Question: Tools To Visualize Hydrogen Bondings Between Two Different Binding Proteins?
8
gravatar for Lynn
8.3 years ago by
Lynn150
Lynn150 wrote:

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 structural • 18k views
ADD COMMENTlink modified 5.9 years ago by bluewoodtree60 • written 8.3 years ago by Lynn150

i am facing the same problem could you please farward me the code u used. my mailing adress is amber.qadir@yahoo.com

ADD REPLYlink written 7.9 years ago by Amber0

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

ADD REPLYlink written 7.9 years ago by Amber0
10
gravatar for Thaman
8.3 years ago by
Thaman3.2k
Finland
Thaman3.2k wrote:

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)
ADD COMMENTlink modified 8.3 years ago • written 8.3 years ago by Thaman3.2k
2

I have edited my answer according to your requirement, hope this works for you.

ADD REPLYlink written 8.3 years ago by Thaman3.2k

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

ADD REPLYlink written 8.3 years ago by Lynn150

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

ADD REPLYlink written 8.3 years ago by Lynn150

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

ADD REPLYlink written 8.3 years ago by Thaman3.2k
5
gravatar for Anuraj Nayarisseri
8.3 years ago by
Indore
Anuraj Nayarisseri740 wrote:

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. Go through the following link. http://www.molegro.com/mvd-product.php

Hope this will help you.

ADD COMMENTlink written 8.3 years ago by Anuraj Nayarisseri740

Thanks for the helpful information! :)

ADD REPLYlink written 8.3 years ago by Lynn150
2
gravatar for Michael Kuhn
8.3 years ago by
Michael Kuhn5.0k
EMBL Heidelberg
Michael Kuhn5.0k wrote:

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

ADD COMMENTlink written 8.3 years ago by Michael Kuhn5.0k

Thanks for the helpful information! :)

ADD REPLYlink written 8.3 years ago by Lynn150
2
gravatar for Neilfws
8.3 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 8.3 years ago by Neilfws48k

Thanks for the helpful information! =)

ADD REPLYlink written 8.3 years ago by Lynn150
2
gravatar for Pierre Poulain
7.9 years ago by
France
Pierre Poulain440 wrote:

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:

[?]

ADD COMMENTlink written 7.9 years ago by Pierre Poulain440
1
gravatar for Egon Willighagen
8.3 years ago by
Maastricht
Egon Willighagen5.2k wrote:

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.

ADD COMMENTlink written 8.3 years ago by Egon Willighagen5.2k

Thanks for the helpful information! :)

ADD REPLYlink written 8.3 years ago by Lynn150
1
gravatar for Khader Shameer
8.3 years ago by
Manhattan, NY
Khader Shameer18k wrote:

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

ADD COMMENTlink written 8.3 years ago by Khader Shameer18k

Thanks for the helpful information! =)

ADD REPLYlink written 8.3 years ago by Lynn150

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?

ADD REPLYlink written 7.9 years ago by Flow1.5k
0
gravatar for Keith Callenberg
7.9 years ago by
Pittsburgh, PA
Keith Callenberg890 wrote:

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/

ADD COMMENTlink written 7.9 years ago by Keith Callenberg890

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.

ADD REPLYlink written 4.5 years ago by devanand.t.19860
0
gravatar for bluewoodtree
5.9 years ago by
bluewoodtree60
bluewoodtree60 wrote:

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

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by bluewoodtree60
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