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Viewing G-factors in 3D

The G-factors provide a measure of how "normal", or alternatively how "unusual", a given stereochemical property is. There are two types computed by PROCHECK: torsion angle G-factors and covalent geometry G-factors.

The former can be viewed mapped onto the 3D structure of the protein in question if you have your browser configured to view RasMol scripts. (For more information on this, click here).

The torsion angle G-factors are as follows:

  • 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

Where a particular torsion angle's G-factor is unusual (ie <-2.0) the central bond defined by the torsion angle is highlighted in the structure as follows:

 G-factor range   Bond colour   Bond thickness (Å) 
 -2.0 to -2.2   YELLOW   0.2 
 -2.2 to -2.4   GOLD   0.2 
 -2.4 to -2.6   ORANGE   0.2 
 -2.6 to -2.8   ORANGE-RED   0.2 
 -2.8 to -3.0   DEEP PINK   0.2 
 -3.0 to -3.5   RED   0.2 
 -3.5 to -4.0   "   0.3 
 -4.0 to -4.5   "   0.4 
 -4.5 to -5.0   "   0.5 

Thus a quick look at the structure can often show the regions, or merely the isolated residues, that appear to have unusual geometry.

 

Roman Laskowski Jul 2005 spacer
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