Tool to access to protein-protein exact interactions domains

Question

[elisabetta.punzi]

I have a set of proteins, all of them are encoded by the mitochondrial genome (e.g. atp6) . I would like to retrieve information about their physical interactions with other proteins from their complex; more precisely, I want to have info on which amino acid range (or nucleotide range) of my protein interacts with another protein and with which amino acids it interacts. More or less like this:

Protein 1    Domain range for protein1    Protein2    Domain range for protein2    Notes
MT-ATP6      Val13-Glu50                  ATP5C1      Gly67-Pro89
MT-ATP6      Arg148-Val170                ATP5F1      Phe200-Ileu212

(of course I'm guessing about the interactions...)

I tried with STRING, InterPro and a few other tools but I couldn't find the exact information I want. Is there any way I can find it?

I don't know if it's an evident question, I'm very new to all of this.

[zizigolu]

Don't worry Elisabetta, everyone has been new someday, I think the below links have something to read...

• http://www.nigms.nih.gov/Initiatives/PSI/
• http://luna.bioc.columbia.edu/honiglab/mark-us

[elisabetta.punzi]

@Sarah: I can't open none of your links, the first one says that the page doesn't exist and the second leads me to an "insecurity warning"...

[zizigolu]

Sorry Elisabetta,

• http://www.geneinfinity.org/sp/sp_proteininteraction.html
• http://www.researchgate.net/post/Can_anyone_help_with_potential_protein-protein_interaction_prediction

[Pallab Bhowmick]

From sequence level it is really hard to predict which residue of your protein A will interact with protein B. As you have mentioned, you know domains of your proteins which suppose to interact with each other (although for protein ATP5F1, its not domain I think it will be peptide which may act as a short linear motif) so it is better to look for structure in PDB! if you are lucky, may be you will find pdb complex of your protein otherwise you have to do docking!

Answer 1

[zizigolu]

http://compbio.ornl.gov/structure/domainparser/