Finding residues physically interacting in a PDB structure and sequence related to that structure
My reputation isn't high enough to make a comment, but have you considered a modelling software such as PyMol or Chimera? You can execute a command line script with softwares such as these and these have the functionality to predict H-bonds. 

In the PDB files there is information regarding the GenBank and UNIPROT info of the protein, and you can find more information here: 

http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html. 

If you want RefSeq ID, you can use GenBank info you extract and convert by piping into a biomaRt (Bioconducor) script, although maybe there is a more direct way.

As for finding which residues in the sequence are interacting, I'm fairly certain that the software packages like PyMol or Chimera will give you information about the interacting residues. 

From what I understand, you will want to filter out only the residues that interact and are on different chains (e.g, Chain A vs. Chain B). This process will require you to work with the syntax of the different software packages when you are scripting. For example, Chimera has a basic primer here:

https://www.cgl.ucsf.edu/chimera/current/docs/ProgrammersGuide/basicPrimer.html

Note that I only gave a reference to Chimera because I am more comfortable with that then other packages and there is likely a more efficient way to do this. With Chimera, you can find the position within the chain of residues participating in the interaction and then you'd store these in a file to do whatever you want later.

I hope this helps.