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Dissecting protein–protein recognition sites
Abstract
The recognition sites in 70 pairwise protein–protein complexes of known three‐dimensional structure are dissected in a set of surface patches by clustering atoms at the interface. When the interface buries <2000 Å 2 of protein surface, the recognition sites usually form a single patch on the surface of each component protein. In contrast, larger interfaces are generally multipatch, with at least one pair of patches that are equivalent in size to a single‐patch interface. Each recognition site, or patch within a site, contains a core made of buried interface atoms, surrounded by a rim of atoms that remain accessible to solvent in the complex. A simple geometric model reproduces the number and distribution of atoms within a patch. The rim is similar in composition to the rest of the protein surface, but the core has a distinctive amino acid composition, which may help in identifying potential protein recognition sites on single proteins of known structures. Proteins 2002;47:334–343. © 2002 Wiley‐Liss, Inc.
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Cites
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“These observations confirm previous findings highlighting the dominant role of aromatic residues in stabilizing protein interfaces through π-π stacking, hydrogen bonding, and hydrophobic interactions (Mohamed, Degac, and Helms 2015; Chakrabarti and Janin 2002).”
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Metadata
- Authors
- Chakrabarti, P., & Janin, J.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2002-03-26
- Volume
- 47
- Issue
- 3
- Pages
- 334-343
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W1985153601
- Cited by
- 570
- References
- 2
- FWCI
- 8.53
- Type
- journal article
- Language
- en
- Open access
- closed
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