Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron
Date
Authors
Major Professor
Advisor
Committee Member
Journal Title
Journal ISSN
Volume Title
Publisher
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.
Series Number
Journal Issue
Is Version Of
Versions
Series
Academic or Administrative Unit
Type
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.