The Use of Amino Acid Patterns of Classified Helices and Strands in Secondary Structure Prediction

Elements of secondary structure from known protein three-dimensional structures have been classified with respect to their environments in tertiary structures. The size of the solvent-inaccessible face of an alpha-helix and the accessibility patterns on the two sides of a beta-strand have been used to classify the secondary structures. For each class, we have derived a sequence template, giving the amino acid propensity at each position. A prediction is made by calculating the compatibility of segments of polypeptide sequence against templates for each type of secondary structure. This method predicts not only position of a secondary structure in a protein sequence but also the orientation of the secondary structure with respect to the core of the protein tertiary structure. A jack-knife test is applied to 78 proteins of known structure solved at better than 2 A resolution. It shows that this method predicts between 13% and 17% better than the methods of Lim, GOR and Chou and Fasman at the level of secondary structure. The orientations of inaccessible faces are predicted within 50 degrees of correct value for about two-thirds of alpha-helices.