Aminoacid Propensity/Enrichment In Protein-Protein Interaction Site

Question

[Burlappsack]

Hello, Does any one know of any references/papers that describe the distribution of amino acid types in site of protein-protein interactions vs. the rest of the surface? I have calculated the amino acid propensity for interface vs. rest of the surface for one data set, and I would like to check it against other datasets to ensure its accuracy and reliability.
Thank you very much your time, Adam

Answer 1

[Woa]

There are quite a few. Depending upon the nature of the protein-protein complexes like homo/heterodimer, permanent/transient obligate/non obligate etc. you can check the following articles (and related references cited in them). Search also in related groups in Connotea etc.

http://www.ncbi.nlm.nih.gov/pubmed/12527304 http://www.ncbi.nlm.nih.gov/pubmed/8552589 http://www.ncbi.nlm.nih.gov/pubmed/10944393 http://www.ncbi.nlm.nih.gov/pubmed/15895504 http://www.ncbi.nlm.nih.gov/pubmed/16423290 http://www.ncbi.nlm.nih.gov/pubmed/16105176 http://www.ncbi.nlm.nih.gov/pubmed/18080088

Check also papers from these groups:

http://bic.boseinst.ernet.in/pinak/pinakpublication.html http://www.btc.iitkgp.ernet.in/rpb.html

[Woa]

and two more: http://www.ncbi.nlm.nih.gov/pubmed/16043700 http://www.ncbi.nlm.nih.gov/pubmed/17623839

[Burlappsack]

+1 for citing my department head

Answer 2

[Khader Shameer]

See the section 2.3.Residue Interface Propensities / FIG.6. of review article by Jones & Thornton in PNAS. Ref: Principles of protein-protein interaction.

Answer 3

[Reyhaneh]

have a look at this 2011 paper. They have done a perfect comparison:

"Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database" http://www.biomedcentral.com/content/pdf/1471-2105-12-313.pdf

Here is a comparison chart from their paper (http://www.biomedcentral.com/1471-2105/12/313/figure/F1):