Schellman loop

Schellman loops (also called Schellman motifs or paperclips) are commonly occurring structural features of proteins and polypeptides. Each has six amino acid residues (labelled residues i to i+5) with two specific inter-mainchain hydrogen bonds (as in lower figure, i) and a characteristic main chain dihedral angle conformation. The CO group of residue i is hydrogen-bonded to the NH of residue i+5 (colored orange in upper figure), and the CO group of residue i+1 is hydrogen-bonded to the NH of residue i+4 (beta turn, colored purple). Residues i+1, i+2, and i+3 have negative φ (phi) angle values and the phi value of residue i+4 is positive. Schellman loops incorporate a three amino acid residue RL nest (protein structural motif), in which three mainchain NH groups (from Schellman loop residues i+3 to i+5) 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: [1]; or PDBeMotif: [2].

The majority of Schellman loops (82%) 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 (28%) 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.

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