Taxonomy and conformational analysis of loops in proteins

We propose a general classification scheme for loops, aperiodic segments of protein structure. In an effort to avoid the geometric complexity created by non-repeating phi psi angles, a morphologic definition that focuses upon the linearity and planarity of loops is utilized. Out of 432 loops (4 to 20 residues in length) extracted from 67 proteins, 205 are classified as linear (straps), 133 as non-linear and planar (omegas), and 86 as non-linear and non-planar (zetas). The remaining 8 are classified as compound loops because they contain a combination of strap, omega, and zeta morphologies. We introduce a structural alphabet as a shorthand notation for describing local conformation. The symbols of this alphabet are based on the virtual dihedral angle joining four consecutive alpha carbons. The notation is used to provide a compact description of loop motifs in phosphate binding and calcium binding proteins. Since similar loop conformations form similar "words", the structural sequence facilitates the search for common structural motifs in a family of loops. Contrary to the view of loops as "random coils", we find loops to have positional preferences for amino acid residues analogous to those previously described for beta-turns.