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non-proline cis amino acid residues in pdb

Kim Henrick henrick at ebi.ac.uk
Fri Mar 6 11:08:51 EST 1998

re the request

From: Mark Banfield <m.banfield at bristol.ac.uk>
I have a non-proline cis-peptide bond in a structure i've recently 
determined, and would like to know how many other's there are.

Has anyone compiled a list of protein structures containing such bonds?
Or have any idea how i could go about compiling such a list? I've been
unable to design a database search for these bond types, without calling
up all the cis-prolines.

There is a list of

1. all pdb entries that have an angle of (absolute value) less than 15.0deg
for the bonds 
 proline     O(-1)----C(-1)----N(pro)----CD(pro)
in the file


in the form
_cis_Proline   PRO    26              -0.1 125d
_cis_Proline   PRO    30             -12.4 12ca
_cis_Proline   PRO   202              13.1 12ca
_cis_Proline   PRO A 210             -12.0 13pk
_cis_Proline   PRO B 210              -8.3 13pk
For NMR entries only the 1st MODEL was looked at
          3251 cis-prolines

2. For all residues in the PDB that have an angle (absolute value)
less than 15.0deg for the bonds 
are listed in the file


in the form

_cis_AminoAcid HIS    27               0.4 1aao
_cis_AminoAcid LEU    71              -4.2 1aao
_cis_AminoAcid GLU   137              -5.2 1aao
_cis_AminoAcid GLY   204             -11.6 1aao
_cis_AminoAcid LEU   207              -5.8 1aao

For NMR entries only the 1st MODEL was looked at
           770  cis-other aminoacids

a clear correct cis-THR is in 1cse, 
  _cis_AminoAcid THR E 211              -3.3 1cse
however not all of the listed cis-non-proline residues that are 
found in the PDB may be correct.

3. For all CYS listed in the pdb di-sulphides are given in the file


in the form

_di_sulphide  CYS     6            ... CYS   127               2.0 132l
_di_sulphide  CYS    30            ... CYS   115               2.0 132l
_di_sulphide  CYS    64            ... CYS    80               2.0 132l
_di_sulphide  CYS    76            ... CYS    94               2.0 132l
_di_sulphide  CYS     6            ... CYS   128               2.0 133l

For NMR entries only the 1st MODEL was looked at

          5934  di-sulphides listed

These are all SQL requests from a database. A public front end
to the database for this type of query is not yet available.

Kim Henrick

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