Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron

Proteins. 2008 Nov 15;73(3):730-41. 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 (Bagci et al., Proteins 2003;53:56-67; Raghunathan et al., Protein Sci 1997;6:2072-2083). 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 < 1.5 A). 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 are considered in detail and a theoretical description of these packing regularities is proposed.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein
  • Models, Molecular
  • Proteins / chemistry*
  • Regression Analysis

Substances

  • Proteins