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Prediction of prolyl residues in cis ‐conformation in protein structures on the basis of the amino acid sequence
Author(s) -
Frömmel Cornelius,
Preissner Robert
Publication year - 1990
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/0014-5793(90)80833-5
Subject(s) - sequence (biology) , peptide sequence , basis (linear algebra) , chemistry , stereochemistry , amino acid , amino acid residue , protein structure , biochemistry , computational biology , biology , mathematics , gene , geometry
In proteins most peptide bonds are in trans ‐conformation: the torsion angle ω = 180°. Only few show cis ‐conformation in known protein structures (ω = 0°). Most of them are prolyl residues. About 6% of about 4000 prolyl residues are in cis ‐conformation. Between trans ‐ and cis ‐prolyl residues significant differences are observed in the surrounding sequences. E.g. there are large amounts of aromatic residues N‐terminally in case of cis ‐prolyl residues, but in the case of trans ‐prolyl residues more aromatic amino acids occur C‐terminally. But in all cases there are only complex patterns which are indicative of cis ‐ and trans ‐conformation, respectively. Considering the neighbours (±6 residues) of prolyl residues and their physicochemical properties we find 6 different patterns which allow one to assign correctly about 75% of known cis ‐structured prolyl residues, whereby no false positive one is predicted.