Hi Neena -
PyMOL shows all the potential H-bonds, but not all of them will be formed at
all times. Any single proton can only participate in one H-bond at a time, but
remember a crystal structure is an average structure based on the ensemble of
states present in the protein crystal (or on the EM grid for cryo-EM
structures). It's ok to have "too many" polar contacts...it just means the
atoms have options for where to interact.
Also, a carbonyl oxygen has 2 lone pairs, so can accept 2 H-bonds. See perhaps
McDonald & Thornton, JMB (1994) https://doi.org/10.1006/jmbi.1994.1334 for a
more detailed discussion.
Hope that helps.
Cheers,
Jared
On April 4, 2019 at 11:25:17 PM, Neena Susan Eappen (neenasusan...@gmail.com)
wrote:
Hello PyMOL users,
Hydrogen bond finder on Pymol sometimes gave me unexpected observations like:
more than 3 H bonds to Lysine, more than 1 to a carbonyl oxygen and so on. This
is even after setting H-bond center cutoff to 3.0 A. Any insight would be
appreciated.
Thank you for sharing your knowledge,
Neena
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