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Author Topic: Water H-Bonding with surrounding residues  (Read 485 times)

Offline kanavkalra

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Water H-Bonding with surrounding residues
« on: May 20, 2018, 09:36:50 am »
Dear Dr. Xiang-Jun Lu,
May I know if there exists any option that could help me get data for the Water H-Bonding with the surrounding residues?

Regards,
Kanav Kalra

Offline xiangjun

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Re: Water H-Bonding with surrounding residues
« Reply #1 on: May 20, 2018, 10:26:30 am »
Hi,

Thanks for posting on the 3DNA Forum!

Could you elaborate on what you want to achieve specifically? Please use a concrete example so that I (and others) can better understand you.

Best regards,

Xiang-Jun


Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline kanavkalra

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Re: Water H-Bonding with surrounding residues
« Reply #2 on: May 20, 2018, 05:23:54 pm »
Hi,
Below is an example:

In PDB id: 2GDI,

For instance, if we want to find out possible H-bonds between a water molecule 'HOH-373' from chain X with the surrounding atoms from the environment. The output could be as follows:

1) O2P atom of G76 chain X;   with the distance between O atom of HOH-373 and O2P atom of G76 of 2.79 Angstrom.
2) HOH 492X;  with the distance between O atom of HOH 373 and O atom of HOH492X of 2.58  Angstrom.
3) N7 of G76 X; with the distance between O of HOH 373 and N7 atom of G76X of 2.84 Angstrom.

So the above three atoms are within the H-bonding distances if we consider the distance criterion of less than 3.5 Angstrom between the donor and acceptor atoms.

Offline xiangjun

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Re: Water H-Bonding with surrounding residues
« Reply #3 on: May 20, 2018, 06:21:41 pm »
Try running DSSR with the --h2o (or --water) option. For example,

Code: [Select]
x3dna-dssr -i=2gdi.pdb --h2o --get-hbond | grep X.HOH373

 1415  3572  #400   o    2.790 O:O OP2@X.G76 O@X.HOH373
 1427  3572  #407   o    2.836 N:O N7@X.G76 O@X.HOH373

By design, DSSR does not output H-bond between waters. So your item 2), i.e. the H-bond between X.HOH373 and X.HOH492, is not available. It should be straightforward to add X.HOH494 to the list, based on available info and a distance cutoff. You're welcome to contribute back your code/script with examples so the community could benefit from it.

HTH,

Xiang-Jun
« Last Edit: May 21, 2018, 09:38:14 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.