[Chimera-users] Contact area between 2 Proteins

[Elaine Meng]

As I already said in the previous message,  if the purpose is to get a buried surface area value for atomic structures (not just to make a figure), then use “measure buriedArea”:

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

The other two methods don’t calculate SAS or SES values, and you said you wanted buried SAS.

The “measure buriedArea” command does not have a cutoff parameter.  Just make sure to specify only the proteins in the command so that water, etc. will not affect the calculation.

Elaine

> On May 10, 2019, at 1:01 PM, Fernando Villa <fer.vdl1928 at gmail.com> wrote:
> 
> 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.png>
> 
> <image.png>
> <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) identifies atom-atom contacts with Find Clashes/Contacts or its command equivalent, findclash.
> 
> With the proteins in the bound state:
> 
> Command: findclash  #0.1  test #0.2  intersub true  overlap  -1  hb 0  make false  select true 
> Command: namesel contacts 
> Command: ~select 
> Command: color yellow contacts&#0.1 
> Command: color hot pink contacts&#0.2
> In the findclash 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) to identify interface atoms.
> With the proteins in the bound state:
> Command: measure buriedArea  #0.1  #0.2 
> Command: color yellow  #0.1@/buriedSESArea>1 
> Command: color hot pink  #0.2@/buriedSESArea>1
> The total buried area and details of the calculation are given in the Reply Log. 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 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  #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  #0.1  #0.2  2.5  color yellow offset 0 
> Command: measure 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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