PDB structure with multiple chains¶
This time we will use protein with two chains, lipoxygenase (PDB: 7LAF) which contain chain A and chain B. First, we will add missing hydrogens to the protein structures and then we will perform analysis of interactions between two chains.
Add missing hydrogen atoms to the structure¶
We start by fetching the PDB file and adding missing hydrogens using Openbabel.
In [1]: fetchPDB('7laf', compressed=False)
In [2]: addMissingAtoms('7laf.pdb', method='openbabel')
In [3]: atoms = parsePDB('addH_7laf.pdb').select('protein')
@> Connecting wwPDB FTP server RCSB PDB (USA).
@> 7laf downloaded (7laf.pdb)
@> PDB download via FTP completed (1 downloaded, 0 failed).
@> Hydrogens were added to the structure. Structure addH_7laf.pdb is saved in the local directry.
@> 21970 atoms and 1 coordinate set(s) were parsed in 0.24s.
In [4]: interactions = Interactions('7laf')
To compute all interactions:
In [5]: all_interactions = interactions.calcProteinInteractions(atoms)
@> Calculating interations.
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ASP505 A OD2_3935 <---> TYR496 A OH_3867 2.2 29.5
@> ASP666 B OD1_10390 <---> SER648 B OG_10241 2.3 17.8
@> HIS394 A N_3026 <---> GLU141 A OE2_1006 2.4 35.5
@> ARG390 B NH1_8204 <---> TYR149 B O_6273 2.4 35.6
@> GLN641 A NE2_4984 <---> GLY621 A O_4815 2.4 8.5
@> ARG649 B NH1_10251 <---> GLU653 B OE1_10281 2.4 4.9
@> ARG463 B NH1_8796 <---> ASP459 B OD1_8759 2.4 30.6
@> TYR318 B N_7621 <---> LEU327 B O_7687 2.4 4.3
@> ASN301 A ND2_2299 <---> ASP428 A O_3307 2.4 29.3
@> ARG474 A NH1_3686 <---> ILE468 A O_3625 2.5 37.5
@> ARG474 B NH1_8890 <---> VAL465 B O_8805 2.5 21.1
@> SER517 B OG_9247 <---> ASN522 B ND2_9287 2.5 26.7
@> ASN522 B ND2_9287 <---> SER517 B OG_9247 2.5 33.0
@> TRP481 B N_8937 <---> GLY477 B O_8911 2.5 7.9
@> LEU36 A N_274 <---> VAL24 A O_194 2.5 21.5
@> SER526 A OG_4113 <---> GLN523 A O_4087 2.5 24.9
@> ARG138 B NH2_6183 <---> GLU507 B OE1_9158 2.5 28.0
@> TRP109 A N_743 <---> ASN173 A OD1_1279 2.5 7.1
@> THR431 B OG1_8538 <---> VAL427 B O_8504 2.5 24.5
@> SER501 B OG_9107 <---> SER498 B O_9082 2.5 35.7
@> GLN143 B N_6219 <---> GLN139 B O_6187 2.5 11.9
@> LEU329 A N_2495 <---> LEU316 A O_2404 2.5 21.1
@> LEU110 A N_757 <---> TRP87 A O_551 2.6 33.6
@> HIS373 A N_2854 <---> HIS368 A O_2818 2.6 19.3
@> ASN413 B ND2_8402 <---> GLU382 B OE1_8140 2.6 20.3
@> ARG535 B NH1_9382 <---> TYR496 B O_9063 2.6 29.4
@> ARG649 A NH1_5047 <---> GLU653 A OE2_5078 2.6 19.6
@> TRP109 B N_5947 <---> ASN173 B OD1_6483 2.6 37.3
@> ARG429 B N_8516 <---> GLN425 B O_8488 2.6 23.9
@> GLN575 B NE2_9683 <---> LEU594 B O_9812 2.6 14.9
@> ARG68 A N_482 <---> SER25 A O_201 2.6 14.5
@> HIS70 A N_500 <---> SER23 A O_188 2.6 12.3
@> ARG215 A NH2_1620 <---> GLU168 B OE1_6442 2.6 24.8
@> THR462 A N_3576 <---> GLU458 A O_3543 2.6 22.5
@> ARG463 B NH2_8797 <---> TYR471 B OH_8856 2.6 19.7
@> HIS405 A ND1_3124 <---> ASN672 A O_5230 2.6 25.8
@> GLN335 A NE2_2547 <---> ALA312 A O_2377 2.6 10.5
@> LEU110 B N_5961 <---> TRP87 B O_5770 2.6 37.7
@> TYR495 B OH_9059 <---> GLU630 B OE1_10098 2.6 12.0
@> ARG463 A NH2_3593 <---> ILE251 A O_1918 2.6 39.3
@> GLN319 B NE2_7641 <---> GLY324 B O_7668 2.6 28.2
@> HIS373 B N_8058 <---> HIS368 B O_8022 2.6 20.9
@> GLU364 B N_7982 <---> VAL360 B O_7954 2.6 28.1
@> TRP87 A N_548 <---> LEU110 A O_760 2.6 8.9
@> TYR408 A OH_3157 <---> ASP616 A OD1_4775 2.6 37.7
@> GLY493 B N_9036 <---> SER489 B O_9008 2.6 32.4
@> LEU354 B N_7900 <---> LYS350 B O_7858 2.6 22.3
@> LEU142 A N_1007 <---> ARG138 A O_972 2.6 5.8
@> VAL488 A N_3794 <---> VAL484 A O_3759 2.6 11.4
@> ASN655 A ND2_5097 <---> TYR662 A O_5144 2.6 17.4
@> THR95 A N_632 <---> ARG5 A O_52 2.6 12.4
@> ARG208 A N_1551 <---> GLU212 A OE1_1591 2.6 21.7
@> ARG463 A NH2_3593 <---> TYR471 A OH_3652 2.6 35.2
@> ARG208 B N_6755 <---> GLU212 B OE1_6795 2.6 34.4
@> SER550 B OG_9500 <---> ILE546 B O_9466 2.6 22.5
@> GLN119 B NE2_6029 <---> GLN137 B OE1_6171 2.6 28.1
@> LEU327 B N_7684 <---> TYR318 B O_7624 2.6 6.3
@> LEU420 A N_3247 <---> ALA416 A O_3217 2.6 34.5
@> CYS106 A N_716 <---> ARG90 A O_582 2.7 36.5
@> LEU607 B N_9900 <---> VAL603 B O_9875 2.7 12.6
@> VAL488 B N_8998 <---> VAL484 B O_8963 2.7 4.8
@> GLY583 B N_9735 <---> ASP352 B OD2_7885 2.7 15.8
@> SER25 A N_198 <---> ARG68 A O_485 2.7 38.0
@> ASN301 A ND2_2299 <---> THR431 A O_3332 2.7 28.3
@> ARG407 A NH2_3145 <---> ASP616 A O_4772 2.7 29.7
@> GLN509 B NE2_9176 <---> LEU532 B O_9352 2.7 37.1
@> ARG407 A NH1_3144 <---> ASP616 A OD2_4776 2.7 11.0
@> SER489 A N_3801 <---> GLU485 A O_3766 2.7 24.6
@> ARG215 A NH1_1619 <---> GLU168 B OE2_6443 2.7 28.7
@> ARG253 A N_1934 <---> ARG463 A O_3586 2.7 10.7
@> PHE288 B N_7398 <---> LEU317 B O_7616 2.7 18.1
@> GLN509 A NE2_3972 <---> LEU532 A O_4148 2.7 27.8
@> THR409 A OG1_3163 <---> VAL674 A O_5244 2.7 37.9
@> PHE309 B N_7556 <---> MET574 B O_9670 2.7 12.8
@> ASN445 B N_8639 <---> LEU441 B O_8606 2.7 23.6
@> GLY583 A N_4531 <---> ASP352 A OD2_2681 2.7 14.6
@> TYR451 B N_8689 <---> SER526 B O_9315 2.7 38.7
@> ARG5 A N_49 <---> THR95 A O_635 2.7 15.9
@> CYS106 B N_5920 <---> ARG90 B O_5801 2.7 32.5
@> TYR149 A N_1066 <---> ARG145 A O_1032 2.7 8.1
@> GLN575 A N_4471 <---> THR593 A O_4601 2.7 15.0
@> HIS160 A N_1167 <---> LYS518 A O_4047 2.7 35.5
@> PHE547 B N_9471 <---> THR543 B O_9444 2.7 33.0
@> ARG253 B N_7138 <---> ARG463 B O_8790 2.7 16.2
@> ASN655 A N_5090 <---> ILE651 A O_5056 2.7 28.0
@> LEU345 B N_7817 <---> ASP348 B OD2_7846 2.7 14.0
@> ASP504 A N_3920 <---> GLU500 A O_3892 2.7 37.2
@> ARG203 A NH1_1514 <---> GLU212 A OE2_1592 2.7 38.1
@> ASN569 A ND2_4434 <---> SER563 A O_4384 2.7 2.5
@> TRP481 A N_3733 <---> GLY477 A O_3707 2.7 5.8
@> ASN362 A N_2765 <---> THR358 A O_2729 2.7 34.3
@> MET314 A N_2386 <---> GLN332 A O_2519 2.7 23.3
@> SER430 B N_8527 <---> VAL426 B O_8497 2.7 13.0
@> TRP87 B N_5767 <---> LEU110 B O_5964 2.7 31.2
@> HIS368 B N_8019 <---> GLU364 B O_7985 2.7 24.6
@> ILE492 B N_9028 <---> VAL488 B O_9001 2.7 2.1
@> ASN413 A ND2_3198 <---> HIS378 A O_2899 2.7 35.7
@> ARG390 A NH1_3000 <---> TYR149 A O_1069 2.7 18.4
@> ARG407 B NH2_8349 <---> ASP616 B O_9976 2.7 31.8
@> SER430 A N_3323 <---> VAL426 A O_3293 2.7 37.6
@> ARG654 A N_5079 <---> GLY650 A O_5052 2.7 22.2
@> ASN445 A N_3435 <---> LEU441 A O_3402 2.7 9.8
@> HIS376 B N_8084 <---> LEU371 B O_8046 2.7 15.5
@> LYS518 B N_9248 <---> GLU514 B O_9217 2.7 30.5
@> ARG444 B NH2_8638 <---> SER296 B O_7465 2.7 14.5
@> GLU440 A N_3390 <---> GLU436 A O_3363 2.7 23.1
@> LEU607 A N_4696 <---> VAL603 A O_4671 2.7 6.3
@> GLN641 A N_4976 <---> ILE637 A O_4948 2.7 35.5
@> ARG444 B N_8628 <---> GLU440 B O_8597 2.7 20.9
@> ASP202 A OD2_1504 <---> GLU418 B OE2_8442 2.7 31.6
@> ILE403 B N_8307 <---> PHE399 B O_8274 2.7 13.4
@> LEU278 A N_2119 <---> ASP265 A OD1_2043 2.7 32.7
@> GLN575 B N_9675 <---> THR593 B O_9805 2.7 22.3
@> GLN136 A NE2_959 <---> GLU140 A OE2_997 2.7 16.6
@> TYR496 B N_9060 <---> ILE492 B O_9031 2.7 35.5
@> GLU364 A N_2778 <---> VAL360 A O_2750 2.8 29.9
@> ALA188 A N_1398 <---> PHE184 A O_1361 2.8 22.9
@> ASN672 B N_10431 <---> ARG618 B O_9993 3.3 14.1
@> ARG461 A N_3565 <---> PRO457 A O_3536 3.3 31.9
@> SER636 A N_4939 <---> ALA632 A O_4908 3.3 26.8
@> GLN136 B NE2_6163 <---> GLU140 B OE2_6201 3.3 15.4
@> ALA370 A N_2834 <---> SER366 A O_2801 3.3 16.7
@> VAL360 A N_2747 <---> ALA356 A O_2715 3.3 23.8
@> PHE229 A N_1729 <---> ALA225 A O_1703 3.3 33.3
@> ASN362 A ND2_2772 <---> PRO571 A O_4446 3.3 10.2
@> CYS161 A N_1177 <---> LYS152 A O_1104 3.3 8.3
@> ALA370 B N_8038 <---> SER366 B O_8005 3.3 30.9
@> ASN413 B N_8395 <---> THR409 B O_8365 3.3 36.3
@> THR372 A N_2847 <---> PHE367 A O_2807 3.3 18.6
@> ARG215 B NH1_6823 <---> GLU212 B OE2_6796 3.3 34.9
@> ASN598 B ND2_9845 <---> ASN304 B OD1_7525 3.3 7.3
@> GLY424 B N_8481 <---> ASP428 B OD2_8515 3.3 25.2
@> ILE515 B N_9223 <---> TRP511 B O_9185 3.3 19.4
@> ARG361 A NH1_2763 <---> ASN569 A O_4430 3.3 27.9
@> CYS161 B N_6381 <---> LYS152 B O_6308 3.3 19.0
@> THR95 B OG1_5856 <---> ARG5 B O_5309 3.3 14.8
@> SER517 B OG_9247 <---> ASN522 B OD1_9286 3.3 36.6
@> ARG474 B NH1_8890 <---> ILE468 B N_8826 3.3 28.8
@> VAL268 A N_2058 <---> THR264 A O_2033 3.3 27.6
@> SER377 B N_8094 <---> THR372 B O_8054 3.3 31.9
@> ARG535 A N_4169 <---> ASP499 A OD1_3887 3.3 1.1
@> ARG634 B NH2_10131 <---> GLU626 B OE1_10061 3.3 31.2
@> ILE421 B N_8459 <---> ALA416 B O_8421 3.3 24.8
@> THR10 A N_91 <---> ALA49 A O_335 3.3 21.1
@> TYR473 B N_8869 <---> ASN244 B OD1_7075 3.3 39.9
@> GLN241 A NE2_1845 <---> ASN569 A OD1_4433 3.3 38.6
@> TYR495 A N_3844 <---> ILE491 A O_3819 3.3 30.8
@> ILE421 A N_3255 <---> ALA416 A O_3217 3.3 34.5
@> ARG5 B N_5306 <---> THR95 B O_5854 3.3 34.8
@> GLN139 A N_980 <---> GLN135 A O_945 3.4 11.3
@> GLN479 A N_3716 <---> ASP475 A O_3691 3.4 33.6
@> SER286 B N_7384 <---> GLU281 B O_7348 3.4 16.8
@> MET195 B N_6647 <---> ALA191 B O_6620 3.4 27.9
@> ARG618 A NH1_4795 <---> ASP625 A OD2_4849 3.4 9.3
@> VAL502 B N_9108 <---> SER498 B O_9082 3.4 32.3
@> ILE515 A N_4019 <---> TRP511 A O_3981 3.4 28.7
@> ARG407 B NH2_8349 <---> GLU671 B OE2_10430 3.4 26.5
@> ASN672 A N_5227 <---> ARG618 A O_4789 3.4 31.4
@> VAL167 B N_6428 <---> GLU418 B OE1_8441 3.4 23.0
@> SER320 B N_7642 <---> PRO325 B O_7672 3.4 32.0
@> HIS394 B N_8230 <---> GLU141 B OE1_6209 3.4 4.5
@> ARG203 A NH1_1514 <---> GLU212 A OE1_1591 3.4 24.9
..
..
@> Number of detected hydrogen bonds: 669.
@> Calculating salt bridges.
@> LYS196 A NZ_1459 <---> ASP202 A OD1_1503_1504 2.4
@> GLU168 B OE1_6442_6443 <---> ARG215 A NH1_1619_1620 2.6
@> ASP202 B OD1_6707_6708 <---> LYS196 B NZ_6663 2.7
@> ARG654 A NH1_5088_5089 <---> ASP476 A OD1_3702_3703 2.8
@> ASP505 B OD1_9138_9139 <---> HIS396 B NE2_8255 2.9
@> ARG203 A NH1_1514_1515 <---> GLU212 A OE1_1591_1592 3.0
@> GLU281 B OE1_7352_7353 <---> LYS284 B NZ_7379 3.0
@> ASP616 A OD1_4775_4776 <---> ARG407 A NH1_3144_3145 3.0
@> ASP505 A OD1_3934_3935 <---> HIS396 A NE2_3051 3.0
@> LYS582 B NZ_9734 <---> ASP348 B OD1_7845_7846 3.1
@> ARG635 A NH1_4937_4938 <---> GLU631 A OE1_4903_4904 3.2
@> GLU32 B OE1_5509_5510 <---> ARG68 B NH1_5729_5730 3.3
@> GLU212 B OE1_6795_6796 <---> ARG203 B NH1_6718_6719 3.3
@> ASP625 B OD1_10052_10053 <---> ARG618 B NH1_9999_10000 3.3
@> ASP616 B OD1_9979_9980 <---> ARG407 B NH1_8348_8349 3.3
@> HIS292 A NE2_2237 <---> GLU364 A OE1_2785_2786 3.4
@> ARG618 A NH1_4795_4796 <---> ASP625 A OD1_4848_4849 3.4
@> ASP476 B OD1_8906_8907 <---> ARG654 B NH1_10292_10293 3.5
@> ARG138 B NH1_6182_6183 <---> GLU507 B OE1_9158_9159 3.5
@> ARG649 B NH1_10251_10252 <---> GLU653 B OE1_10281_10282 3.6
@> ARG649 A NH1_5047_5048 <---> GLU653 A OE1_5077_5078 3.6
@> ARG634 B NH1_10130_10131 <---> GLU626 B OE1_10061_10062 3.7
@> GLU364 B OE1_7989_7990 <---> HIS292 B NE2_7441 3.7
@> ARG220 B NH1_6872_6873 <---> GLU194 B OE1_6645_6646 3.8
@> GLU507 A OE1_3954_3955 <---> ARG138 A NH1_978_979 3.8
@> ASP602 A OD1_4666_4667 <---> ARG429 A NH1_3321_3322 3.9
@> GLU626 A OE1_4857_4858 <---> ARG634 A NH1_4926_4927 3.9
@> ARG220 A NH1_1668_1669 <---> GLU194 A OE1_1441_1442 3.9
@> LYS357 B NZ_7929 <---> ASP235 B OD1_7001_7002 3.9
@> LYS175 A NZ_1297 <---> GLU168 A OE1_1238_1239 4.0
@> ASP235 A OD1_1797_1798 <---> LYS357 A NZ_2725 4.0
@> GLU141 B OE1_6209_6210 <---> ARG145 B NH1_6242_6243 4.0
@> ARG429 B NH1_8525_8526 <---> ASP602 B OD1_9870_9871 4.0
@> GLU613 A OE1_4756_4757 <---> LYS180 A NZ_1336 4.0
@> ARG7 A NH1_76_77 <---> ASP52 A OD1_361_362 4.1
@> ARG463 B NH1_8796_8797 <---> ASP459 B OD1_8759_8760 4.1
@> GLU382 A OE1_2936_2937 <---> ARG417 A NH1_3228_3229 4.1
@> ASP348 A OD1_2641_2642 <---> LYS582 A NZ_4530 4.2
@> ASP20 B OD1_5424_5425 <---> LYS71 B NZ_5756 4.2
@> GLU194 A OE1_1441_1442 <---> LYS198 A NZ_1476 4.2
@> GLU32 A OE1_252_253 <---> ARG68 A NH1_491_492 4.3
@> ARG463 A NH1_3592_3593 <---> ASP459 A OD1_3555_3556 4.3
@> ARG208 A NH1_1560_1561 <---> GLU111 B OE1_5976_5977 4.3
@> GLU141 A OE1_1005_1006 <---> ARG145 A NH1_1038_1039 4.4
@> ASP475 A OD1_3694_3695 <---> ARG474 A NH1_3686_3687 4.4
@> ASP616 A OD1_4775_4776 <---> LYS180 A NZ_1336 4.5
@> ARG390 A NH1_3000_3001 <---> GLU514 A OE1_4017_4018 4.6
@> ARG63 B NH1_5687_5688 <---> ASP129 B OD1_6102_6103 4.6
@> ARG461 B NH1_8778_8779 <---> GLU458 B OE1_8751_8752 4.6
@> ARG444 A NH1_3433_3434 <---> GLU440 A OE1_3397_3398 4.6
@> GLU369 A OE1_2832_2833 <---> HIS368 A NE2_2824 4.6
@> HIS231 B NE2_6962 <---> GLU234 B OE1_6993_6994 4.6
@> LYS165 A NZ_1216 <---> ASP163 A OD1_1197_1198 4.6
@> LYS612 B NZ_9952 <---> ASP562 B OD1_9583_9584 4.7
@> ASP20 A OD1_167_168 <---> LYS71 A NZ_518 4.7
@> GLU212 B OE1_6795_6796 <---> ARG208 B NH1_6764_6765 4.7
@> GLU369 B OE1_8036_8037 <---> HIS368 B NE2_8028 4.8
@> HIS231 A NE2_1758 <---> GLU234 A OE1_1789_1790 4.8
@> GLU168 B OE1_6442_6443 <---> LYS175 B NZ_6501 4.8
@> ARG417 B NH1_8432_8433 <---> GLU382 B OE1_8140_8141 4.9
@> ARG474 B NH1_8890_8891 <---> ASP475 B OD1_8898_8899 4.9
@> ARG215 A NH1_1619_1620 <---> GLU212 A OE1_1591_1592 4.9
@> GLU12 B OE1_5366_5367 <---> ARG90 B NH1_5807_5808 4.9
@> LYS198 B NZ_6680 <---> GLU194 B OE1_6645_6646 5.0
@> Number of detected salt bridges: 64.
@> Calculating repulsive ionic bonding.
@> ASP352 A OD1_2680_2681 <---> ASP349 A OD1_2649_2650 3.3
@> LYS165 A NZ_1216 <---> LYS152 A NZ_1109 3.8
@> ARG203 B NH1_6718_6719 <---> ARG208 B NH1_6764_6765 4.3
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Calculating Pi stacking interactions.
@> HIS227 B 6923_6924_6925_6926_6927 <---> HIS231 B 6958_6959_6960_6961_6962 4.1 23.4
@> HIS227 A 1719_1720_1721_1722_1723 <---> HIS231 A 1754_1755_1756_1757_1758 4.1 29.7
@> PHE640 A 4970_4971_4972_4973_4974_4975 <---> PHE487 A 3788_3789_3790_3791_3792_3793 4.3 177.8
@> HIS411 B 8382_8383_8384_8385_8386 <---> TYR176 B 6507_6508_6509_6510_6511_6512 4.5 173.1
@> TRP566 B 9609_9611_9612_9613_9614_9615 <---> PHE229 B 6938_6939_6940_6941_6942_6943 4.5 105.4
@> PHE640 B10174_10175_10176_10177_10178_10179 <---> PHE487 B 8992_8993_8994_8995_8996_8997 4.5 166.4
@> HIS373 B 8063_8064_8065_8066_8067 <---> HIS378 B 8105_8106_8107_8108_8109 4.5 123.3
@> PHE229 A 1734_1735_1736_1737_1738_1739 <---> TRP566 A 4405_4407_4408_4409_4410_4411 4.6 75.3
@> TYR176 A 1303_1304_1305_1306_1307_1308 <---> HIS411 A 3178_3179_3180_3181_3182 4.7 87.1
@> TYR256 B 7170_7171_7172_7173_7174_7175 <---> HIS255 B 7160_7161_7162_7163_7164 4.7 82.3
@> HIS553 B 9520_9521_9522_9523_9524 <---> HIS378 B 8105_8106_8107_8108_8109 4.7 99.2
@> HIS255 A 1956_1957_1958_1959_1960 <---> TYR256 A 1966_1967_1968_1969_1970_1971 4.8 66.4
@> PHE399 A 3072_3073_3074_3075_3076_3077 <---> HIS394 A 3031_3032_3033_3034_3035 4.8 125.6
@> TRP109 B 5954_5956_5957_5958_5959_5960 <---> PHE88 B 5786_5787_5788_5789_5790_5791 4.9 45.5
@> HIS553 A 4316_4317_4318_4319_4320 <---> HIS378 A 2901_2902_2903_2904_2905 4.9 95.9
@> HIS373 A 2859_2860_2861_2862_2863 <---> HIS378 A 2901_2902_2903_2904_2905 5.0 85.4
@> Number of detected Pi stacking interactions: 16.
@> Calculating cation-Pi interactions.
@> PHE399 B 8276_8277_8278_8279_8280_8281 <---> ARG145 B NH1_6242_6243 3.8
@> PHE229 B 6938_6939_6940_6941_6942_6943 <---> LYS214 B NZ_6813 4.4
@> PHE219 B 6857_6858_6859_6860_6861_6862 <---> ARG220 B NH1_6872_6873 4.5
@> HIS376 A 2885_2886_2887_2888_2889 <---> LYS552 A NZ_4310 4.5
@> PHE219 A 1653_1654_1655_1656_1657_1658 <---> ARG220 A NH1_1668_1669 4.6
@> TYR408 B 8355_8356_8357_8358_8359_8360 <---> ARG407 B NH1_8348_8349 4.6
@> PHE399 A 3072_3073_3074_3075_3076_3077 <---> ARG145 A NH1_1038_1039 4.6
@> TYR408 A 3151_3152_3153_3154_3155_3156 <---> ARG407 A NH1_3144_3145 4.6
@> TYR154 B 6324_6325_6326_6327_6328_6329 <---> LYS152 B NZ_6313 4.6
@> PHE344 A 2607_2608_2609_2610_2611_2612 <---> LYS582 A NZ_4530 4.7
@> TYR408 B 8355_8356_8357_8358_8359_8360 <---> LYS180 B NZ_6540 4.7
@> TYR472 B 8862_8863_8864_8865_8866_8867 <---> ARG654 B NH1_10292_10293 4.8
@> HIS160 B 6376_6377_6378_6379_6380 <---> LYS518 B NZ_9256 4.8
@> TYR107 A 727_728_729_730_731_732 <---> ARG90 A NH1_588_589 4.9
@> TYR472 A 3658_3659_3660_3661_3662_3663 <---> ARG654 A NH1_5088_5089 4.9
@> Number of detected cation-pi interactions: 15.
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@> ILE433 B CD1_855114s <---> PHE438 B CD1_8583 2.2 42.8
@> MET446 A SD_344914s <---> LEU449 A CD1_3475 2.8 43.8
@> ALA179 B CB_653114s <---> PHE14 B CE2_5382 2.9 48.5
@> ILE421 A CD1_326214s <---> TYR154 A OH_1126 2.9 21.4
@> PHE92 A CE2_61314s <---> VAL69 A CG2_499 3.0 33.3
@> PHE438 A CD1_337914s <---> ILE433 A CG2_3346 3.0 43.4
@> MET478 A SD_371414s <---> ILE460 A CD1_3564 3.0 30.7
@> ILE460 B CG2_876714s <---> VAL465 B CG2_8808 3.0 42.3
@> VAL6 B CG2_532314s <---> LEU94 B CD2_5850 3.1 23.4
@> ARG474 B CG_888614s <---> ILE460 B CD1_8768 3.1 37.5
@> LEU210 B CD1_677814s <---> ILE591 B CG1_9794 3.1 33.1
@> TRP207 B NE1_674914s <---> MET567 B CE_9623 3.1 22.5
@> VAL55 B CG1_562614s <---> LEU36 B CD1_5537 3.1 20.4
@> ILE515 A CG2_402514s <---> TYR541 A OH_4229 3.2 29.9
@> TYR472 B OH_886814s <---> LEU658 B CD2_10322 3.2 31.2
@> ALA123 B CB_605414s <---> TYR495 B CE1_9056 3.2 30.9
@> ARG220 B CG_686814s <---> PHE219 B CE2_6861 3.2 81.3
@> LEU594 A CD1_461114s <---> MET213 A CE_1600 3.2 14.0
@> ILE515 B CG2_922914s <---> TYR541 B OH_9433 3.2 29.6
@> TRP158 B CH2_636314s <---> ILE442 B CD1_8618 3.2 45.7
@> PHE367 A CE2_281314s <---> ILE294 A CG2_2248 3.2 17.1
@> VAL8 A CG2_8414s <---> PHE92 A CD1_610 3.2 28.0
@> PHE184 B CD2_656914s <---> ILE197 A CD1_1467 3.3 29.5
@> TYR664 A CD1_516614s <---> ALA558 A CB_4348 3.3 38.4
@> TRP608 B NE1_991614s <---> ARG220 B CG_6868 3.3 46.3
@> LEU605 B CD1_989314s <---> ALA191 B CB_6621 3.3 16.4
@> TYR472 A OH_366414s <---> LEU658 A CD2_5118 3.3 33.0
@> LEU594 B CD1_981514s <---> MET213 B CE_6804 3.3 16.0
@> ALA188 B CB_660614s <---> LEU609 B CD1_9928 3.3 30.9
@> ALA370 A CB_283814s <---> PHE438 A CD2_3380 3.3 42.4
@> LEU521 A CD1_407414s <---> MET446 A CE_3450 3.3 11.8
@> LEU538 A CD2_420114s <---> ILE492 A CD1_3831 3.3 25.6
@> LEU401 B CD1_829714s <---> PHE487 B CE2_8996 3.3 21.3
@> TYR495 A CE1_385214s <---> ALA123 A CB_850 3.3 28.2
@> VAL24 B CG1_545314s <---> LEU67 B CD1_5718 3.3 11.0
@> PHE104 A CE1_70614s <---> LEU94 A CD1_630 3.3 16.3
@> ILE468 A CG2_362814s <---> TYR471 A CD2_3648 3.3 15.5
@> TRP359 B CZ3_794914s <---> MET574 B CG_9672 3.3 43.2
@> LEU201 B CD1_669914s <---> PHE192 B CE1_6630 3.3 31.1
@> PHE92 B CE2_583214s <---> VAL8 B CG2_5341 3.3 31.8
@> TYR318 A CD1_242314s <---> LEU272 A CD2_2090 3.4 34.9
@> LEU250 B CD2_711814s <---> PHE367 B CZ_8018 3.4 47.0
@> LEU317 A CD1_241514s <---> ILE251 A CD1_1922 3.4 14.3
@> ARG90 A CG_58414s <---> PHE88 A CE2_571 3.4 31.2
@> PHE4 A CD2_4514s <---> LEU57 A CD1_403 3.4 14.5
@> LEU441 A CD1_340514s <---> ILE433 A CD1_3347 3.4 15.4
@> VAL290 A CG2_221914s <---> LEU317 A CD1_2415 3.4 9.6
@> PHE547 A CE1_427514s <---> ALA551 A CB_4301 3.4 31.0
@> PHE219 A CE2_165714s <---> ARG220 A CG_1664 3.4 91.6
@> PHE45 A CZ_31514s <---> LEU38 A CD1_295 3.4 14.4
@> MET148 A CG_106314s <---> TYR149 A CE2_1075 3.4 68.6
@> LEU110 A CD2_76414s <---> TRP87 A CZ3_560 3.4 54.2
@> PHE192 A CZ_142814s <---> LYS196 A CG_1456 3.4 36.2
@> TYR473 A CE2_367414s <---> ALA555 A CB_4330 3.4 13.4
@> PHE384 B CD2_815614s <---> VAL545 B CG1_9461 3.4 38.5
@> TYR496 B CD1_906614s <---> VAL502 B CG2_9114 3.4 32.3
@> ARG417 A CG_322414s <---> ILE421 A CD1_3262 3.4 19.2
@> LEU210 A CD2_157514s <---> MET213 A CE_1600 3.4 42.7
@> LEU456 B CD1_873514s <---> ILE460 B CD1_8768 3.4 39.6
@> VAL263 A CG2_202914s <---> PHE261 A CZ_2015 3.4 35.6
@> VAL597 A CG2_463314s <---> TRP207 A CD2_1544 3.4 51.7
@> LEU355 B CD1_791414s <---> TRP359 B NE1_7945 3.4 38.6
@> TRP511 A CE3_398814s <---> LEU508 A CD1_3962 3.4 36.6
@> LEU605 A CD1_468914s <---> ALA191 A CB_1417 3.4 12.4
@> LEU420 B CD1_845714s <---> VAL426 B CG1_8499 3.4 20.8
@> VAL69 B CG2_573714s <---> PHE92 B CE1_5831 3.4 28.2
@> LEU354 B CD2_790714s <---> TRP232 B CH2_6976 3.4 36.8
@> VAL542 A CG1_423514s <---> LEU401 A CD2_3094 3.4 9.3
@> VAL360 A CG2_275314s <---> ILE331 A CG2_2514 3.5 14.1
@> VAL125 B CG1_606914s <---> TRP127 B CE2_6086 3.5 50.8
@> LYS214 A CD_160714s <---> PHE229 A CZ_1739 3.5 36.1
@> LEU329 B CD2_770614s <---> VAL271 B CG1_7285 3.5 17.7
@> ILE294 B CG2_745214s <---> LEU295 B CD1_7460 3.5 41.1
@> LEU419 B CD1_844914s <---> LYS196 A CD_1457 3.5 34.6
@> LYS518 B CG_925314s <---> TRP151 B CE2_6300 3.5 61.9
@> MET574 A CG_446814s <---> TRP359 A CZ3_2745 3.5 46.6
@> PHE590 B CE2_978714s <---> LEU594 B CD1_9815 3.5 37.1
@> ILE343 B CG2_780414s <---> ALA330 B CB_7711 3.5 3.4
@> PHE547 B CE2_948014s <---> ALA551 B CB_9505 3.5 25.8
..
..
@> Number of detected hydrophobic interactions: 324.
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
To extract the interactions between protein’s complex, specify selection and selection2 and interaction type:
For hydrogen bonds:
In [6]: interactions.getHydrogenBonds(selection='chain A', selection2='chain B')
[['ARG215', 'NH2_1620', 'A', 'GLU168', 'OE1_6442', 'B', 2.5802, 24.8343],
['ARG215', 'NH1_1619', 'A', 'GLU168', 'OE2_6443', 'B', 2.6778, 28.6548],
['ASP202', 'OD2_1504', 'A', 'GLU418', 'OE2_8442', 'B', 2.744, 31.6383]]
For salt bridges:
In [7]: interactions.getSaltBridges(selection='chain A', selection2='chain B')
[['GLU168', 'OE1_6442_6443', 'B', 'ARG215', 'NH1_1619_1620', 'A', 2.6066],
['ARG208', 'NH1_1560_1561', 'A', 'GLU111', 'OE1_5976_5977', 'B', 4.3468]]
For hydrophobic interactions:
In [8]: interactions.getHydrophobic(selection='chain A', selection2='chain B')
[['PHE184', 'CD2_6569', 'B', 'ILE197', 'CD1_1467', 'A', 3.2502, 29.5284],
['LEU419', 'CD1_8449', 'B', 'LYS196', 'CD_1457', 'A', 3.4645, 34.5683],
['ALA182', 'CB_1349', 'A', 'ILE197', 'CD1_6671', 'B', 3.7348, 34.1782],
['ALA193', 'CB_6637', 'B', 'LEU186', 'CD1_1387', 'A', 4.2965, 20.2503]]
For Pi-stacking interaction:
In [9]: interactions.getPiStacking(selection='chain A', selection2='chain B')
[]
For Pi-cation interactions:
In [10]: interactions.getPiCation(selection='chain A', selection2='chain B')
[]
For repulsive ionic bonding interactions:
In [11]: interactions.getRepulsiveIonicBonding(selection='chain A', selection2='chain B')
[]
Non-zero interactions could be futher saved and used in VMD program to display them:
In [12]: showProteinInteractions_VMD(atoms, interactions.getHydrogenBonds(),
....: color='blue', filename='HBs_7laf.tcl')
....:
In [13]: showProteinInteractions_VMD(atoms, interactions.getSaltBridges(),
....: color='yellow',filename='SBs_7laf.tcl')
....:
In [14]: showProteinInteractions_VMD(atoms, interactions.getHydrophobic(),
....: color='silver',filename='HPh_7laf.tcl')
....:
@> TCL file saved
@> TCL file saved
@> TCL file saved