Pseudo-dihedral Angles in Proteins Providing a New Description of the Ramachandran Map

Abstract

Since the first years of structural biology, the Ramachandran map has provided a simple definition of the curvilinear geometry of the protein backbone. Its definition is mainly based on the values of the dihedral angles ϕ and ψ measured between the heavy atoms of the protein backbone. Discontinuities in angle values are observed, particularly in the region of the β -strand secondary structure. We introduce new pseudo-dihedral angles involving hydrogen positions instead of some of the positions of the heavy atoms. We determine simple relationships between the old and new dihedral angles. We show that combining the old and new parameters allows us to overcome the discontinuity problem encountered in the Ramachandran map.