The alpha-helix as seen from the protein tertiary structure: a 3-D structural classification.

Helices are selected from globular protein structures defined at high resolution by X-ray analysis. We cluster alpha-helices in two ways: according to their position in the tertiary structure by considering patterns of solvent inaccessible residues and according to the arc of the solvent inaccessible face. For each class of helices we have defined propensities for amino acids at each position; these can be used to calculate templates for recognition of a member of that class. The analysis provides a basis for the prediction of alpha-helices and estimation of their approximate position in a protein tertiary structure. It also provides an approach to estimating the probability of finding amino acid sequences as helices in solution and in a folded protein, thus indicating those helices that might be involved in nucleation of protein folding.