[Chimera-users] classifying contact interactions

[Elaine Meng]

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,
> 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 at cgl.ucsf.edu>  
> wrote:
>
> (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.
>
>
> On Oct 24, 2009, at 8:00 AM, M. Shahid wrote:
>
> 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
> .......... .... ... .. .