Campus Units

Bioinformatics and Computational Biology

Document Type

Conference Proceeding

Publication Version

Accepted Manuscript

Publication Date

2007

First Page

35

Last Page

41

DOI

10.1109/BIBM.2007.60

Conference Title

2007 IEEE International Conference on Bioinformatics and Biomedicine

Conference Date

November 2-4, 2007

City

Fremont, California

Abstract

We analyzed the structural properties and the local surface environment of surface amino acid residues of proteins using a large, non-redundant dataset of 2383 protein chains in dimeric complexes from PDB. We compared the interface residues and non-interface residues based on six properties: side chain orientation, surface roughness, solid angle, cx value, hydrophobicity and interface cluster size. The results of our analysis show that interface residues have side chains pointing inward; interfaces are rougher, tend to be flat, moderately convex or concave and protrude more relative to non-interface surface residues. Interface residues tend to be surrounded by hydrophobic neighbors and tend to form clusters consisting of three or more interfaces residues. These findings are consistent with previous published studies using much smaller datasets, while allowing for more qualitative conclusions due to our larger dataset. Preliminary results suggest the possibility of using the six the properties to identify putative interface residues.

Comments

This is a proceeding from IEEE International Conference on Bioinformatics and Biomedicine (2007): 35, doi: 10.1109/BIBM.2007.60. Posted with permission.

Rights

© 2007 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.

Copyright Owner

IEEE

Language

en

File Format

application/pdf

Share

Article Location

 
COinS