3
$\begingroup$

I am analyzing the 7VF2 structure, from the RCSB-database. I noticed that some residues belonging to one of its chains interact with the other chains that are present within the assembly. My question is if there is a method to extract a list of interacting residues that are present in a PDB.

EDIT: enter image description here

Just as an example, we have Lys 1616 belonging to ZC3H13 chain that interacts with Glu 621 of the protein virilizer homolog (the first chain)

Mol* 3D visualizer can be used for major information in the 3D View in the link page I provided

$\endgroup$
3
  • 1
    $\begingroup$ do you need alpha chain hydrogen interactions or side chains hydrogen interactions ? I believe most of the alpha helics and beta sheets emerge from apha carbon hydrogen bonds so thet'll be a huge number of interaction to be shown, but could be wrong $\endgroup$
    – pippo1980
    Mar 2, 2023 at 14:14
  • 1
    $\begingroup$ files.rcsb.org/pub/pdb/validation_reports/vf/7vf2/… : Atom-1 Atom-2 Interatomic distance (Å) Clash overlap (Å) : 2:B:1616:LYS:HA 2:B:1616:LYS:HD2 1.71 0.42 there is something wrong with k1616 as per validation report states ... see atoms nomenclature in Lys ligand-expo.rcsb.org/reports/L/LYS/LYS_D3L3.gif $\endgroup$
    – pippo1980
    Mar 2, 2023 at 14:46
  • 1
    $\begingroup$ DSSP gives you hydrogen bonds, not sure how it works for complexes though. $\endgroup$
    – jgreener
    Mar 6, 2023 at 11:53

1 Answer 1

1
$\begingroup$

You can do that with GROMACS. You probably need to check the manual for this, but roughly these are the steps:

gmx pdb2gmx -f input.pdb -o output.gro -water spc
gmx solvate -cp output.gro -cs spc216.gro -o output_solv.gro -p output.top
gmx pdb2gmx -f output_solv.gro -o output_processed.gro -p output.top -ignh
gmx make_ndx -f output_processed.gro -o index.ndx
gmx hbond -f output_processed.gro -n index.ndx -s output.tpr -num hbond.xvg -hbn hbond.ndx

First, you convert the PDB file into a GROMACS topology file using the pdb2gmx command. Then you can solvate the system with water molecules and add hydrogen atoms. Then you cCreate an index file containing the groups of atoms you want to analyze. Then you can use the hbond command to calculate the hydrogen bonds.

I have not used GROMACS in a while. Hope that provides a starting point. With GROMACS you can even run a simulation and monitor the h-bonds over time.

You actually might need to run an energy minimziation first, as the PDB might not in an optimal state for the h-bonds detection.

$\endgroup$
1
  • $\begingroup$ Great comment! I will keep this question open so that more possible answers can be added. Meanwhile, thank you for the suggestion! I will try and let you know! $\endgroup$ Mar 8, 2023 at 8:27

This site is temporarily in read-only mode and not accepting new answers.

Not the answer you're looking for? Browse other questions tagged .