Dear All, I have a question regarding the contact interactions between a protein-ligand complex. I can retrieve the contacts by the findclash command in --nogui mode as below: chimera --nogui protligcomplex.pdb clash.com and similarly I can find the hbonds. The output I am getting is as below: -------------------------------------------------------------------------------- 32 contacts atom1 atom2 overlap distance LIG 1 H ALA 265.A O 1.045 1.435 LIG 1 O ALA 265.A O 0.550 2.430 LIG 1 N GLU 169.A OE2 0.439 2.666 LIG 1 H GLU 169.A CD 0.116 2.584 LIG 1 O ASN 253.A 1HD2 0.094 2.386 LIG 1 H ALA 265.A C 0.090 2.610 LIG 1 C ALA 265.A O 0.059 3.121 LIG 1 N ASN 253.A OD1 -0.037 3.142 LIG 1 C ALA 265.A O -0.039 3.219 LIG 1 N GLU 169.A HG3 -0.072 2.697 LIG 1 C PHE 168.A HB2 -0.081 2.781 LIG 1 N GLU 169.A CG -0.113 3.438 LIG 1 N GLU 169.A CD -0.125 3.450 LIG 1 N GLU 169.A CD -0.128 3.453 LIG 1 C MET 270.A HG2 -0.140 2.840 LIG 1 N PHE 168.A CD2 -0.163 3.488 .......... .... ... .. . -------------------------------------------------------------------------------- Now I want to further classify these contact interactions into more other types: Aromatic and Ionic (anion < - > cation). Is there any way in Chimera to achieve this? Or if I want to do it with some scripting, which atoms I would say are involved in ionic and aromatic interactions considering the distance value as well? I would be very much grateful if someone suggest me a way to do this. Thanks, Best regards, -- Shahid.
Hi Shahid, It certainly would be easier if Chimera allowed you to find contacts/ H-bonds between two arbitrary sets of atoms rather than between one set and "everything else". I will open a feature-request ticket in our Trac database for this with you on the recipient list so you will know when it gets implemented. It will probably be several months before I have time to get to it. In the interim there is an uglier method for getting what you want -- at least for contacts. Basically you delete away all the atoms you don't care about. So to find the aromatic contacts between ligand and non-ligand do this (Favorites->Command Line): del ~aromatic sel :LIG then find contacts between selected atoms and all other atoms. You would have to open a new copy of your system (and close the mutilated one!) to find other interactions. To get charge interactions first add charges to your atoms with the Add Charge tool. You can then select ligand atoms with more than a certain negative charge and non-ligand with more than a certain positive charge (say .1 for this example) with: sel :LIG & @/charge<-0.1 | ~:LIG & @/charge>0.1 then delete all other atoms with: del ~sel then find clashes as above. Then on a new copy of the system find contacts between atoms with the charges reversed. Like I said: ugly! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 24, 2009, at 8:00 AM, M. Shahid wrote:
Hello, Just some additions to what Eric said... (a) you would probably want to use "aromatic ring" instead of "aromatic" -- "aromatic" specifies entire aromatic amino acids, "aromatic ring" specifies aromatic rings in all kinds of molecules. In Eric's example, the ligand residue name was LIG ... so of course, if it has some other name you would use that instead. (b) you could select most (but not all) charged groups based on atom type, for example with the command: select Ng+ | N3+ | N2+ | O2- | O3- That gets atom types in charged groups commonly found in amino acids and nucleotides, except histidines. To include histidines, but only the ones that are charged, you would need to add hydrogens (AddH tool or command addh), add charge (Add Charge tool or command addcharge), and then use select Ng+ | N3+ | N2+ | O2- | O3- | :/amberName=HIP & @nd1,ne2 (The charge assignment process identifies which histidines are doubly protonated and assigns them the AMBER residue name HIP.) A limitation of using this atom type approach is that we do not have thiolate sulfur atom type; if there is specific Cys thiolate you wish to consider, you would have to add that sulfur to the selection manually. There are additional atom types for charged functional groups, but they would not occur in proteins. If manmade ligands are involved, however, you may want to take a look at the list of atom types and possibly add N1+,P3+,S3+,S3- (no, that's not thiolate even though it sounds like it) to the selection command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html> Here is an earlier posting about finding salt bridges: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003602.html
(c) I wasn't sure if you were also interested in ion-aromatic (cation- pi) interactions. Here some example commands for looking at possible cation-pi interactions. addh addcharge sel aromatic ring | N1+ | N2+ | N3+ | Ng+ | :/amberName=HIP & nd1,ne2 del ~ sel sel aromatic ring findclash sel overlap -1 hbond 0 log true (d) yet another approach is to just get all the contacts of all types and filter them afterwards. However, that would require you to figure out the types of interactions based on the residue and atom names, which might be a lot of work. If using this approach, you might want to remove all the hydrogens first, since they would generally provide a large amount of redundant information. I hope this helps, Elaine On Oct 26, 2009, at 12:06 PM, Eric Pettersen wrote:
Dear Elaine, Dear Eric, Thanks a lot for suggestion of using an alternate way of classifying the contact interactions. I am currently using it with step by step selection of different types. And its working great!!! thanks again. Could you please also give me some hints on the other way you mentioned in (d) below in conversation? Best regards, -- Shahid. On Mon, Oct 26, 2009 at 9:02 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Shahid, For (d) there is not really any trick, it is just using the residue and atom names. For example, if you knew C1-C6 in LIG are an aromatic ring, for aromatic-aromatic contacts to PHE you could look for lines in the contacts output with PHE CG,CD1,CD2,CE1,CE2,CZ such as:
LIG 1 C1 PHE 168.A CD2 -0.163 3.488
As I mentioned this would be a lot of work since you would have to know all the atom/res names for a particular type of functional group such as aromatic ring. Also, I don't think this would work for your system because looking at what you sent below, your LIG atoms are not named uniquely (all the carbons are just named C, all the nitrogens named N, etc.). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 29, 2009, at 4:10 AM, M. Shahid wrote:
Dear Elaine, Thanks again for the good information. I have done it the way you said and it is really a lot of work, but i was thinking was it the right way or not. When I select aromatic ring, all aromatic-aromatic contacts between both residues and ligand aromatic atoms are displayed. Best regards, -- Shahid. On Thu, Oct 29, 2009 at 6:11 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Shahid, It depends what you want. If those are the results you want (all aromatic-aromatic contacts), it would be the right approach. If not, you would want to use more filtering on the output using names, or deleting some atoms before the calculation as Eric described, to narrow down the results. Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 31, 2009, at 2:32 AM, M. Shahid wrote:
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M. Shahid