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Protein Engineering vol. 16 no. 11 pp. 799-807, 2003
© 2003 Oxford University Press

Exploring the sequence patterns in the {alpha}-helices of proteins

Junwen Wang1,2 and Jin-An Feng1,2,3

1Department of Chemistry and 2Center for Biotechnology, Temple University, 1901 North 13th Street, Philadelphia, PA 19122, USA

3 To whom correspondence should be addressed. e-mail: feng{at}astro.temple.edu

This paper reports an extensive sequence analysis of the {alpha}-helices of proteins. {alpha}-Helices were extracted from the Protein Data Bank (PDB) and were divided into groups according to their sizes. It was found that some amino acids had differential propensity values for adopting helical conformation in short, medium and long {alpha}-helices. Pro and Trp had a significantly higher propensity for helical conformation in short helices than in medium and long helices. Trp was the strongest helix conformer in short helices. Sequence patterns favoring helical conformation were derived from a neighbor-dependent sequence analysis of proteins, which calculated the effect of neighboring amino acid type on the propensity of residues for adopting a particular secondary structure in proteins. This method produced an enhanced statistical significance scale that allowed us to explore the positional preference of amino acids for {alpha}-helical conformations. It was shown that the amino acid pair preference for {alpha}-helix had a unique pattern and this pattern was not always predictable by assuming proportional contributions from the individual propensity values of the amino acids. Our analysis also yielded a series of amino acid dyads that showed preference for {alpha}-helix conformation. The data presented in this study, along with our previous study on loop sequences of proteins, should prove useful for developing potential ‘codes’ for recognizing sequence patterns that are favorable for specific secondary structural elements in proteins.

Received January 5, 2003; revised June 25, 2003; accepted September 4, 2003.


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