[Chimera-users] classifying contact interactions

[Elaine Meng]

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:

> 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:
>
>> 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.
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