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
