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Published online before print April 9, 2004, 10.1110/ps.03505804
Protein Science (2004), 13:1426-1429. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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FOR THE RECORD

Shorter side chains optimize helix–helix packing

Sulin Jiang1 and Ilya A. Vakser2

1 Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA
2 Bioinformatics Laboratory, Department of Applied Mathematics and Statistics, State University of New York at Stony Brook, Stony Brook, New York 11794-3600, USA

(RECEIVED November 3, 2003; FINAL REVISION January 16, 2004; ACCEPTED January 19, 2004)



Abstract

A systematic study of helix–helix packing in a comprehensive database of protein structures revealed that the side chains inside helix–helix interfaces on average are shorter than those in the noninterface parts of the helices. The study follows our earlier study of this effect in transmembrane helices. The results obtained on the entire database of protein structures are consistent with those obtained on the transmembrane helices. The difference in the length of interface and noninterface side chains is small but statistically significant. It indicates that helices, if viewed along their main axis, statistically are not circular, but have a flattened interface. This effect brings the helices closer to each other and creates a tighter structural packing. The results provide an interesting insight into the aspects of protein structure and folding.

Keywords: protein modeling; structure prediction; protein folding; secondary structure packing; docking

Reprint requests to: Ilya A. Vakser, Bioinformatics Laboratory, Department of Applied Mathematics and Statistics, State University of New York at Stony Brook, Stony Brook, NY 11794-3600, USA; e-mail: vakser{at}ams.sunysb.edu; fax: (631) 632-8490.

Article published ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03505804.


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