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Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps
Author(s) -
Seeliger Daniel,
de Groot Bert L.
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21447
Subject(s) - sphere packing , atomic radius , resolution (logic) , atomic packing factor , chemistry , biological system , crystallography , chemical physics , materials science , computer science , mathematics , geometry , biology , artificial intelligence , organic chemistry
A rigorous quantitative assessment of atomic contacts and packing in native protein structures is presented. The analysis is based on optimized atomic radii derived from a set of high‐resolution protein structures and reveals that the distribution of atomic contacts and overlaps is a structural constraint in proteins, irrespective of structural or functional classification and size. Furthermore, a newly developed method for calculating packing properties is introduced and applied to sets of protein structures at different levels of resolution. The results show that limited resolution yields decreasing packing quality, which underscores the relevance of packing considerations for structure prediction, design, dynamics, and docking. Proteins 2007. © 2007 Wiley‐Liss, Inc.