Residue Contact Map - Program And/Or Database

Question

[Lyco]

Can anybody recommend a good program/server for identifying contact residues from a given PDB-formatted file (protein-protein or protein-ligand contacts). No fancy graphics required, just a list of residues in molecule A that make a contact with residues of molecule B (assuming that a distance threshold is specified). It would be great if the kind of contact would also be provided (backbone or side chain ? salt bridge, polar, hydrophobic ?).

I am aware of several interactive structure viewers that helps with getting this information(dsv, yasara, vmd? ...), I would prefer a tool that does this with minimal user interaction, ideally in batch mode.

A second, related question: is there a database or table where these kind of information is collected for many/all multi-molecule PDF files ?

Answer 1

[Khader Shameer]

A second, related question: is there a database or table where these kind of information is collected for many/all multi-molecule PDF files?

Yes, such a data set is available at PDBSum. See an example of domain-swapped CYANOVIRIN-N dimer here.

List of interactions in a text file is available here.

Also see my answer / Hari's reply here on downloading .gro files used to generate LigPlots in PDBSum.

[Wayne]

I made some scripts to parse that text file you point out and make it a nice form for working with Python, and also generate some summary reports when you compare the same proteins in different, related structures, for example when the structure of a complex is solved with different ligands. The scripts are demonstrated in a series of Jupyter notebooks here. Go there and press launch binder to get started with an active Jupyter session in your browser. The actual scripts being used are here; however, the accompanying Jupyter notebook is really needed to make a couple of them work. Best to start at https://github.com/fomightez/pdbsum-binder

Answer 2

[Neilfws]

Try the WHAT IF Server. If by "batch mode" you mean "upload multiple PDB files" then no, it does not do that, but it is quick and easy to use.

Select "Atomic contacts" from the menu, choose the appropriate option, upload PDB file (or paste PDB ID) and submit. The server returns a nice, simple easy-to-parse ASCII output format.

Answer 3

[Lyco]

A recent addition to the ranks of programs/servers for the task: COCOMAPS has been described in a recent article in Bioinformatics. The link to the online server ist https://www.molnac.unisa.it/BioTools/cocomaps/