Xiaoyi,
When I'm interested in dimer interfaces, or protein ligand contacts I
usually use Molprobity to define the interface.
http://molprobity.biochem.duke.edu/
It is a bit of a process, but here's the rundown:
Load your .pdb into molprobity
Add hydrogens
Visualize interface contacts
Then select your two 'half-interfaces' and run probe
One of the outputs from this is a list that has:
residue from half 1 : residue from half 2 : contact type : details
I usually will take this list of residues and display them in pymol,
then add dashes for hydrogen bonds using the dist command
-bob
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