Campus Units

Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Baker Center for Bioinformatics and Biological Statistics

Document Type

Article

Publication Version

Accepted Manuscript

Publication Date

11-15-2008

Journal or Book Title

Proteins: Structure, Function, and Bioinformatics

Volume

73

Issue

3

First Page

730

Last Page

741

DOI

10.1002/prot.22092

Abstract

The orientational geometry of residue packing in proteins was studied in the past by superimposing clusters of neighboring residues with several simple lattices.1,2 In this work, instead of a lattice we use the regular polyhedron, the icosahedron, as the model to describe the orientational distribution of contacts in clusters derived from a high-resolution protein dataset (522 protein structures with high resolution < 1.5Å). We find that the order parameter (orientation function) measuring the angular overlap of directions in coordination clusters with directions of the icosahedron is 0.91, which is a significant improvement in comparison with the value 0.82 for the order parameter with the face-centered cubic (fcc) lattice. Close packing tendencies and patterns of residue packing in proteins is considered in detail and a theoretical description of these packing regularities is proposed.

Comments

This is the peer reviewed version of the following article: Feng, Yaping, Robert L. Jernigan, and Andrzej Kloczkowski. "Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron." Proteins: Structure, Function, and Bioinformatics 73, no. 3 (2008): 730-741, which has been published in final form at doi: 10.1002/prot.22092. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.

Copyright Owner

Wiley-Liss, Inc.

Language

en

File Format

application/pdf

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