Abstract of the prepress paper: Structure Validation by Ca Geometry: f,y and Cb Deviation
Proteins: Structure, Function, and Genetics © copyright 2002 WILEY-LISS, INC.

Geometrical validation around the Ca is described, with a new Cb measure and updated Ramachandran plot. Deviation of the observed Cb atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cb deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new f,y plot using density-dependent smoothing, for 81,234 non-Gly, non-Pro, 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 g-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 over-represented near functional sites, and strain is partly compensated by the g-turn H-bond. Favored and allowed f,y regions are also defined for Pro, pre-Pro, and Gly (important because Gly f,y 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 a-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.1 (this issue) for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our non-repetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu/) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage).

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