[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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