Re: [ccp4bb] stacking interaction!

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CCP4bb <-- 2007 <-- August 2007 <-- 03 August 2007

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Subject: Re: stacking interaction!
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-08-03

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Subject: some resources for working with new pdbv3 format
From: Robert Immormino immormino {- at -} GMAIL {- dot -} COM
Date: 2007-08-03

Subject: Re: stacking interaction!
From: Kim Henrick henrick {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2007-08-03

using
http://www.ebi.ac.uk/msd-srv/msdsite/
and then under "Ligand environment:"
click Edit and draw the interaction
The oval shape is a ligand - click on it
and say make it GAL

you can say add a TRP connected to a ligand
(it is a rectangle shape)
and click on the "bond" circle and change it to
type "two-planes"

click SUBMIT tehn SEARCH and you will have
all interactions of TRP---GAL in a planar like manner
there are 84 of these
variations can be used for making the ligands
TRP/HIS/TYR/PHE as an or

you can look for sandwiches TRP--XXX--TRP

#----------------------------------------------
but for pure protein protein side chain interactions
as clusters of aromatics interacting try
http://www.ebi.ac.uk/msd-srv/MSDtemplate/
you can upload your pdb file and search for all
your file for any of the known custers or
or browse looking for our type of interaction
say 'TRP TRP PHE'
it will automatically assume TRP/PHE/TYR are equivalent
there are 6 known clusters of at least 3 aromatics
where the side chains are in the same place for the
unqiue set of PDB entries by sequence

e.g. click on
-PHE- -PHE- -PHE- -ASN- -ASN- -HIS- -SER-
then DETAIL
then Overlaid of this site

you will see the 7 structures not related by sequence
with the pattern
FWWNQHS*** where 6 side chains are identical in 3d space
(this isnt a pure stacking but the clustalw alignment
of the 7 hydrolase sequences shows only 32 '*'
out of lengths 212 to 316 amino acids)

the view overlay of the 1st PHE-PHE-PHE set of 16 structures
is impressive cnsiering that al the structures in this case have no
relationship - all know clusters are searched for in any upload structure

The service is under continued improvement and you may wish
to contact Tom Oldfield on specific requests as there is a newer
unreleased version

kim

On Fri, 3 Aug 2007, Eleanor Dodson wrote:

> Try submitting your coordinates to www.ebi.ac.uk/ msd and choose the task
> MSDpisa
>
> It gives you lots of info including that..
>
> Eleanor
>
> 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.
>>
>>
>>
>

--
Kim HENRICK henrick@ebi.ac.uk ::telephone: +44 (0) 1223 494629

CCP4bb navigation

CCP4bb <-- 2007 <-- August 2007 <-- 03 August 2007

Previous message:
Subject: Re: stacking interaction!
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-08-03

Next message:
Subject: some resources for working with new pdbv3 format
From: Robert Immormino immormino {- at -} GMAIL {- dot -} COM
Date: 2007-08-03