[phenixbb] close contact and torsion angle
Nathaniel Echols
nechols at lbl.gov
Fri Oct 12 09:01:39 PDT 2012
On Fri, Oct 12, 2012 at 6:54 AM, Edward A. Berry <BerryE at upstate.edu> wrote:
> From a recent PDB validation:
> ==> The following table contains a list of torsion angles outside the
> expected
> Ramachandran regions [GJ. Kleywegt and TA. Jones, PHI/PSI-chology:
> Ramachandran Revisited, Structure 1996, 4, 1395 - 1400].
>
> Residue Chain Sequence PSI PHI
> ASN A 35 -101.76 -94.29
> LYS A 45 -111.15 60.76
> LEU B 12 84.56 -68.33
> ASN B 35 -102.05 -94.34
> LYS B 45 -127.20 70.13
>
> Looking at Kleywegt's paper, their allowed region contains 98% of residues
> in hi-res structures.
> So if your protein has, say 1000 residues, you would expect about 20 true
> "outliers".
This may be appropriate for the PDB validation - for
Phenix/Molprobity, where the meaning of "outlier" is probably
different, the guideline we use is a maximum of 0.2% outliers, with
98% in "favored" regions.
-Nat
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