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Nucleic Acids Research Advance Access published online on May 25, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm307
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© 2007 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.

Web Server Issue

A server and database for dipole moments of proteins

Clifford E. Felder1, Jaime Prilusky2, Israel Silman3 and Joel L. Sussman1,*

1Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, 2Department of Biological Services, Weizmann Institute of Science, 76100 Rehovot, Israel and 3Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel

*To whom correspondence should be addressed. Tel: +972-8-934-4531; Fax: +972-8-934-4159; Email: Joel.Sussman{at}weizmann.ac.il

Received January 31, 2007. Revised April 1, 2007. Accepted April 14, 2007.

An Internet server at http://bip.weizmann.ac.il/dipol calculates the net charge, dipole moment and mean radius of any 3D protein structure or its constituent peptide chains, and displays the dipole vector superimposed on a ribbon backbone of the protein. The server can also display the angle between the dipole and a selected list of amino acid residues in the protein. When the net charges and dipole moments of ~12 000 non-homologous PDB biological units (PISCES set), and their unique chains of length 50 residues or longer, were examined, the great majority of both charges and dipoles fell into a very narrow range of values, with long extended tails containing a few extreme outliers. In general, there is no obvious relation between a protein's charge or dipole moment and its structure or function, so that its electrostatic properties are highly specific to the particular protein, except that the majority of chains with very large positive charges or dipoles bind to ribosomes or interact with nucleic acids.


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