Tools To Visualize Hydrogen Bondings Between Two Different Binding Proteins?
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10.3 years ago
Lynn ▴ 150

I'm studying the interaction between two binding proteins (two chains) using Rasmol but it only shows the hydrogen bonds within the chain itself.

Is there any way to show the h-bonds between the two chains using Rasmol or any other tools available? Thank you in advance!!

ppi protein protein structural • 20k views
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i am facing the same problem could you please farward me the code u used. my mailing adress is amber.qadir@yahoo.com

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i am facing the same problem could you please farward me the code u used for finding hydrogen bond between two docked proteins? my mailing adress is amber.qadir@yahoo.com

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10.3 years ago
Thaman ★ 3.3k

Maybe you should focus in this PyMOLWiki example

# EXAMPLE 2
# Show hydrogen bonds between two proteins

load prot1.pdb
load prot2.pdb

h_add prot1
h_add prot2

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (prot1 and acc),(prot2 and don), 3.2
dist HBD, (prot1 and don),(prot2 and acc), 3.2
delete don
delete acc
hide (hydro)

hide labels,HBA
hide labels,HBD

# NOTE: that you could also use this approach between two
# non-overlapping selections within a single object.

Edit: RasMol shows only the backbone hydrogen bonds (hbonds). It is not capable of displaying hbonds between sidechains, between chains, between ligands and their binding sites, etc.

Addition

  • Load your structure through PyMOL>Plugin>PDB Loader Service> 317H
  • There are object menus:- A (action),S (show),H (Hide), L (label), C (color) from where you can do most of the operations
  • First Click on H>Hide everything, then S>Cartoon, then C>by chain>by chain (e, c) then L>chains (Now you can see the chains of your structure)
  • Click on Display>Sequence (to see which residues lies in different chain)
  • Now rest of the steps are done through PyMOL command terminal, commands can be type to perform specific operation. PyMOL is generally open in two mode which is similiar to RasMol.
PyMOL>select ChA, chain A  //ChA is selection of Chain A residues, ChA is used just for convinence 
 Selector: selection "ChA" defined with 8726 atoms.
PyMOL>select ChB, chain B
 Selector: selection "ChB" defined with 111 atoms.
PyMOL>dist name, ChA, ChB, mode=2
 Executive: object "name" created.
  

To know more about different mode please visit PyMOLWiki

Now you can see hydrogen bonding with distances between bonding residues. You can rotate to clear the view of the structure. If you want to perform more complicated bonding then these commands can be use.

h_add 317H
select protein, chain A or chain B or chain C
select substrate, chain D
select don, (elem n+o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (substrate and acc), (protein and don), 3.2
dist HBD, (substrate and don), (protein and acc), 3.2
delete don
delete acc
hide (hydro)
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I have edited my answer according to your requirement, hope this works for you.

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Thanks for the helpful explanation. But the 3D structure that I am studying is already binding together forming one protein structure with two chains. I need to analyze the hbonds between both the chains. Is it possible with Pymol?

Attached here is the link to the protein structure I am currently studying. Thank you, once again! Sorry for any inconveniences caused.

http://www.mediafire.com/?hpzqoxt6t6sf1j2

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Thank you so much!! That is very, very helpful of you, Thaman!! I really appreciate it alot. =)

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It's my pleasure but accept the answer if you want

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10.3 years ago

Molegro Virtual Docker you can use for visualization of Hydrogen Bond Interactions between two intercted Protein. You may import the out of docking result in Molegro and in Display you will have an option to view H-Bond Interaction. Molegro is a commercial tool but trial version is available for one month.

Hope this will help you.

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Thanks for the helpful information! :)

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10.3 years ago

PyMol might be able to do what you want, see the PyMOLWiki.

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Thanks for the helpful information! :)

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10.3 years ago
Neilfws 49k

From this Rasmol documentation:

The hbonds command displays only backbone-to-backbone hydrogen bonds in regions of defined secondary structure, and Watson-Crick inter-nucleotide bonds in DNA double helix. RasMol and Chime have no built-in mechanism to locate and display other types of hydrogen bonds, such as any involving sidechains, inter-chain hbonds, ligand-protein hbonds, etc.

So using Rasmol - no. It is rather old software and is no longer actively developed.

As others suggested, look at PyMol instead.

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Thanks for the helpful information! =)

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9.8 years ago

Hello,

Another way to visualize H-bond between two proteins, but not in 3D, could be with the MONSTER web server : http://monster.northwestern.edu/

You have an overview of the interface and the result below:

[?]

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10.3 years ago

You can also have a look at Jmol, which has a very powerful scripting language. I do not know the exact commands to do it, but it has means to detect close contacts, such as to find hydrogen bonds.

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Thanks for the helpful information! :)

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10.3 years ago

LIGPLOT / DIMPLOT can generate publication quality inter & intra chain hydrogen bonds in protein structures. You need an academic license for installation.

alt text

Manuscript describing LIGPLOT is here and detailed tutorial available here

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Thanks for the helpful information! =)

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it is a very limited program since it can not show anythin but hydrophobic and hydrogen bond interactions; what about relevant electrostatics, aromatic and metal interactions?

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9.8 years ago

The HBonds plugin in the [?]VMD[?] software package is very handy for analyzing hydrogen bonding. It has both an easy graphical interface, as well as a command-line interface if you need to do any scripting with it. It is included in the normal VMD package when you [?]download VMD[?].

Here is a link to a description of the HBonds plugin itself: http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/

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I tried VMD according to the link given by you. But it never shows me any output graphics. Its simply blank. I adjusted the values according to the recommendation in link, still nothing.

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7.9 years ago
bluewoodtree ▴ 60

The Swiss PDB viewer is also a nice alternative to PyMOL for showing H-bonds. It uses distance constraints and angle constraints.
You can find the tutorial here: http://spdbv.vital-it.ch/activsit_tut.html

And the manual with a more detailed description: http://spdbv.vital-it.ch/Swiss-PdbViewerManualv3.7.pdf

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