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alpha helix
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noun
  1. A secondary structure found in many proteins, where the amino acids are arranged in a coil, or helix, with almost no free space on the inside and all side chains being pointed towards the outside.
  2. Alpha helices in living organisms have a right-handed geometry, because of the unique chirality of the natural amino acids.
  3. The backbone dihedral angles of each amino acid in a right-handed alpha helix are φ = -57° and ψ = -47°.
  4. The repeating unit of a helix follows the n_r nomenclature, where n = number of residues per turn and r = number of atoms in ring formed by a hydrogen bond and the segment of main chain connecting its extremities. An alpha helix is 3.6_13. The first alpha helical residue is taken as the first residue whose backbone carbonyl group (C=O) is regularly hydrogen bonded (...) to the amide hydrogen (N-H) along the helix, such that C=0...H-N. Correspondingly, the last helical residue is the last whose backbone amide hydrogen is regularly hydrogen bonded to the backbone carbonyl oxygen along the helix. Thus in an alpha helix, the ith residue's carbonyl oxygen forms a hydrogen bond with the ith + 4 residue's amide hydrogen in the polypeptide sequence. When this pattern is broken the helix is broken, and irregular hydrogen-bonding arrangements are not considered part of an alpha helix.
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