Any cis peptides out there......

Mischa Machius machius at CHOP.SWMED.EDU
Thu Mar 5 11:11:35 EST 1998



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

-------------------------------------------------------------------------------
 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
-------------------------------------------------------------------------------






More information about the X-plor mailing list