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Statistical analysis of predominantly transient protein–protein interfaces



A non-redundant set of 170 protein–protein interfaces of known structure was statistically analyzed for residue and secondary-structure compositions, pairing preferences and side-chain–backbone interaction frequencies. By focussing mainly on transient protein–protein interfaces, the results underline previous findings for protein–protein interfaces but also show some new interesting aspects of transient interfaces. The residue compositions at interfaces found in this study correlate well with the results of other studies. On average, contacts between pairs of hydrophobic and polar residues were unfavorable, and the charged residues tended to pair subject to charge complementarity. Secondary structure composition analysis shows that neither helices nor β-sheets are dominantly populated at interfaces. Analyzing the pairing preferences of the secondary structure elements revealed a higher affinity within the same elements and alludes to tight packings. In addition, the results for the side-chain and backbone interaction frequencies, which were measured under more stringent conditions, showed a high occurrence of side-chain–backbone interactions. Taking a closer look at the helix and β-sheet binding frequencies for a given side-chain and backbone interaction underlined the relevance of tight packings. The polarity of interfaces increased with decreasing interface size. These types of information may be useful for scoring complexes in protein–protein docking studies or for prediction of protein–protein interfaces from the sequences alone. Proteins 2005. © 2005 Wiley-Liss, Inc.