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<mailto: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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