Hi,
I have a question about QtPISA that ships with the latest ccp4
(7.1.003). Analyzing one of our recent structures, I came across what
appears to be a hydrogen bond at a protein-protein interface, but it is
not being picked by QtPISA (built from PISA v 2.1.2). It is a 2.9 Å
(donor to acceptor) distance between the Trp side chain Nitrogen and a
main chain carbonyl oxygen.
See https://www.dropbox.com/s/yebyomdqu9ukjys/coot.png?dl=0
The N-H...O angle is 134 degrees (after adding hydrogens with
phenix.reduce), and while that is not great, it is not horrible.
Artificially changing the angle to >160 degrees did not make PISA detect
the hydrogen bond.
I thought that maybe PISA ignored Trp side chains altogether, but an
earlier version running on PDBe's webpage (v. 1.52) reports this H bond
using the identical pdb file as input.
So, it appears that the developers removed the detection of these close
contacts as hydrogen bonds at some point between versions 1.52 and
2.1.2. Could anyone help me explain this, or what I might be doing wrong
here?
Thank you,
Engin
P.S. The source code or a version history may be available somewhere to
check this, but the CCP4 page is down, and I don't know where to look.
--
Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
http://voices.uchicago.edu/ozkanlab
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