Hello everybody,

i am a freshman in structural biology. Right now i encountered two questions and need help from all of you:

1) from the paper, i saw there are three different interactions between the ligand and the residue:(i) hydrogen bonding, (ii) π–π stacking and (iii) cation–π interactions, how can i determine which kind of interaction did happen in my protein. i had chencked that there are no  hydrogen bonds between the ligand and the residue.

2) my protein is dimeric in the crystal, when i want to find the polar contacts of one residue (pymol) and found that this residue has differnet polar contacts in the two monomer. Is this acceptable?

 

Thanks in advance!

quanju