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Bioinformatics Advance Access originally published online on October 23, 2006
Bioinformatics 2006 22(22):2735-2738; doi:10.1093/bioinformatics/btl274
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins

Anne E. Counterman Burba , Ursula Lehnert , Eric Z. Yu and Mark Gerstein *

Department of Molecular Biophysics and Biochemistry, Yale University New Haven, CT 06520, USA

*To whom correspondence should be addressed.

Motivation: In many proteins, helix–helix interactions can be critical to establishing protein conformation (folding) and dynamics, as well as determining associations between protein units. However, the determination of a set of rules that guide helix–helix interaction has been elusive. In order to gain further insight into the helix–helix interface, we have developed a comprehensive package of tools for analyzing helix–helix packing in proteins. These tools are available at http://helix.gersteinlab.org. They include quantitative measures of the helix interaction surface area and helix crossing angle, as well as several methods for visualizing the helical interaction. These methods can be used for analysis of individual protein conformations or to gain insight into dynamic changes in helix interactions. For the latter purpose, a direct interface from entries in the Molecular Motions Database to the HIT site has been provided.

Contact: Mark.Gerstein{at}yale.edu

Received on May 9, 2006; accepted on May 25, 2006

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