[Chimera-users] Contact area between 2 Proteins

[Fernando Villa]

Dear Elaine C. Meng ... Thank you very much for the help, and I am more
clear, the differences between the methods before mentioned.
So, if I want to calculate the contact area between two proteins  (solvent
accesible surface area)



[image: image.png]

[image: image.png]
[image: image.png]
Is it correct to use a 2.5A cuttoff?
which of the three methods should I use?

*Method 1* (used for the figures
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#figures>)
identifies atom-atom contacts with *Find Clashes/Contacts*
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
or
its command equivalent, *findclash
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>*.

With the proteins in the bound state:

*Command*: *findclash
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
 #0.1  test #0.2  intersub true  overlap  -1  hb 0  make false  select
true*

*Command*: *namesel
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/namesel.html> contacts*

*Command*: *~select
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer>*
*Command*: *color
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> yellow
contacts&#0.1*
*Command*: *color
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> hot
pink contacts&#0.2*

In the *findclash
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>*
command,
the *overlap* and *hb* parameters are adjustable, with values of 0.0-(–1.0)
Å and 0.0 Å, respectively, recommended for finding *contacts*. An
*overlap* cutoff
of –1.0 identifies pairs of atoms with VDW surfaces up to 1.0 Å apart. When
the command is instead used to find only *clashes* (unfavorable, too-close
contacts), *hb* values > 0.0 help to exclude H-bonding atom pairs. The two
sets of atoms are specified with model numbers (*e.g.* *#0.1*), but chain
identifiers could have been used instead (*e.g.* *:.a*), and if water had
not been deleted, the calculation could have been limited explicitly to
protein (*e.g.* *#0.1&protein* or *:.a&protein*).

*Method 2* first calculates buried surface area, then uses the resulting
per-atom values (assigned as atom attributes
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef>)
to identify interface atoms.

With the proteins in the bound state:

*Command*: *measure buriedArea
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>
 #0.1  #0.2*

*Command*: *color
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>
yellow  #0.1@/buriedSESArea>1*

*Command*: *color
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>
hot pink  #0.2@/buriedSESArea>1*

The total buried area and details of the calculation are given in the *Reply
Log* <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/reply.html>.
Different cutoff values could be used, but in this case, atoms with > 1.0 Å2 of
solvent-excluded surface area buried in the interface are similar to the
set of atoms found in the method 1
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#method1>
example.
Although solvent, ions, and ligands are not enclosed in the displayed
surfaces, the buried-area calculation will include all specified atoms.
Thus it is important to specify only the intended atoms; for example, if
nonprotein atoms were present:

*Command*: *measure buriedArea
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>
 #0.1&protein  #0.2&protein*

*Method 3* identifies where surfaces are close to one another and does not
involve atoms.

With the proteins in the bound state and surfaces shown:

*Command*: *measure contactArea
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#contactArea>
 #0.1  #0.2  2.5  color yellow offset 0*

*Command*: *measure contactArea
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#contactArea>
 #0.2  #0.1  2.5  color hotpink offset 0*

These commands identify where the surfaces are within 2.5 Å of each other.
Again, different cutoffs could be used, but 2.5 gave a result roughly
similar to the preceding examples. The specifications in the contact-area
command (*e.g.* *#0.1*) refer to the surface models, which happen to have
the same model numbers as the corresponding atomic structures.

I apologize to you and the entire community for asking things that may be
obvious to you and the research community.
I am very new in this area and I would be very helpful in completing my
doctoral thesis.


Sincerely, Fernando Villa

best regards!



El vie., 10 de may. de 2019 a la(s) 10:59, Elaine Meng (meng at cgl.ucsf.edu)
escribió:

> Dear Fer Villa,
> (better to send questions to chimera-users at cgl.ucsf.edu, CC’d here)
>
> It is not really a matter of right and wrong.  Instead it depends on what
> you want…
>
> If you want to measure buried solvent-accessible and solvent-excluded
> surface areas of atomic structures, use “measure buriedArea”.
>
> The “measure contactArea” command is similar but if the goal is
> measurement (rather than coloring for a figure), it is generally used for
> other kinds of surfaces that are not necessarily associated with any atoms,
> like density map isosurfaces.  In that case, the appropriate cutoff value
> really depends on the judgment of the user based on what kinds of surfaces
> these are and what the user is trying to do.
>
> The tutorial you mention is for making a figure where the interaction
> surfaces of two proteins are colored, which is a different purpose than
> getting a measurement value.  It explains that different cutoffs could be
> used with “measure contactArea", but the example has 2.5 because it gave
> similar appearance to using the other (buriedArea) method.  The tutorial
> shows both methods because if you are making a figure, you could use either
> one as you like.  It actually discusses three methods.
>
> For the other people on the list, here is that tutorial:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
> … 3 methods of coloring the interface:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#interface
> >
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On May 10, 2019, at 12:17 AM, Fernando Villa <fer.vdl1928 at gmail.com>
> wrote:
> >
> > Dear Chimera users,
> > I would like to know which is the correct method to know what is the
> surface area of contact between two proteins:
> > measure contactArea or measure buriedArea?
> > When I apply the command: measure contactArea # 0.1 # 0.2 2.5 color
> yellow offset 0 that comes in the tutorial, it says that the cutting
> distance is equal to 2.5 A2
> > But, is it correct?
> > How can I know that?
> > this example states that if this cut-off distance (2.5 A) is applied
> compared with a cut distance for measure buriedArea:
> > Command: measure buriedArea # 0.1 # 0.2
> > Command: color yellow #0.1@/buriedSESArea> 1
> > Command: color hot pink #0.2@/buriedSESArea> 1
> > measure buried Area # 0.1 & protein # 0.2 & protein
> > atoms with> 1.0 Å2
> > How can I know which is the correct contact area (protein protein
> interaction) of two models or crystals?
> > What is the correct cutting area that I should apply?
> > Could it be the default cut area of 1A?
> > Which method of calculation is better, measure contactArea or measure
> buriedArea?
> > I would thank you in advance for a possible solution to my problem.
> >
> > Best regards.
> >
> > Fer Villa.
> > Enviar comentarios
> > Historial
> > Guardadas
> > Comunidad
> >
> > <image.png>
> >
> > Command:open 1avx
> > Command: ~longbond
> > Command: split
> > Command: preset apply int 2
> > Command: repr stick
> > Command: delete solvent
> > Command: color sea green #0.1
> > Command: color medium purple #0.2
> > Command: surface
> > Command: measure contactArea  #0.1  #0.2  2.5  color yellow offset 0
> > Command: measure contactArea  #0.2  #0.1  2.5  color hotpink offset 0
> >
> >
> > or
> >
> > Command: measure buriedArea  #0.1  #0.2
> > Command: color yellow  #0.1@/buriedSESArea>1
> > Command: color hot pink  #0.2@/buriedSESArea>1
> >
> > Command: measure buriedArea  #0.1&protein  #0.2&protein
> >
> > ATTE
> > Fernando Villa Díaz
> >
>
>
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