Title
Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron
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.
Copyright Owner
Wiley-Liss, Inc.
Copyright Date
2008
Language
en
File Format
application/pdf
Recommended Citation
Feng, Yaping; Jernigan, Robert L.; and Kloczkowski, Andrzej, "Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron" (2008). Biochemistry, Biophysics and Molecular Biology Publications. 177.
https://lib.dr.iastate.edu/bbmb_ag_pubs/177
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.