Comprehensive statistical analysis of residues interaction specificity at protein-protein interfaces

We calculated interchain contacts on the atomic level for nonredundant set of 4602 protein-protein interfaces using an unbiased Voronoi-Delaune tessellation method, and made 20X20 residue contact matrixes both for homodimers and heterocomplexes. The area of contacts and the distance distribution for these contacts were calculated on both the residue and the atomic levels. We analyzed residue area distribution and showed the existence of two types of interresidue contacts: stochastic and specific. We also derived formulas describing the distribution of contact area for stochastic and specific interactions in parametric form. Maximum pairing preference index was found for Cys-Cys contacts and for oppositely charged interactions. A significant difference in residue contacts was observed between homodimers and heterocomplexes. Interfaces in homodimers were enriched with contacts between residues of the same type due to the effects of structure symmetry. Proteins 2007;67:1060-1077. (C) 2007 Wiley-Liss, Inc.