Entering edit mode
3.8 years ago
srdjanmasirevic2
▴
10
Does anybody knows a software or already build up module in python that calculates distance between protein and ligand C atoms.
The point is that I have a PDB file that has protein binding pocket atom coordinates, together with the number of 10 different ligand coordinates in. Something like this:
ATOM 1 N VAL A 1 16.084 31.820 28.427 1.00 27.25 N
ATOM 2 CA VAL A 1 14.861 30.935 28.224 1.00 25.37 C
ATOM 3 C VAL A 1 14.253 31.406 26.892 1.00 22.19 C
ATOM 4 O VAL A 1 14.324 32.566 26.580 1.00 23.58 O
ATOM 5 CB VAL A 1 13.842 31.151 29.349 1.00 27.51 C
ATOM 6 CG1 VAL A 1 12.499 30.433 29.111 1.00 26.28 C
...
TER
HETATM 1539 C 3TZ A 187 4.075 12.355 25.223 1.00 35.58 C
HETATM 1540 N 3TZ A 187 1.696 11.836 25.442 1.00 40.54 N
HETATM 1541 O 3TZ A 187 5.202 11.813 25.232 1.00 33.14 O
HETATM 1542 N1 3TZ A 187 -3.584 17.685 22.560 1.00 13.51 N
...
TER
HETATM 1547 C6 2JP A 102 -3.679 17.145 23.785 1.00 15.83 C
HETATM 1548 O6 2JP A 102 -4.191 15.926 23.690 1.00 19.66 O
HETATM 1549 CA 2JP A 102 3.015 11.233 25.256 1.00 38.90 C
HETATM 1550 CB 2JP A 102 3.172 10.552 23.884 1.00 41.37 C
...
TER
etc, there are coordinates for 10 different ligands.
What I am interested in is to see for any C atom in each ligand, within distance of 4 Angstroms, how many protein C atoms would be identified? So that the final conclusion is: within 4A distance from ligand C atoms for all 10 ligands there are 35 protein C atoms identified.
