Nonglycine Residues in Proteins should most likely have an Allowed Conformation with a Negative Value for Backbone Torsion Angle ɸ

Abstract

Backbone torsion angles ɸ, ψ of a vast majority of nonglycine residues in proteins lay within the peculiar insulated regions in the (ɸ,ψ) space assigned to the conformations allowed for nonglycine residues that embrace the conformations with negative and positive values of ɸ separately. Emphasizing this feature here, the abilities of nonglycine residues to access and reside in the allowed conformations with negative and positive value of angle ɸ evaluated from the alanine dipeptide U(ɸ,ψ) potential energy surface map computations. Established that for nonglycine residues the lowest energy conformation with negative value of ɸ is noticeably favorable than that with positive ɸ and these conformations are separated by unusually higher activation barrier. The occurrences of the residues in the conformations with negative and positive ɸ in a large set of high resolution structures from the Protein Data Bank also investigated. Taken together, the results suggested that nonglycine residues in proteins should most likely have an allowed conformation with negative value of angle ɸ . Residues with positive ɸ angle are considered as outliers with a dubious conformation and should be inspected thoroughly for coordinate errors.