Structural and sequence patterns in the loops of beta alpha beta units

Abstract

The conformation and sequences of the 129 loops of 70 beta alpha beta units from 17 alpha/beta proteins were analysed for patterns. Many different conformations of the loop regions were observed, but 18 of the loops could be classified into one of four loop families with distinctive conformation and sequence patterns. (i) Adjacent alpha beta loops with one residue between the alpha-helix and beta-strand. The residue is a glycine with conformationally restricted phi/psi angles; (ii) adjacent alpha beta loops of three residues with a conformationally restricted glycine as the first of the loop followed by an analine or histidine residue and a third residue with helical phi/psi angles; (iii) adjacent beta alpha loops of 3/4 residues previously reported to bind nucleotides and which have three glycine residues in the loop region; (iv) non-adjacent beta alpha loops of 0 residues with a serine or threonine as the last residue of the beta-strand. The analysis provides information for the model building of loops and prediction of secondary structure from amino acid sequences.