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Environmental features are important in determining protein secondary structure

Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA

Reprint requests to: Dr. W. Curtis Johnson, Jr., Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA; e-mail: johnsowc{at}ucs.orst.edu; fax: (541) 737-0481.

We have investigated amino acid features that determine secondary structure: (1) the solvent accessibility of each side chain, and (2) the interaction of each side chain with others one to four residues apart. Solvent accessibility is a simple model that distinguishes residue environment. The pairwise interactions represent a simple model of local side chain to side chain interactions. To test the importance of these features we developed an algorithm to separate -helices, ß-strands, and "other" structure. Single residue and pairwise probabilities were determined for 25,141 samples from proteins with <30% homology. Combining the features of solvent accessibility with pairwise probabilities allows us to distinguish the three structures after cross validation at the 82.0% level. We gain 1.4% to 2.0% accuracy by optimizing the propensities, demonstrating that probabilities do not necessarily reflect propensities. Optimization of residue exposures, weights of all probabilities, and propensities increased accuracy to 84.0%.

Keywords: Protein folding; prediction secondary structure

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