Thanks you Jared.
I will try CCP4 and get back to you.
Regards,
Bhumika.
On Wed, Sep 10, 2014 at 12:20 AM, Sampson, Jared <jared.samp...@nyumc.org>
wrote:
> Hi Bhumika -
>
> Have a look at the CCP4 program NCONT:
> http://www.ccp4.ac.uk/html/ncont.html.
>
> You can run it within the CCP4 GUI or from the command line. For
> example, for contacts between helices 1 and 2, type these lines at the
> prompt (or copy and paste), substituting the correct path to the PDB file
> and ranges you want to examine.
>
> ncont xyzin 2rh1.pdb <<eof
> source A/29-60
> target A/67-96
> maxdist 5.5
> sort source
> eof
>
>
> You’ll get output that looks like this:
>
> <snip>
>
> 360 contacts found:
>
> SOURCE ATOMS TARGET ATOMS DISTANCE
>
> /1/A/ 32(TRP). / CE3[ C]: /1/A/ 95(LEU). / CD2[ C]: 5.16
> /1/A/ 32(TRP). / CZ3[ C]: /1/A/ 95(LEU). / CD2[ C]: 4.43
> /1/A/ 32(TRP). / CH2[ C]: /1/A/ 94(ILE). / CG2[ C]: 5.39
> /1/A/ 95(LEU). / CD2[ C]: 4.78
> /1/A/ 33(VAL). / CA [ C]: /1/A/ 95(LEU). / CD2[ C]: 4.23
> /1/A/ 33(VAL). / C [ C]: /1/A/ 95(LEU). / CD2[ C]: 4.35
> /1/A/ 95(LEU). / CG [ C]: 5.49
> /1/A/ 33(VAL). / O [ O]: /1/A/ 95(LEU). / CD1[ C]: 4.56
> /1/A/ 95(LEU). / CD2[ C]: 3.64
> /1/A/ 95(LEU). / CB [ C]: 5.41
> /1/A/ 95(LEU). / CG [ C]: 4.69
> /1/A/ 33(VAL). / CB [ C]: /1/A/ 95(LEU). / CB [ C]: 5.44
> /1/A/ 95(LEU). / O [ O]: 5.24
> /1/A/ 95(LEU). / CD2[ C]: 4.50
> /1/A/ 33(VAL). / CG1[ C]: /1/A/ 95(LEU). / C [ C]: 4.92
> /1/A/ 95(LEU). / CG [ C]: 4.47
> /1/A/ 95(LEU). / CD1[ C]: 4.89
> /1/A/ 95(LEU). / CD2[ C]: 3.74
> /1/A/ 95(LEU). / CA [ C]: 4.80
> /1/A/ 95(LEU). / O [ O]: 4.36
> /1/A/ 95(LEU). / CB [ C]: 4.20
> </snip>
>
>
> You can also visualize contact residues in PyMOL using selection algebra
> <http://www.pymolwiki.org/index.php/Selection_algebra>. A simple version
> might look like:
>
> fetch 2rh1, async=0
> as cartoon
>
> # create helix selections
> select helix1, chain A and resi 29-60
> select helix2, chain A and resi 67-96
>
> # create contact selection for the helix pair
> select cont_1_2, (helix2 within 5.5 of helix1) or (helix1 within 5.5 of
> helix2)
>
> # visualize contacts
> show sticks, cont_1_2
>
>
> Hope that helps.
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
>
>
>
> On Sep 7, 2014, at 8:03 PM, bhumika arora <bhumikar...@gmail.com> wrote:
>
> Dear Pymol users,
>
> I wish to know how to calculate residue-residue contacts from a PDB
> file. Where, contact definition is : two residues are considered to be in
> contact if the
> minimal distance of their side chain or backbone heavy atoms is < 5.5A ˚ .
>
> Specifically, I want to calculate inter-helical (helix-helix) contacts
> from a PDB; when two residues from different helices (transmembrane
> helixes) are considered to be in contact if the minimal distance of their
> side chain or backbone heavy atoms is < 5.5A ˚
>
> For example, I want to calculate the inter-helical residue contacts of
> the PDB "2RH1"
>
> Please advise.
>
> Regards,
> Bhumika.
>
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