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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 chain dihedral 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.