Re: [ccp4bb] stacking interaction!

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Molrep question
From: Cynthia Czyrphony cynthia {- dot -} czyrphony {- at -} GMAIL {- dot -} COM
Date: 2007-08-02

Next message:
Subject: Re: stacking interaction!
From: Anthony Addlagatta anthony {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2007-08-02

Subject: Re: stacking interaction!
From: Robert Immormino immormino {- at -} GMAIL {- dot -} COM
Date: 2007-08-02

Sreeram,

This can be done with MolProbity. (http://molprobity.biochem.duke.edu/index.php)

The routine would be to upload your .pdb coordinates, add hydrogens,
and then run "visualize
interface contacts". The details of the flags for this last routine
would be particular to what you are looking for exactly.

The line of output is information rich and therefore a bit confusing,
but in the example below A 78 PHE CE1 contacts other residues with a
sum contact surface area of 2.0 sq. Angstroms.

A 78 PHE CE1 : B 82 VAL CG2 : wc ; B 82 VAL HG22 : cc
; B 82 VAL CG2 : cc ; B 82 VAL HG22 : so ; B 82 VAL
CG2 : so ; : Dots = 32 : Area covered = 2 sq A

For some quite specific queries, it may be necessary to download
reduce, probe, and prekin from: http://kinemage.biochem.duke.edu/

With these programs and some patience you should be able to query a
large variety of van der Waals interactions.

For example,

reduce -build 1TC6.pdb > 1TC6H.pdb
probe -c -both "chainA 282" "chainA 331" 1TC6H.pdb
will produce the following information about the interaction between
two Trp residues in the tryptophan zipper of GRP94.

subgroup: 1->2
atoms selected: 24
potential dots: 2676
potential area: 167.2 A^2
type # % score score/A^2 x 1000
C wide_contact 60 2.2% 0.6 3.56
C close_contact 45 1.7% 2.0 11.74
C small_overlap 13 0.5% -0.2 -1.15
N wide_contact 8 0.3% 0.1 0.60
N close_contact 11 0.4% 0.5 3.16
N small_overlap 1 0.0% -0.0 -0.02
O wide_contact 1 0.0% 0.0 0.01

tot contact: 125 4.7% 3.2 19.07
tot overlap: 14 0.5% -0.2 -1.17
tot H-bond: 0 0.0% 0.0 0.00

grand tot: 139 5.2% 3.0 17.90

contact surface area: 8.7 A^2

This interaction can be visualized in KiNG by adding on a few extra commands.

prekin -lots 1TC6H.pdb > 1TC6H.kin
probe -both "chainA 282" "chainA 331" 1TC6H.pdb >> 1TC6H.kin

The image is available here:
http://richardsons.biochem.duke.edu/~immormino/kingsnap1.jpg

Cheers,

-bob

On 8/2/07, Sreeram Mahesh wrote:
> Hi All!
>
> I have found stacking interaction between aromatic residues of a
> structure of an enzyme. does anybody knows any server which can quantify
> the stacking interaction between side chains of aminoacids.
>
> Thanking very much in advance!
>
>
> Sreeram Mahesh
> Research Student
> Prof S Ramakumar's lab
> PHYSICS department
> IISc Bangalore-560 012.
> ph:080-2293 2718.
> mobile: 9241145183.
>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Molrep question
From: Cynthia Czyrphony cynthia {- dot -} czyrphony {- at -} GMAIL {- dot -} COM
Date: 2007-08-02

Next message:
Subject: Re: stacking interaction!
From: Anthony Addlagatta anthony {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2007-08-02