re the request
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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.
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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
http://pqs.ebi.ac.uk/pqs-doc/CisPro
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
Ca(-1)----C(-1)----N----Ca
are listed in the file
http://pqs.ebi.ac.uk/pqs-doc/CisOther
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
http://pqs.ebi.ac.uk/pqs-doc/Disulphide
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
