I have Blast A against PDB and selected all the complexes. And the results are :
complex1: A1 - B
complex2: A2 - C
where A1,A2,A3 are all blasts of A and B,C,D are the partners in the complexes. Using these complexes I have detected a binding site(BS) on the A.
Now I have selected a known PDB structure (A'-L') where A' is the homolog of A and L' is the partner. [In the calculation above for the binding site I have left out A'-L' complex]. But there is a big difference between the BS of A' -L' and the BS defined above.
It seems that L' is interacting with A' in a totally different manner, while all the other blast complexes of A show similar BS pattern when interacting with partners. Now I think there must be something different between L' and other partners (B,C,D), so my aim is to have a metric to compare these partners with each other and see how different one complex is to others.
Do you have any suggestion on how I can do this?
Thanks in advance;