Structure validation by Cα geometry: ϕ,ψ and Cβ deviation

Abstract

Geometrical validation around the Cα is described, with a new Cβ measure and updated Ramachandran plot. Deviation of the observed Cβ atom from ideal position provides a single measure encapsulating the major structure‐validation information contained in bond angle distortions. Cβ deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new ϕ,ψ plot using density‐dependent smoothing for 81,234 non‐Gly, non‐Pro, and non‐prePro residues with B < 30 from 500 high‐resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the γ‐turn conformation near +75°,−60°, counted as forbidden by common structure‐validation programs; however, it occurs in well‐ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the γ‐turn H‐bond. Favored and allowed ϕ,ψ regions are also defined for Pro, pre‐Pro, and Gly (important because Gly ϕ,ψ angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of α‐helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two‐peptide NHs permits donating only a single H‐bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user‐uploaded file, see M OL P ROBITY (http://kinemage.biochem.duke.edu) or R AM P AGE (http://www‐cryst.bioc.cam.ac.uk/rampage). Proteins 2003;50:437–450.