Schellman loops are commonly occurring structural features of proteins and polypeptides. Each has six amino acid residues with two specific inter-mainchain hydrogen bonds and a characteristic main chaindihedral angle conformation. The CO group of residue i is hydrogen-bonded to the NH of residue i+5, and the CO group of residue i+1 is hydrogen-bonded to the NH of residue i+4. Residues i+1, i+2, and i+3 have negative φ angle values and the phi value of residue i+4 is positive. Schellman loops incorporate a three amino acid residue RL nest, in which three mainchain NH groups form a concavity for hydrogen bonding to carbonyl oxygens. About 2.5% of amino acids in proteins belong to Schellman loops. Two websites are available for examining small motifs in proteins, Motivated Proteins: ; or PDBeMotif: . The majority of Schellman loops occur at the C-terminus of an alpha-helix such that residues i, i+1, i+2 and i+3 are part of the helix. Over a quarter of helices have a C-terminal Schellman loop. Occasional Schellman loops occur with seven instead of six residues. In these, the CO group of residue i is hydrogen-bonded to the NH of residue i+6, and the CO group of residue i+1 is hydrogen-bonded to the NH of residue i+5. Rare “left-handed” six-residue Schellman loops occur; these have the same hydrogen bonds, but residues i+1, i+2, and i+3 have positive φ values while the φ value of residue i+4 is negative; the nest is of the LR, rather than the RL, kind. Amino acid propensities for the residues of the common type of Schellman loop have been described. Residue i+4 is the one most-highly conserved; it has positive φ values; 70% of amino acids are glycine and none are proline. Consideration of the hydrogen bonding in the nests of Schellman loops bound to mainchain oxygens reveals two main types of arrangement: 1,3-bridged or not. In one the first and third nest NH groups are bridged by an oxygen atom. In the other the first NH group is hydrogen bonded to the CO group of an amino acid four residues behind in the sequence, and none of the nest NH groups are bridged. It seems that Schellman loops are less homogeneous than might have been expected. The original Schellman criteria result in the inclusion of features not now regarded as Schellman loops. A newer set of criteria is given in the first paragraph.
