Termination of right handed helices in proteins by residues in left handed helical conformations.
An analysis of 636 helical segments, ranging in length from 4 to 32 residues, from 123 independent protein crystal structures reveals that helix termination by residues in left handed (alpha 1) helical conformations is a common occurrence. Gly and Asn residues are the most frequent alpha L helix terminators, with the former having a very high propensity to adopt such conformations. The alpha R-alpha R-alpha R-alpha L segment at the C termini of protein helices often possesses a 6--> 1 (pi-type) hydrogen bond between the CO of residue i and the NH of residue i + 5 with residue i + 4 occurring in the alpha L conformation. A stereochemical analysis of 216 examples shows that in 62 cases the 6-->1 hydrogen bond is absent. The present analysis provides a quantitative measure of the propensity of the 20 amino acids to adopt alpha L helix terminating conformations.
Nagarajaram
H A
HA
Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
Sowdhamini
R
R
Ramakrishnan
C
C
Balaram
P
P
D006860:Hydrogen Bonding; D008958:Models, Molecular; D017433:Protein Structure, Secondary