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G-factors

The G-factor provides a measure of how "normal", or alternatively how "unusual", a given stereochemical property is. In PROCHECK it is computed for the following properties:-
    Torsion angles:-
    • phi-psi combination
    • chi1-chi2 combination
    • chi1 torsion for those residues that do not have a chi-2
    • combined chi-3 and chi-4 torsion angles
    • omega torsion angles

    Covalent geometry:-

    • main-chain bond lengths
    • main-chain bond angles

The G-factor is essentially just a log-odds score based on the observed distributions of these stereochemical parameters.

When applied to a given residue, a low G-factor indicates that the property corresponds to a low-probability conformation. So, for example, residues falling in the disallowed regions of the Ramachandran plot will have a low (or very negative) G-factor. Similarly for unfavourable chi1-chi2 and chi1 values.

Thus, if a protein has many residues with low G-factors it suggests that something may be amiss with its overall geometry.

Torsion angle G-factors

For the torsion angle G-factors the standards of "normality" have been derived from an analysis of 163 non-homologous, high-resolution protein chains chosen from structures solved by X-ray crystallography to a resolution of 2.0Å or better and an R-factor 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 phi-psi, chi1-chi2, chi-1, chi-3, chi-4 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 phi-psi 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 phi-psi combination. The probabilities were, in turn, used to compute a log-odds score for each cell. Log-odds scores can be summed, rather than multiplied like probabilities; therefore, taking meaningful averages becomes possible.

Bond-length and bond-angle G-factors

For the main-chain bond lengths and bond angles, the G-factors are computed using the Engh & Huber (1991) small-molecule means and standard deviations.

Reference

Engh RA and Huber R (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst., A47, 392-400.

 

Roman Laskowski Sep 1995 spacer
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