
PROCHECK Operating Manual
Appendix E  GfactorsThe Gfactor provides a measure of how "normal", or alternatively how "unusual", a given stereochemical property is. In PROCHECK it is computed for the following properties:
Covalent geometry: The Gfactor is essentially just a logodds score based on the observed distributions of these stereochemical parameters. When applied to a given residue, a low Gfactor indicates that the property corresponds to a lowprobability conformation. So, for example, residues falling in the disallowed regions of the Ramachandran plot will have a low (or very negative) Gfactor. Similarly for unfavourable chi1chi2 and chi1 values. Thus, if a protein has many residues with low Gfactors it suggests that something may be amiss with its overall geometry.
Torsion angle GfactorsFor the torsion angle Gfactors the standards of "normality" have been derived from an analysis of 163 nonhomologous, highresolution protein chains chosen from structures solved by Xray crystallography to a resolution of 2.0Å or better and an Rfactor no greater than 20%. No two of the 163 chains shared a sequence homology greater than 35%, and all atoms having zero occupancy were excluded from the analysis. The analyses provided the observed distributions of phipsi, chi1chi2, chi1, chi3, chi4 and omega values for each of the 20 amino acid types. These distributions were then divided into cells. For example, each residue type's Ramachandran plot of phipsi values was divided into 45 x 45 cells. The numbers of observations in each cell were used to calculate the probability of a given residue type having a given phipsi combination. The probabilities were, in turn, used to compute a logodds score for each cell. Logodds scores can be summed, rather than multiplied like probabilities; therefore, taking meaningful averages becomes possible.
Bondlength and bondangle GfactorsFor the mainchain bond lengths and bond angles, the Gfactors are computed using the Engh & Huber (1991) smallmolecule means and standard deviations.
PROCHECK Operating Manual 