Analysis of protein crystallographic structural data: analysis of the orientation of peptide planes

Abstract

A new dihedral angle parameter θ', defined by C_i-1---|Ni...Ci---|N_i+1, involving pairs of backbone atoms in two adjacent peptide planes is used in this paper to analyse the relative orientation of the peptide planes in a protein chain. The equiangle contours for this parameter on the Φ+Ψ in an approximately linear way. Thus, θ' serves as a good single parameter representation for chainfolding characterization by bringing out the relative orientation of successive peptide planes. Unlike the earlier proposed θ which gives the gross folding features, θ' can be applied for nonregular helical features. Its utility in the detection of bend regions in protein chains is compared with that of θ through theoretically calculated tables as well as examples from actual proteins.