Changes in the default parameters

There are a lot of parameters that can be changed in the water bridge analysis, including the distances, angles, and the number of involved water molecules or residues.

atoms: Atomic object from which atoms are considered

method: 'cluster' or 'chain', where ‘chain’ will find the shortest

water bridging path between two protein atoms default is 'chain'

distDA: maximal distance between water/protein donor and acceptor

default is 3.5

distWR: maximal distance between considered water and any residue

default is 4

anglePDWA: angle range where protein is donor and water is acceptor

default is (100, 200)

anglePAWD: angle range where protein is acceptor and water is donor

default is (100, 140)

angleWW: angle between water donor/acceptor

default is (140, 180)

maxDepth: maximum number of waters in chain/depth of residues in cluster

default is 2

maxNumRes: maximum number of water+protein residues in cluster

default is None

donors: which atoms to count as donors

default is ['N', 'O', 'S', 'F']

acceptors: which atoms to count as acceptors

default is ['N', 'O', 'S', 'F']

output: return information arrays, (protein atoms, water atoms),

or just atom indices per bridge Options are 'info', 'atomic' and 'indices' Default is 'atomic'

isInfoLog: whether to log information

default is True

The above criteria are used to find hydrogen bonds in a PDB structure which are used to predict possible water bridges.

The angles are calculated so that the hydrogen atom that makes the hydrogen bond is the vertex of the angle, where the donor and acceptor atoms form the two ends. The angle is measured between the line connecting the donor to the hydrogen and the line connecting the hydrogen to the acceptor.

Most PDB structures do not have hydrogen atoms, therefore we can ignore this criterium. Hydrogen bonds will be calculated just based on distance and atom types.

Here’s an example of how to apply changes in parameters:

In [1]: waterBridges_2 = calcWaterBridges(atoms, method='cluster', distWR=3.0, distDA=3.2, maxDepth=3)

@> 17 water bridges detected.
@> SER7 OG_21 A LYS110 NZ_838 A 4.70722699686344 1 ['A_1316']
@> GLY14 O_72 A SER47 O_328 A GLU50 N_347 A 5.288116583434976 4.544135231262378 5.10489901956934 1 ['A_1274']
@> PRO20 O_115 A GLU23 OE1_139 A 4.571172934816621 1 ['A_1292']
@> GLU23 OE2_140 A SER71 O_514 A HIS72 ND1_523 A 4.934310286149422 4.127239392136104 4.463734423103597 1 ['A_1244']
@> ASP42 OD2_301 A ARG40 NH2_286 A 5.163938516287738 1 ['A_1246']
@> ASP81 OD1_598 A THR84 OG1_621 A ARG40 NH2_286 A 4.415462942886057 4.365525627000715 3.9229717052255175 1 ['A_1262']
@> GLY14 O_72 A SER47 O_328 A GLU50 N_347 A 5.288116583434976 4.544135231262378 5.10489901956934 1 ['A_1274']
@> GLU50 OE2_355 A TYR131 OH_1009 A 5.157987010452818 1 ['A_1299']
@> ARG65 NH2_473 A ASP135 O_1037 A 4.820906553751068 1 ['A_1267']
@> GLU23 OE2_140 A SER71 O_514 A HIS72 ND1_523 A 4.934310286149422 4.127239392136104 4.463734423103597 1 ['A_1244']
@> GLN105 NE2_800 A LYS102 O_772 A LYS79 NZ_582 A 4.2363221076778395 3.8752885053889865 4.929221236666094 1 ['A_1249']
@> ASP81 OD1_598 A THR84 OG1_621 A ARG40 NH2_286 A 4.415462942886057 4.365525627000715 3.9229717052255175 1 ['A_1262']
@> GLN105 NE2_800 A LYS102 O_772 A LYS79 NZ_582 A 4.2363221076778395 3.8752885053889865 4.929221236666094 1 ['A_1249']
@> SER7 OG_21 A LYS110 NZ_838 A 4.70722699686344 1 ['A_1316']
@> LEU125 O_953 A GLY117 N_886 A 3.8595291163560352 1 ['A_1264']
@> GLU50 OE2_355 A TYR131 OH_1009 A 5.157987010452818 1 ['A_1299']
@> ARG65 NH2_473 A ASP135 O_1037 A 4.820906553751068 1 ['A_1267']