Hi, 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 allAny cis peptides out there......

[islam]

Mark,

This is very easy to do and I recently
(mid Feb) searched for cis
bonds in all PDB files. This list
contains lines like
                              torsion
  1ai9 B GLY 113  GLY 114     -2.393

It should be a trivial matter to re-order/format
for your own purposes. If this is of use please
let me know and I can email/ftp the file to you.

regards suhail
____________________________________________
Suhail A Islam
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44 Lincoln's Inn Fields, London WC2A 3PX
Tel:   +44 (0)171 269 3380
Fax:   +44 (0)171 269 3258
email: islam at icrf.icnet.uk
www:   http://www.icnet.uk/bmm/
____________________________________________


Mark Banfield wrote:
> 
> Hi,
> 
> 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.
> 
> Thanks for any help.....
> 
> Mark Banfield
> 
> Dept. of Biochem.
> University of Bristol
> Bristol
> UK