Recurring loop motif in proteins that occurs in right-handed and left-handed forms. Its relationship with alpha-helices and beta-bulge loops

A common feature of alpha-helices in proteins is a loop at the C-terminal end, with a characteristic hydrogen bond pattern. It is noted that several loops with the same structural features occur independently of alpha-helices; two are even situated at the loop ends of beta-hairpins. The name paperclip is suggested for loops possessing the appropriate hydrogen bonds. A number of features of paperclips are described: they exist in two classes, depending on the number of residues at the loop end; one class is very much commoner than the other. Two paperclips are found that belong to the common class, except that the main-chain conformation of each is the mirror image of that normally found. The majority of paperclips are shown to have tightly clustered sets of main-chain dihedral angles. These are somewhat similar to, but distinct from, a subgroup of another common family of loops that have been called beta-bulge loops; in the latter, the dihedral angles are also tightly clustered. The high degree of clustering in both cases is likely to be a result of steric constraints associated with hydrogen bond patterns at the ends of loops.