DNA-Protein Interactions between S/MARs and Nuclear matrix Protein

Question

[adurrahfaizal]

Hi all.

I have recently started working on the protein-DNA interactions. My focus is on the interaction between S/MARs and the nuclear matrix protein. I would like to find where is the specific location within the S/MARs that interact with the protein.

I have done the docking by using NPDock server and for the visualization purpose, I used Chimera. However, I can only find the clashes and contacts between S/MARs and the protein. I would like to find what are the interactions in terms of what types of bonds occurred between them, whether its H-bonds, hydrophobic interactions, salt bridges or base stacking.

Anyone knows what software or server which I can use to determine what are the interactions exactly? Can anyone help me?