On Thu, 5 Mar 1998, 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.....
I have recently (08/97) compiled a list of cis-peptide bonds in the PDB. I
can send everyone who is interested a (huge) list of all cis-peptide
bonds, which looks like that:
...
pdb1aa1.ent LYS 175 <--> PRO 176 0.0
pdb1zio.ent PHE 86 <--> PRO 87 -0.4
...
The last number is the omega angle.
I also have a table which summarizes how many cis-peptide bonds of a given
kind there are, like this:
----------------------------------
AA | ALA ARG ASN ASP CYS GLN ...
-----|----------------------------
ALA | 1 - - 62 - 1
ARG | - - - 16 - -
ASN | 1 - 2 1 - -
ASP | 1 - 1 1 - -
...
Interestingly, CYS and MET are the only amino acids which do not take part
in a cis-peptide bond.
Mischa
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Mischa Machius, Ph.D.
University of Texas
Southwestern Medical Center at Dallas
Howard Hughes Medical Institute tel: +1 214 648 5002
5323 Harry Hines Blvd. fax: +1 214 648 5095
Dallas, TX 75235-9050, U.S.A. e-mail: machius at chop.swmed.edu
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