 5.4
@> Number of detected cation-pi interactions: 2.
@> Frame: 17
@> Calculating cation-Pi interactions.
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.4
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.6
@> Number of detected cation-pi interactions: 2.
@> Frame: 18
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.5
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.2
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.3
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.7
@> HSE72 P 1038_1039_1040_1042_1044 <---> ARG27 P NH1_356_359 5.8
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 6.0
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 6.0
@> Number of detected cation-pi interactions: 7.
@> Frame: 19
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.9
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.0
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.2
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 5.9
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 5.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 20
@> Calculating cation-Pi interactions.
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.0
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.6
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 5.7
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 5.8
@> Number of detected cation-pi interactions: 4.
Pi-Cation interactions are replaced
We can check whether the interactions were replaced. The repulsive ionic
bonding can be found by using getInteractions() and selecting 2
(0 - hydrogen bonds, 1 - salt bridges, 2 - repulsive ionic bonding,
3 - Pi-Stacking, 4 - Pi-Cation, 5 - hydrophobic, 6 - disulfide bonds).
In [32]: interactionsTrajectory.getInteractions()[2]
[[['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 6.666],
['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 6.9843],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.6316]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.5002],
['ASP92', 'OD1_1368_1369', 'P', 'GLU93', 'OE1_1383_1384', 'P', 7.9458]],
[['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.8023],
['ASP137', 'OD1_2090_2091', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.7429],
['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 7.9228]],
[['GLU80', 'OE1_1181_1182', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.2655],
['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.8064]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 6.0034],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.8451],
['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 7.0306]],
[['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.1332],
['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.6231],
['LYS79', 'NZ_1164', 'P', 'LYS102', 'NZ_1540', 'P', 7.81]],
[['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.1141],
['LYS112', 'NZ_1699', 'P', 'LYS6', 'NZ_32', 'P', 6.4258],
['LYS79', 'NZ_1164', 'P', 'LYS107', 'NZ_1620', 'P', 7.0898]],
[['ARG147', 'NH1_2257_2260', 'P', 'LYS123', 'NZ_1875', 'P', 4.8418],
['ASP42', 'OD1_609_610', 'P', 'GLU23', 'OE1_290_291', 'P', 5.8605],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.3776],
['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 6.9162]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 5.1095],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.9653],
['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 7.1885]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.3093],
['GLU93', 'OE1_1383_1384', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.2251],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.3655]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.6267],
['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.6563],
['ASP92', 'OD1_1368_1369', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.4486],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.3554]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 5.2803],
['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.6125],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.7231]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 5.903],
['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 6.2264],
['ARG150', 'NH1_2303_2306', 'P', 'ARG147', 'NH1_2257_2260', 'P', 7.2115]],
[['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.5807],
['ASP129', 'OD1_1978_1979', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.6156],
['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 7.7691],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.8267]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 6.9607],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.0793],
['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 7.1994],
['ASP92', 'OD1_1368_1369', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.9662]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 6.4558],
['GLU154', 'OE1_2371_2372', 'P', 'ASP120', 'OD1_1824_1825', 'P', 6.5391],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.6406]],
[['ASP42', 'OD1_609_610', 'P', 'GLU23', 'OE1_290_291', 'P', 5.5599],
['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 7.1302],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.1991],
['ASP129', 'OD1_1978_1979', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.2499]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.913],
['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.4678],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.3594],
['GLU128', 'OE1_1966_1967', 'P', 'ASP129', 'OD1_1978_1979', 'P', 7.9788]],
[['ASP42', 'OD1_609_610', 'P', 'GLU23', 'OE1_290_291', 'P', 5.6704],
['ASP135', 'OD1_2067_2068', 'P', 'GLU139', 'OE1_2125_2126', 'P', 5.9135],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.7566],
['ASP92', 'OD1_1368_1369', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.7899],
['GLU93', 'OE1_1383_1384', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.3464]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 5.3159],
['GLU139', 'OE1_2125_2126', 'P', 'ASP135', 'OD1_2067_2068', 'P', 6.0087],
['LYS79', 'NZ_1164', 'P', 'LYS107', 'NZ_1620', 'P', 6.0679],
['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 6.9706]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.4846],
['ASP135', 'OD1_2067_2068', 'P', 'GLU139', 'OE1_2125_2126', 'P', 5.4686],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.0978],
['LYS79', 'NZ_1164', 'P', 'LYS102', 'NZ_1540', 'P', 7.9242]]]
In [33]: interactionsTrajectory.getInteractions()[4]
[[['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.6523],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.5323],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
4.828],
['PHE138',
'2101_2102_2104_2106_2108_2110',
'P',
'ARG58',
'NH1_829_832',
'P',
5.0448],
['TYR131',
'2003_2004_2006_2008_2011_2013',
'P',
'ARG58',
'NH1_829_832',
'P',
5.0915]],
..
..
Statistics¶
Using calcStatisticsInteractions() function, we can compute the statistics
of interaction in the trajectory, such as the average distance between residues
(usually the center of the mass; details are described in the function which
computes the specific type of interactions), standard deviation for the
distance value and weight. Weight is the number of counts for the whole
trajectory and is divided by the number of frames in the dcd file. Weight equal to 1
corresponds to the contact that was main the whole time of the simulation.
Note that weight can be >1 when multiple contacts are present between the same
residues.
For example:
In [34]: interactions = interactionsTrajectory.getPiCation()
In [35]: calcStatisticsInteractions(interactions)
@> Statistics for PHE85P-ARG40P:
@> Average [Ang.]: 4.385379791259766
@> Standard deviation [Ang.]: 0.5366479754447937
@> Weight: 0.952381
@> Statistics for HSE66P-ARG65P:
@> Average [Ang.]: 4.717772006988525
@> Standard deviation [Ang.]: 0.6487299799919128
@> Weight: 0.857143
@> Statistics for HSE157P-LYS112P:
@> Average [Ang.]: 4.388020038604736
@> Standard deviation [Ang.]: 1.0506110191345215
@> Weight: 0.47619
@> Statistics for PHE138P-ARG58P:
@> Average [Ang.]: 5.318399906158447
@> Standard deviation [Ang.]: 0.24265700578689575
@> Weight: 0.809524
@> Statistics for TYR87P-LYS112P:
@> Average [Ang.]: 5.441559791564941
@> Standard deviation [Ang.]: 0.25401198863983154
@> Weight: 0.47619
@> Statistics for TRP39P-LYS6P:
@> Average [Ang.]: 5.522061824798584
@> Standard deviation [Ang.]: 0.31886300444602966
@> Weight: 0.380952
@> Statistics for PHE85P-ARG75P:
@> Average [Ang.]: 5.877999782562256
@> Standard deviation [Ang.]: 0.06788399815559387
@> Weight: 0.285714
In [36]: calcStatisticsInteractions(interactionsTrajectory.getHydrogenBonds())
@> Statistics for ARG101P-ASP98P:
@> Average [Ang.]: 2.793931
@> Standard deviation [Ang.]: 0.205527
@> Weight: 1.52381
@> Statistics for HSE72P-ASN15P:
@> Average [Ang.]: 2.989283
@> Standard deviation [Ang.]: 0.270697
@> Weight: 0.285714
@> Statistics for GLN143P-GLU139P:
@> Average [Ang.]: 3.051633
@> Standard deviation [Ang.]: 0.20753
@> Weight: 1.285714
@> Statistics for HSE66P-GLU139P:
@> Average [Ang.]: 2.900411
@> Standard deviation [Ang.]: 0.169455
@> Weight: 0.428571
@> Statistics for ARG40P-LYS6P:
@> Average [Ang.]: 3.055475
@> Standard deviation [Ang.]: 0.213814
@> Weight: 0.380952
@> Statistics for ARG58P-ASP56P:
@> Average [Ang.]: 2.827481
@> Standard deviation [Ang.]: 0.171087
@> Weight: 2.952381
@> Statistics for ALA45P-ARG75P:
@> Average [Ang.]: 2.840721
@> Standard deviation [Ang.]: 0.105565
@> Weight: 0.904762
@> Statistics for ASN53P-GLU50P:
@> Average [Ang.]: 2.980214
@> Standard deviation [Ang.]: 0.147229
@> Weight: 0.333333
@> Statistics for ALA74P-ASN53P:
@> Average [Ang.]: 2.98522
@> Standard deviation [Ang.]: 0.148331
@> Weight: 0.952381
@> Statistics for ASP56P-ILE16P:
@> Average [Ang.]: 3.085957
@> Standard deviation [Ang.]: 0.21134
@> Weight: 0.666667
@> Statistics for LYS110P-THR84P:
@> Average [Ang.]: 2.774475
@> Standard deviation [Ang.]: 0.080304
@> Weight: 0.380952
@> Statistics for LEU116P-CYS90P:
@> Average [Ang.]: 2.887425
@> Standard deviation [Ang.]: 0.118768
@> Weight: 0.952381
@> Statistics for SER103P-LEU99P:
@> Average [Ang.]: 2.897324
@> Standard deviation [Ang.]: 0.17182
@> Weight: 1.380952
@> Statistics for ASN134P-ASP137P:
@> Average [Ang.]: 2.917242
@> Standard deviation [Ang.]: 0.160488
@> Weight: 0.904762
@> Statistics for PHE152P-CYS148P:
@> Average [Ang.]: 2.956784
@> Standard deviation [Ang.]: 0.160039
@> Weight: 0.904762
@> Statistics for ASN95P-ASP92P:
@> Average [Ang.]: 3.061373
@> Standard deviation [Ang.]: 0.215848
@> Weight: 0.714286
@> Statistics for LYS6P-ASN38P:
@> Average [Ang.]: 3.006786
@> Standard deviation [Ang.]: 0.154497
@> Weight: 0.333333
@> Statistics for ILE77P-ALA45P:
@> Average [Ang.]: 2.819429
@> Standard deviation [Ang.]: 0.092538
@> Weight: 0.666667
@> Statistics for LEU99P-ASN95P:
@> Average [Ang.]: 3.027242
@> Standard deviation [Ang.]: 0.19744
@> Weight: 0.904762
@> Statistics for CYS149P-CYS145P:
@> Average [Ang.]: 2.928052
@> Standard deviation [Ang.]: 0.146811
@> Weight: 1.190476
@> Statistics for GLY52P-ALA74P:
@> Average [Ang.]: 2.887583
@> Standard deviation [Ang.]: 0.088417
@> Weight: 0.285714
@> Statistics for ASP32P-LYS28P:
@> Average [Ang.]: 2.86277
@> Standard deviation [Ang.]: 0.119982
@> Weight: 0.952381
@> Statistics for ILE88P-LYS112P:
@> Average [Ang.]: 2.906433
@> Standard deviation [Ang.]: 0.147086
@> Weight: 1.0
@> Statistics for ARG27P-GLU23P:
@> Average [Ang.]: 2.790357
@> Standard deviation [Ang.]: 0.140396
@> Weight: 2.0
@> Statistics for TYR142P-PHE138P:
@> Average [Ang.]: 3.094219
@> Standard deviation [Ang.]: 0.152889
@> Weight: 1.0
@> Statistics for PHE26P-ALA22P:
@> Average [Ang.]: 3.023619
@> Standard deviation [Ang.]: 0.150087
@> Weight: 1.0
@> Statistics for ASN15P-SER19P:
@> Average [Ang.]: 2.96532
@> Standard deviation [Ang.]: 0.213496
@> Weight: 0.238095
@> Statistics for ARG75P-ASP81P:
@> Average [Ang.]: 2.782441
@> Standard deviation [Ang.]: 0.185369
@> Weight: 2.095238
@> Statistics for ARG75P-ASP42P:
@> Average [Ang.]: 2.760572
@> Standard deviation [Ang.]: 0.134486
@> Weight: 1.380952
@> Statistics for ARG97P-GLU93P:
@> Average [Ang.]: 2.881173
@> Standard deviation [Ang.]: 0.223159
@> Weight: 1.952381
@> Statistics for ARG65P-GLU139P:
@> Average [Ang.]: 2.826732
@> Standard deviation [Ang.]: 0.198775
@> Weight: 1.047619
@> Statistics for VAL25P-ILE21P:
@> Average [Ang.]: 2.975267
@> Standard deviation [Ang.]: 0.121046
@> Weight: 1.0
@> Statistics for LEU153P-CYS149P:
@> Average [Ang.]: 3.04695
@> Standard deviation [Ang.]: 0.1793
@> Weight: 0.952381
@> Statistics for SER7P-ASP86P:
@> Average [Ang.]: 2.758983
@> Standard deviation [Ang.]: 0.122097
@> Weight: 1.142857
..
..
@> Statistics for ALA83P-LYS79P:
@> Average [Ang.]: 3.225643
@> Standard deviation [Ang.]: 0.148806
@> Weight: 0.333333
@> Statistics for GLN60P-MET70P:
@> Average [Ang.]: 2.902757
@> Standard deviation [Ang.]: 0.162208
@> Weight: 0.333333
@> Statistics for GLN124P-ILE126P:
@> Average [Ang.]: 2.98456
@> Standard deviation [Ang.]: 0.198396
@> Weight: 0.238095
@> Statistics for SER19P-ASN15P:
@> Average [Ang.]: 2.691612
@> Standard deviation [Ang.]: 0.10843
@> Weight: 0.380952
@> Statistics for ASN95P-THR46P:
@> Average [Ang.]: 3.056129
@> Standard deviation [Ang.]: 0.197107
@> Weight: 0.333333
@> Statistics for ARG150P-ASP120P:
@> Average [Ang.]: 2.752571
@> Standard deviation [Ang.]: 0.112541
@> Weight: 0.333333
@> Statistics for LYS155P-HSE157P:
@> Average [Ang.]: 2.833843
@> Standard deviation [Ang.]: 0.185712
@> Weight: 0.333333
@> Statistics for ARG65P-ASP135P:
@> Average [Ang.]: 2.86488
@> Standard deviation [Ang.]: 0.213607
@> Weight: 0.47619
For better visualization of the results, we can use
showInteractionsGraph(), which displays results as a graph with
residue-residue pairs of interactions. The intensity of the color of the
lines connecting two residues corresponds to the number of counts. Darker
lines are assigned to the most frequent appearance of interaction. The
distance between pairs corresponds to the average distance across
all the frames. Moreover, ovals with residue names are color-coded: acidic
residues: red, basic: blue, polar: green, non-polar: silver, and
proline: pink. The same function can be applied to ensemble PDB (more
examples can be found there).
We will also change the region of protein structure, which we would like to
analyze from residue 1 to 100.
In [37]: statistics = calcStatisticsInteractions(interactionsTrajectory.getHydrogenBonds(selection='resid 5 to 100'))
In [38]: showInteractionsGraph(statistics, code='1-letter', cutoff=0.5)
@> Statistics for ARG101P-ASP98P:
@> Average [Ang.]: 2.793931
@> Standard deviation [Ang.]: 0.205527
@> Weight: 1.52381
@> Statistics for HSE72P-ASN15P:
@> Average [Ang.]: 2.989283
@> Standard deviation [Ang.]: 0.270697
@> Weight: 0.285714
@> Statistics for HSE66P-GLU139P:
@> Average [Ang.]: 2.900411
@> Standard deviation [Ang.]: 0.169455
@> Weight: 0.428571
@> Statistics for ARG40P-LYS6P:
@> Average [Ang.]: 3.055475
@> Standard deviation [Ang.]: 0.213814
@> Weight: 0.380952
@> Statistics for ARG58P-ASP56P:
@> Average [Ang.]: 2.827481
@> Standard deviation [Ang.]: 0.171087
@> Weight: 2.952381
@> Statistics for ALA45P-ARG75P:
@> Average [Ang.]: 2.840721
@> Standard deviation [Ang.]: 0.105565
@> Weight: 0.904762
@> Statistics for ASN53P-GLU50P:
@> Average [Ang.]: 2.980214
@> Standard deviation [Ang.]: 0.147229
@> Weight: 0.333333
@> Statistics for ALA74P-ASN53P:
@> Average [Ang.]: 2.98522
@> Standard deviation [Ang.]: 0.148331
@> Weight: 0.952381
@> Statistics for ASP56P-ILE16P:
@> Average [Ang.]: 3.085957
@> Standard deviation [Ang.]: 0.21134
@> Weight: 0.666667
@> Statistics for LYS110P-THR84P:
@> Average [Ang.]: 2.774475
@> Standard deviation [Ang.]: 0.080304
@> Weight: 0.380952
@> Statistics for LEU116P-CYS90P:
@> Average [Ang.]: 2.887425
@> Standard deviation [Ang.]: 0.118768
@> Weight: 0.952381
@> Statistics for SER103P-LEU99P:
@> Average [Ang.]: 2.897324
@> Standard deviation [Ang.]: 0.17182
@> Weight: 1.380952
@> Statistics for ASN95P-ASP92P:
@> Average [Ang.]: 3.061373
@> Standard deviation [Ang.]: 0.215848
@> Weight: 0.714286
@> Statistics for LYS6P-ASN38P:
@> Average [Ang.]: 3.006786
@> Standard deviation [Ang.]: 0.154497
@> Weight: 0.333333
@> Statistics for ILE77P-ALA45P:
@> Average [Ang.]: 2.819429
@> Standard deviation [Ang.]: 0.092538
@> Weight: 0.666667
@> Statistics for LEU99P-ASN95P:
@> Average [Ang.]: 3.027242
@> Standard deviation [Ang.]: 0.19744
@> Weight: 0.904762
@> Statistics for GLY52P-ALA74P:
@> Average [Ang.]: 2.887583
@> Standard deviation [Ang.]: 0.088417
@> Weight: 0.285714
..
..
Compare two independent frames¶
With this analysis, we can also compare interactions between frames. Below, we
will compute hydrogen bonds for frame 0 and frame 18 and we will compare
them using the compareInteractions() function. That function will be helpful
in checking the difference between interactions. The results will be saved
as diff_fr0_vsfr18.dat file.
Let’s check the interactions for the initail frame in our trajectory:
In [39]: frame0 = dcd.getFrame(0)
In [40]: at0 = frame0.getAtoms()
In [41]: hb0 = calcHydrogenBonds(at0.select('protein'))
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG101 P NH1_1516 <---> ASP98 P OD1_1463 2.0 33.1
@> HSE72 P NE2_1042 <---> ASN15 P OD1_165 2.6 34.8
@> GLN143 P NE2_2192 <---> GLU139 P OE2_2126 2.7 9.2
@> HSE66 P NE2_957 <---> GLU139 P OE1_2125 2.7 6.4
@> ARG40 P N_561 <---> LYS6 P O_37 2.7 17.1
@> ARG58 P N_813 <---> ASP56 P OD1_788 2.7 30.0
@> ALA45 P N_634 <---> ARG75 P O_1097 2.8 35.1
@> ASN53 P ND2_747 <---> GLU50 P OE1_708 2.8 18.2
@> ALA74 P N_1064 <---> ASN53 P O_751 2.8 21.3
@> ASP56 P N_780 <---> ILE16 P O_189 2.8 27.0
@> LYS110 P NZ_1667 <---> THR84 P O_1240 2.8 38.2
@> LEU116 P N_1758 <---> CYS90 P O_1342 2.8 15.0
@> SER103 P N_1546 <---> LEU99 P O_1485 2.8 29.1
@> ASN134 P N_2045 <---> ASP137 P OD2_2091 2.8 22.6
@> PHE152 P N_2321 <---> CYS148 P O_2275 2.8 8.3
@> ASN95 P N_1398 <---> ASP92 P OD1_1368 2.8 12.6
@> LYS6 P N_16 <---> ASN38 P O_536 2.8 25.0
@> ILE77 P N_1115 <---> ALA45 P O_643 2.8 12.2
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.8 27.7
@> LEU99 P N_1467 <---> ASN95 P O_1411 2.8 15.5
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.8 9.6
@> GLY52 P N_731 <---> ALA74 P O_1073 2.8 6.6
@> ASP32 P N_435 <---> LYS28 P O_385 2.8 8.8
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.8 17.7
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 21.7
@> ARG27 P N_340 <---> GLU23 P O_293 2.8 15.4
@> TYR142 P N_2159 <---> PHE138 P O_2113 2.9 14.2
@> GLY133 P N_2038 <---> PRO130 P O_1995 2.9 25.4
@> PHE26 P N_320 <---> ALA22 P O_278 2.9 4.9
@> ASN15 P ND2_166 <---> SER19 P OG_232 2.9 32.1
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.9 19.7
@> ARG75 P NH2_1093 <---> ASP42 P OD2_610 2.9 23.5
@> ARG97 P N_1431 <---> GLU93 P O_1386 2.9 22.2
@> ARG65 P NH2_941 <---> GLU139 P OE1_2125 2.9 32.3
@> VAL25 P N_304 <---> ILE21 P O_268 2.9 8.2
@> LEU153 P N_2341 <---> CYS149 P O_2286 2.9 12.5
@> SER7 P N_38 <---> ASP86 P OD2_1270 2.9 39.9
@> ASP86 P N_1261 <---> SER7 P OG_45 2.9 34.7
@> ARG58 P NH2_832 <---> TYR131 P O_2016 2.9 33.1
@> THR46 P N_644 <---> CYS12 P O_130 2.9 36.1
@> GLN144 P N_2197 <---> THR140 P O_2142 2.9 23.3
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.9 12.4
@> LEU89 P N_1313 <---> LEU9 P O_83 2.9 29.5
@> THR31 P N_421 <---> ARG27 P O_363 2.9 24.1
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.9 24.6
@> CYS148 P N_2265 <---> GLN144 P O_2213 2.9 9.3
@> GLU23 P N_279 <---> SER19 P O_235 2.9 15.4
@> ILE68 P N_970 <---> MET63 P O_899 2.9 13.0
@> PHE10 P N_84 <---> ASP42 P O_612 2.9 22.8
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.9 10.1
@> SER61 P N_861 <---> TYR57 P O_812 2.9 35.1
@> CYS145 P N_2214 <---> VAL141 P O_2158 2.9 15.9
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.9 31.5
@> LYS64 P N_900 <---> GLN60 P O_860 2.9 22.9
@> LEU9 P N_65 <---> TYR87 P O_1293 2.9 16.4
@> ASN38 P N_523 <---> ILE35 P O_496 2.9 29.1
@> VAL11 P N_104 <---> LEU89 P O_1331 2.9 29.7
@> ASN100 P N_1486 <---> LEU96 P O_1430 2.9 10.3
@> GLN124 P N_1881 <---> ASP120 P OD2_1825 2.9 27.5
@> LYS102 P N_1524 <---> ASP98 P O_1466 2.9 9.3
@> GLN76 P NE2_1110 <---> THR46 P O_657 2.9 31.4
@> ARG40 P NH1_577 <---> THR84 P OG1_1233 2.9 8.4
@> ALA44 P N_624 <---> PHE10 P O_103 2.9 33.2
@> GLU154 P N_2360 <---> ARG150 P O_2310 3.0 22.6
@> VAL8 P N_49 <---> ARG40 P O_584 3.0 25.0
@> MET63 P N_883 <---> GLY59 P O_843 3.0 18.3
@> GLN60 P N_844 <---> ASP56 P O_791 3.0 35.5
@> ILE35 P N_478 <---> VAL30 P O_420 3.0 23.5
@> VAL146 P N_2225 <---> TYR142 P O_2179 3.0 31.5
@> ARG58 P NH1_829 <---> TYR131 P O_2016 3.0 38.1
@> ASN53 P N_738 <---> GLU50 P O_711 3.0 28.6
@> ARG101 P N_1500 <---> ARG97 P O_1454 3.0 32.3
@> ARG18 P NH1_217 <---> ILE127 P O_1954 3.0 26.0
@> ARG75 P N_1074 <---> ASN15 P OD1_165 3.0 25.1
@> GLN144 P NE2_2209 <---> ILE126 P O_1935 3.0 18.3
@> ASN34 P N_464 <---> THR31 P O_434 3.0 18.2
@> ASN15 P ND2_166 <---> SER43 P OG_620 3.0 25.7
@> ARG58 P NE_826 <---> ASP56 P OD1_788 3.0 22.2
@> ARG27 P NH1_356 <---> GLU23 P OE2_291 3.0 36.9
@> ILE127 P N_1936 <---> MET91 P O_1359 3.0 17.6
@> TYR119 P OH_1808 <---> HSE157 P N_2407 3.0 28.1
@> HSE157 P N_2407 <---> TYR119 P OH_1808 3.0 19.2
@> GLU139 P N_2114 <---> ASP135 P O_2070 3.0 27.9
@> LEU29 P N_386 <---> VAL25 P O_319 3.0 19.1
@> SER47 P N_658 <---> LEU13 P O_149 3.0 28.8
@> VAL30 P N_405 <---> PHE26 P O_339 3.0 17.7
@> GLN105 P N_1571 <---> LYS102 P O_1545 3.0 19.7
@> SER118 P N_1784 <---> LEU115 P O_1757 3.1 21.4
@> LYS155 P N_2375 <---> ALA151 P O_2320 3.1 21.3
@> GLU114 P N_1724 <---> ILE88 P O_1312 3.1 24.2
@> ASP120 P N_1816 <---> GLY117 P O_1783 3.1 12.7
@> CYS62 P N_872 <---> ARG58 P O_836 3.1 20.4
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 3.1 4.3
@> ALA24 P N_294 <---> PRO20 P O_249 3.1 29.9
@> ARG150 P N_2287 <---> VAL146 P O_2240 3.1 12.7
@> LYS28 P N_364 <---> ALA24 P O_303 3.1 20.0
@> VAL141 P N_2143 <---> ASP137 P O_2093 3.1 18.5
@> ASP98 P N_1455 <---> SER94 P O_1397 3.1 19.6
@> LEU96 P N_1412 <---> ASP92 P O_1371 3.1 36.3
@> ALA22 P N_269 <---> ARG18 P O_224 3.1 21.9
@> ALA151 P N_2311 <---> ARG147 P O_2264 3.1 15.6
@> GLY67 P N_963 <---> LYS64 P O_921 3.1 22.8
@> ASP42 P N_601 <---> VAL8 P O_64 3.1 35.6
@> ARG65 P N_922 <---> SER61 P O_871 3.1 23.4
@> TRP39 P N_537 <---> SER36 P O_507 3.1 15.2
@> LYS123 P N_1859 <---> ASP120 P O_1827 3.1 18.7
@> MET91 P N_1343 <---> ASN95 P OD1_1406 3.2 39.0
@> THR140 P N_2129 <---> SER136 P O_2081 3.2 30.3
@> PHE85 P N_1241 <---> ASP81 P O_1196 3.2 20.2
@> ASN15 P N_157 <---> CYS12 P SG_127 3.2 37.5
@> ALA111 P N_1673 <---> PHE82 P O_1216 3.2 20.6
@> ARG147 P N_2241 <---> GLN143 P O_2196 3.2 12.1
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 3.2 29.3
@> LYS112 P NZ_1699 <---> HSE157 P OT2_2424 3.3 28.7
@> ARG147 P NH1_2257 <---> GLN124 P OE1_1892 3.3 29.9
@> PHE138 P N_2094 <---> ASN134 P O_2058 3.3 31.0
@> SER7 P OG_45 <---> THR84 P O_1240 3.3 35.5
@> CYS12 P N_120 <---> ALA44 P O_633 3.3 36.1
@> SER19 P N_225 <---> CYS12 P SG_127 3.3 8.0
@> PHE82 P N_1197 <---> LYS79 P O_1169 3.4 37.7
@> ASP81 P N_1185 <---> THR78 P OG1_1140 3.5 39.5
@> LYS102 P NZ_1540 <---> ASP98 P OD2_1464 3.5 26.1
@> ARG147 P NH2_2260 <---> GLN124 P OE1_1892 3.5 33.9
@> VAL106 P N_1588 <---> SER103 P O_1556 3.5 34.2
@> Number of detected hydrogen bonds: 124.
Let’s check the interactions for frame number 18 in our trajectory:
In [42]: frame18 = dcd.getFrame(18)
In [43]: at18 = frame18.getAtoms()
In [44]: hb18 = calcHydrogenBonds(at18.select('protein'))
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 2.6 18.5
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.6 21.5
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.7 18.4
@> LYS28 P NZ_380 <---> ASP32 P OD2_444 2.7 25.9
@> ARG150 P NE_2300 <---> GLU154 P OE1_2371 2.7 22.4
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.7 25.9
@> ARG75 P NE_1087 <---> ASP42 P OD1_609 2.7 16.1
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.7 2.1
@> SER19 P OG_232 <---> ASN15 P OD1_165 2.7 8.1
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.7 1.4
@> VAL8 P N_49 <---> ARG40 P O_584 2.7 11.5
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.7 28.1
@> ASN134 P N_2045 <---> ASP137 P OD1_2090 2.7 12.5
@> LYS155 P NZ_2391 <---> HSE157 P OT2_2424 2.7 38.9
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.7 25.8
@> CYS145 P N_2214 <---> VAL141 P O_2158 2.7 13.7
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463 2.8 29.5
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 21.3
@> LEU29 P N_386 <---> VAL25 P O_319 2.8 16.9
@> THR84 P OG1_1233 <---> GLU80 P O_1184 2.8 10.5
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.8 4.9
@> THR31 P OG1_427 <---> ARG27 P O_363 2.8 21.2
@> ASP98 P N_1455 <---> SER94 P O_1397 2.8 6.1
@> SER43 P OG_620 <---> GLU23 P OE1_290 2.8 13.9
@> LYS110 P N_1651 <---> PHE82 P O_1216 2.8 36.4
@> SER118 P OG_1791 <---> GLU114 P OE2_1736 2.8 20.1
@> ARG65 P NH1_938 <---> ASP135 P OD2_2068 2.8 12.3
@> LYS64 P N_900 <---> GLN60 P O_860 2.8 3.3
@> ARG101 P NH2_1519 <---> ASP98 P OD2_1464 2.8 8.9
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.8 25.1
@> ARG65 P N_922 <---> SER61 P O_871 2.8 24.3
@> ARG58 P NH1_829 <---> GLY133 P O_2044 2.8 34.0
@> ILE127 P N_1936 <---> MET91 P O_1359 2.8 22.3
@> THR78 P OG1_1140 <---> ASP81 P OD2_1194 2.8 12.4
@> THR84 P N_1227 <---> GLU80 P O_1184 2.8 10.8
@> GLN33 P N_447 <---> LEU29 P O_404 2.8 6.2
@> SER7 P N_38 <---> ASP86 P OD1_1269 2.8 25.3
@> ASP32 P N_435 <---> LYS28 P O_385 2.8 16.9
@> ASP86 P N_1261 <---> SER7 P O_48 2.8 35.1
@> LYS102 P N_1524 <---> ASP98 P O_1466 2.8 29.0
@> ASP42 P N_601 <---> VAL8 P O_64 2.9 25.5
@> SER61 P N_861 <---> TYR57 P O_812 2.9 32.8
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.9 2.6
@> VAL146 P N_2225 <---> TYR142 P O_2179 2.9 9.7
@> GLN60 P N_844 <---> ASP56 P O_791 2.9 25.1
@> LYS155 P N_2375 <---> ARG150 P O_2310 2.9 13.4
@> ALA74 P N_1064 <---> ASN53 P O_751 2.9 16.2
@> TYR87 P N_1273 <---> SER7 P O_48 2.9 18.2
@> GLN144 P N_2197 <---> THR140 P O_2142 2.9 16.3
@> LEU89 P N_1313 <---> LEU9 P O_83 2.9 28.6
@> ARG101 P N_1500 <---> ARG97 P O_1454 2.9 3.1
@> CYS12 P SG_127 <---> SER19 P OG_232 3.0 35.8
@> ASN53 P ND2_747 <---> GLU50 P OE2_709 3.0 21.4
@> ALA45 P N_634 <---> ARG75 P O_1097 3.0 11.5
@> ASP56 P N_780 <---> ILE16 P O_189 3.0 15.2
@> ARG58 P N_813 <---> ASP56 P OD1_788 3.0 14.2
@> ILE77 P N_1115 <---> ALA45 P O_643 3.0 12.8
@> GLY67 P N_963 <---> MET63 P O_899 3.0 16.3
@> ARG18 P NH1_217 <---> ILE127 P O_1954 3.0 33.1
@> ARG75 P NH1_1090 <---> ASP81 P OD1_1193 3.0 39.7
@> THR140 P N_2129 <---> SER136 P O_2081 3.0 18.5
@> LEU153 P N_2341 <---> CYS149 P O_2286 3.0 12.0
@> ASN104 P N_1557 <---> ASN100 P O_1499 3.0 38.4
@> CYS62 P N_872 <---> ARG58 P O_836 3.0 39.7
@> VAL11 P N_104 <---> LEU89 P O_1331 3.0 15.4
@> VAL106 P N_1588 <---> LYS102 P O_1545 3.0 2.4
@> ALA151 P N_2311 <---> ARG147 P O_2264 3.0 21.7
@> ARG40 P N_561 <---> LYS6 P O_37 3.0 33.0
@> LEU9 P N_65 <---> TYR87 P O_1293 3.0 39.7
@> ARG27 P N_340 <---> GLU23 P O_293 3.0 17.9
@> ASN95 P ND2_1407 <---> THR46 P OG1_650 3.0 38.8
@> ARG27 P NH2_359 <---> VAL41 P O_600 3.0 32.9
@> LEU99 P N_1467 <---> ASN95 P O_1411 3.0 21.7
@> GLU154 P N_2360 <---> ARG150 P O_2310 3.0 37.1
@> ALA111 P N_1673 <---> PHE82 P O_1216 3.0 18.4
@> ARG150 P NH2_2306 <---> GLU154 P OE1_2371 3.0 31.0
@> VAL25 P N_304 <---> ILE21 P O_268 3.0 10.3
@> ASN15 P ND2_166 <---> SER43 P OG_620 3.1 18.8
@> MET63 P N_883 <---> GLY59 P O_843 3.1 15.7
@> VAL30 P N_405 <---> PHE26 P O_339 3.1 6.2
@> ARG150 P N_2287 <---> VAL146 P O_2240 3.1 30.1
@> PHE138 P N_2094 <---> ASN134 P O_2058 3.1 10.8
@> VAL141 P N_2143 <---> ASP137 P O_2093 3.1 10.8
@> PHE10 P N_84 <---> ASP42 P O_612 3.1 17.6
@> CYS148 P N_2265 <---> GLN144 P O_2213 3.1 23.2
@> PHE26 P N_320 <---> ALA22 P O_278 3.1 9.0
@> GLN76 P NE2_1110 <---> THR46 P O_657 3.1 11.9
@> LEU116 P N_1758 <---> CYS90 P O_1342 3.2 18.5
@> GLU23 P N_279 <---> SER19 P O_235 3.2 2.4
@> ALA44 P N_624 <---> PHE10 P O_103 3.2 38.7
@> ARG65 P NH2_941 <---> ASP135 P OD1_2067 3.2 19.6
@> ASN34 P N_464 <---> THR31 P O_434 3.2 38.6
@> ARG97 P N_1431 <---> GLU93 P O_1386 3.2 17.8
@> ALA22 P N_269 <---> ARG18 P O_224 3.2 11.6
@> GLN105 P N_1571 <---> ARG101 P O_1523 3.2 28.1
@> LYS6 P N_16 <---> ASN38 P O_536 3.2 31.6
@> ASN95 P N_1398 <---> ASP92 P OD1_1368 3.2 11.6
@> CYS145 P SG_2221 <---> VAL141 P O_2158 3.3 30.4
@> HSE66 P N_946 <---> CYS62 P O_882 3.3 14.7
@> ARG147 P N_2241 <---> GLN143 P O_2196 3.3 26.0
@> TYR142 P N_2159 <---> PHE138 P O_2113 3.3 11.5
@> TRP39 P N_537 <---> ILE35 P O_496 3.4 35.3
@> GLN124 P N_1881 <---> GLN144 P OE1_2208 3.4 35.9
@> CYS12 P N_120 <---> ALA44 P O_633 3.4 35.7
@> SER103 P OG_1553 <---> LEU99 P O_1485 3.4 14.9
@> PHE85 P N_1241 <---> ASP81 P O_1196 3.4 24.1
@> SER19 P N_225 <---> CYS12 P SG_127 3.5 7.6
@> Number of detected hydrogen bonds: 107.
And compare them using compareInteractions(). We will obtain
information on which interactions are newly maintained, which are stable,
and which ones were lost.
In [45]: compareInteractions(hb0, hb18, filename='diff_fr0_vsfr18.dat')
@> Which interactions disappeared: 23
@> TYR87P <---> SER7P
@> SER43P <---> GLU23P
@> ASN104P <---> ASN100P
@> LYS155P <---> HSE157P
@> ARG150P <---> GLU154P
@> ASN95P <---> THR46P
@> LYS110P <---> PHE82P
@> SER19P <---> ASN15P
@> LYS155P <---> ARG150P
@> SER118P <---> GLU114P
@> GLY67P <---> MET63P
@> ARG65P <---> ASP135P
@> TRP39P <---> ILE35P
@> THR84P <---> GLU80P
@> HSE66P <---> CYS62P
@> GLN105P <---> ARG101P
@> CYS12P <---> SER19P
@> ARG58P <---> GLY133P
@> VAL106P <---> LYS102P
@> LYS28P <---> ASP32P
@> GLN124P <---> GLN144P
@> ARG27P <---> VAL41P
@> GLN33P <---> LEU29P
Which interactions appeared: 41
@> SER118P <---> LEU115P
@> GLY67P <---> LYS64P
@> GLU139P <---> ASP135P
@> ARG75P <---> ASN15P
@> PHE82P <---> LYS79P
@> ARG147P <---> GLN124P
@> GLY52P <---> ALA74P
@> ASP81P <---> THR78P
@> GLN144P <---> ILE126P
@> ASN38P <---> ILE35P
@> SER47P <---> LEU13P
@> ARG58P <---> TYR131P
@> LYS155P <---> ALA151P
@> MET91P <---> ASN95P
@> PHE152P <---> CYS148P
@> LYS28P <---> ALA24P
@> ASN100P <---> LEU96P
@> VAL106P <---> SER103P
@> SER7P <---> THR84P
@> ALA24P <---> PRO20P
@> HSE66P <---> GLU139P
@> GLU114P <---> ILE88P
@> LEU96P <---> ASP92P
@> GLN105P <---> LYS102P
@> LYS123P <---> ASP120P
@> GLY133P <---> PRO130P
@> TYR119P <---> HSE157P
@> ASN15P <---> SER19P
@> ILE35P <---> VAL30P
@> ARG65P <---> GLU139P
@> HSE157P <---> TYR119P
@> ASP120P <---> GLY117P
@> ARG40P <---> THR84P
@> ILE68P <---> MET63P
@> ASN15P <---> CYS12P
@> HSE72P <---> ASN15P
@> LYS110P <---> THR84P
@> GLN124P <---> ASP120P
@> TRP39P <---> SER36P
@> THR46P <---> CYS12P
@> LYS112P <---> HSE157P
@> Which interactions are the same: 73
@> GLN60P <---> ASP56P
@> ARG150P <---> VAL146P
@> ARG101P <---> ASP98P
@> ILE77P <---> ALA45P
@> VAL11P <---> LEU89P
@> SER61P <---> TYR57P
@> ARG18P <---> ASP92P
@> ALA22P <---> ARG18P
@> THR31P <---> ARG27P
@> ALA44P <---> PHE10P
@> LEU153P <---> CYS149P
@> ARG58P <---> ASP56P
@> ALA111P <---> PHE82P
@> CYS62P <---> ARG58P
@> VAL146P <---> TYR142P
@> GLU23P <---> SER19P
@> ARG27P <---> GLU23P
@> CYS149P <---> CYS145P
@> LYS64P <---> GLN60P
@> VAL8P <---> ARG40P
@> ARG40P <---> LYS6P
@> ARG65P <---> SER61P
@> ASP32P <---> LYS28P
@> ILE88P <---> LYS112P
@> ALA45P <---> ARG75P
@> PHE26P <---> ALA22P
@> ASN95P <---> ASP92P
@> VAL30P <---> PHE26P
@> THR140P <---> SER136P
@> LEU89P <---> LEU9P
@> SER103P <---> LEU99P
@> LEU116P <---> CYS90P
@> PHE10P <---> ASP42P
@> ASN15P <---> SER43P
@> TYR142P <---> PHE138P
@> ASN34P <---> THR31P
@> ASN134P <---> ASP137P
@> LEU99P <---> ASN95P
@> ASP98P <---> SER94P
@> GLN144P <---> THR140P
@> ARG97P <---> GLU93P
@> GLN76P <---> THR46P
@> LYS6P <---> ASN38P
@> ARG75P <---> ASP81P
@> ASN53P <---> GLU50P
@> THR78P <---> ASP81P
@> VAL141P <---> ASP137P
@> SER19P <---> CYS12P
@> GLN143P <---> GLU139P
@> LEU29P <---> VAL25P
@> ALA151P <---> ARG147P
@> GLU154P <---> ARG150P
@> ALA74P <---> ASN53P
@> CYS148P <---> GLN144P
@> SER7P <---> ASP86P
@> LYS102P <---> ASP98P
@> MET63P <---> GLY59P
@> ASP56P <---> ILE16P
@> PHE138P <---> ASN134P
@> CYS90P <---> GLU114P
@> ASP42P <---> VAL8P
@> CYS145P <---> VAL141P
@> ARG147P <---> GLN143P
@> PHE85P <---> ASP81P
@> VAL25P <---> ILE21P
@> LEU9P <---> TYR87P
@> ASP86P <---> SER7P
@> ARG101P <---> ARG97P
@> ILE127P <---> MET91P
@> LYS112P <---> ASP86P
@> CYS12P <---> ALA44P
@> ARG75P <---> ASP42P
@> ARG18P <---> ILE127P
We can also all the tools that are shown for single PDB analysis in this
tutorial. For example, we can compute all interactions for frame0 and
frame18 and display the interactions:
In [46]: interactions0 = Interactions()
In [47]: interactions0.calcProteinInteractions(at0)
In [48]: matrix0 = interactions0.buildInteractionMatrix()
In [49]: interactions0.showCumulativeInteractionTypes()
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
In [50]: interactions18 = Interactions()
In [51]: interactions18.calcProteinInteractions(at18)
In [52]: matrix18 = interactions18.buildInteractionMatrix()
@> Calculating interations.
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 2.6 18.5
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.6 21.5
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.7 18.4
@> LYS28 P NZ_380 <---> ASP32 P OD2_444 2.7 25.9
@> ARG150 P NE_2300 <---> GLU154 P OE1_2371 2.7 22.4
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.7 25.9
@> ARG75 P NE_1087 <---> ASP42 P OD1_609 2.7 16.1
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.7 2.1
@> SER19 P OG_232 <---> ASN15 P OD1_165 2.7 8.1
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.7 1.4
@> VAL8 P N_49 <---> ARG40 P O_584 2.7 11.5
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.7 28.1
@> ASN134 P N_2045 <---> ASP137 P OD1_2090 2.7 12.5
@> LYS155 P NZ_2391 <---> HSE157 P OT2_2424 2.7 38.9
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.7 25.8
In [53]: interactions18.showCumulativeInteractionTypes()
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
Parse previously saved data¶
To upload and further use the interactions data use
InteractionsTrajectory.parseInteractions() function:
In [54]: interactionsTrajectory2 = InteractionsTrajectory('5kqm_import')
In [55]: interactionsTrajectory2.parseInteractions('calcProteinInteractionsTrajectory.pkl')
[[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.5997, 34.752],
['GLN143', 'NE2_2192', 'P', 'GLU139', 'OE2_2126', 'P', 2.7287, 9.1822],
['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7314, 6.3592],
['ARG40', 'N_561', 'P', 'LYS6', 'O_37', 'P', 2.7479, 17.1499],
['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.7499, 29.9737],
['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.7609, 35.0983],
['ASN53', 'ND2_747', 'P', 'GLU50', 'OE1_708', 'P', 2.7702, 18.2336],
['ALA74', 'N_1064', 'P', 'ASN53', 'O_751', 'P', 2.7782, 21.3375],
['ASP56', 'N_780', 'P', 'ILE16', 'O_189', 'P', 2.7793, 27.0481],
['LYS110', 'NZ_1667', 'P', 'THR84', 'O_1240', 'P', 2.7977, 38.2213],
['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.8072, 15.0239],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
['ASN134', 'N_2045', 'P', 'ASP137', 'OD2_2091', 'P', 2.8132, 22.562],
['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8141, 8.2562],
['ASN95', 'N_1398', 'P', 'ASP92', 'OD1_1368', 'P', 2.8148, 12.5701],
['LYS6', 'N_16', 'P', 'ASN38', 'O_536', 'P', 2.8178, 25.0306],
['ILE77', 'N_1115', 'P', 'ALA45', 'O_643', 'P', 2.8179, 12.1856],
['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.8204, 27.6617],
['LEU99', 'N_1467', 'P', 'ASN95', 'O_1411', 'P', 2.8205, 15.4867],
['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.8247, 9.5914],
['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.832, 6.6442],
['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.8357, 8.8318],
..
..
After uploading, we have access to all data, for example:
In [56]: interactionsTrajectory2.getHydrophohic()
[[['ALA156', 'CB_2401', 'P', 'TYR87', 'OH_1286', 'P', 3.0459, 21.959],
['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.3105, 5.1584],
['ILE68', 'CG2_976', 'P', 'MET63', 'CE_894', 'P', 3.3306, 52.4165],
['TYR142', 'CZ_2171', 'P', 'VAL146', 'CG2_2235', 'P', 3.4815, 49.7427],
['PHE10', 'CD1_92', 'P', 'ALA22', 'CB_273', 'P', 3.5334, 31.1973],
['LYS6', 'CD_26', 'P', 'TRP39', 'CZ2_555', 'P', 3.5427, 68.7284],
['PHE26', 'CE2_336', 'P', 'VAL30', 'CG1_411', 'P', 3.5603, 21.127],
['ILE88', 'CD_1307', 'P', 'ALA111', 'CB_1677', 'P', 3.5627, 21.2201],
['VAL11', 'CG2_114', 'P', 'ILE88', 'CG2_1300', 'P', 3.6386, 9.3289],
['VAL41', 'CG2_595', 'P', 'PHE26', 'CD2_334', 'P', 3.6448, 16.55],
['PHE152', 'CE1_2331', 'P', 'ALA156', 'CB_2401', 'P', 3.6594, 17.4765],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.6828, 25.1359],
['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6917, 11.9735],
['PHE82', 'CD1_1205', 'P', 'ILE88', 'CD_1307', 'P', 3.692, 17.6138],
['LEU116', 'CD2_1771', 'P', 'ILE127', 'CD_1949', 'P', 3.7057, 17.4094],
..
..
In [57]: calcStatisticsInteractions(interactionsTrajectory2.getHydrogenBonds())
@> Statistics for ARG101P-ASP98P:
@> Average [Ang.]: 2.793931
@> Standard deviation [Ang.]: 0.205527
@> Weight: 1.52381
@> Statistics for HSE72P-ASN15P:
@> Average [Ang.]: 2.989283
@> Standard deviation [Ang.]: 0.270697
@> Weight: 0.285714
@> Statistics for GLN143P-GLU139P:
@> Average [Ang.]: 3.051633
@> Standard deviation [Ang.]: 0.20753
@> Weight: 1.285714
@> Statistics for HSE66P-GLU139P:
@> Average [Ang.]: 2.900411
@> Standard deviation [Ang.]: 0.169455
@> Weight: 0.428571
@> Statistics for ARG40P-LYS6P:
@> Average [Ang.]: 3.055475
@> Standard deviation [Ang.]: 0.213814
@> Weight: 0.380952
@> Statistics for ARG58P-ASP56P:
@> Average [Ang.]: 2.827481
@> Standard deviation [Ang.]: 0.171087
@> Weight: 2.952381
..
..
In [58]: interactionsTrajectory2.getTimeInteractions()
