Cellular and Molecular Life Sciences

, Volume 65, Issue 7, pp 1059–1072

The interface of protein-protein complexes: Analysis of contacts and prediction of interactions


DOI: 10.1007/s00018-007-7451-x

Cite this article as:
Bahadur, R.P. & Zacharias, M. Cell. Mol. Life Sci. (2008) 65: 1059. doi:10.1007/s00018-007-7451-x


Specific protein-protein interactions are essential for cellular functions. Experimentally determined three-dimensional structures of protein-protein complexes offer the possibility to characterize binding interfaces in terms of size, shape and packing density. Comparison with crystal-packing interfaces representing nonspecific protein-protein contacts gives insight into how specific binding differs from nonspecific low-affinity binding. An overview is given on empirical structural rules for specific protein-protein recognition derived from known complex structures. Although single parameters such as interface size, shape or surface complementary show clear trends for different interface types, each parameter alone is insufficient to fully distinguish between specific versus crystal-packing contacts. A combination of interface parameters is, however, well suited to characterize a specific interface. This knowledge provides us with the essential ingredients that make up a specific protein recognition site. It is also of great value for the prediction of protein binding sites and for the evaluation of predicted complex structures.


Protein-protein interactions protein-protein docking protein-binding region crystal packing nonspecific interaction protein interface description binding site prediction 

Copyright information

© Birkhaueser 2007

Authors and Affiliations

  1. 1.School of Engineering and ScienceJacobs University BremenBremenGermany

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