PREDICTION OF PROLYL RESIDUES IN CIS-CONFORMATION IN PROTEIN STRUCTURES ON THE BASIS OF THE AMINO-ACID-SEQUENCE

In proteins most peptide bonds are in trans-conformation: the torsion angle omega=180-degrees. Only few show cis-conformation in known protein structures (omega=0-degrees). 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-polyl 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.