Hi Quanju, Pymol is good as it will show you polar contacts (h-bonds and electrostatic interactions/salt bridges). However pi-stacking and pi-cation interactions comes with experience to some extent i.e. being able to recognise them. Coot will help as it shows polar contacts as well as “close contacts”. You can tailor the parameters for “close contacts to assist you in identifying other interactions say up to 4 Angstrom.
My instinct still leads to experience. Have a look at a medicinal chemistry text book as a start e.g. Patrick, “An introduction to medicinal chemistry” although from memory there isn’t much on pi stacking. Also keep in mind there are numerous (3) modes of pi stacking; stacked, edge to face as well as triangulated interactions between three rings. For pi-cation, it is somewhat simpler to look at specific amino acids (Arg/Lys) in your protein active site interacting with an aromatic ring (within 4 Angstrom roughly). Hope this helps J From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of xiangquanju Sent: Tuesday, 9 April 2013 8:51 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] 2013年4月9日 16:39:16 自动保存草稿 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�Cπ stacking and (iii) cation�Cπ 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
