[chimerax-users] Inquiry about bond type generated by the "contacts" command with default settings for AlphaFold-generated protein structure

[Elaine Meng]

Dear James,
These are just lines drawn to show which pairs of atoms are within the distance criteria you used when running the contacts command.  If you ran the command on all types of atoms, these could include all types of interactions (polar, nonpolar, hydrogen bonds, hydrophobic interactions, etc.) but it depends on the types of the two atoms in each contact.  These lines may or may not indicate any kind of bonding in the chemical sense.  

See "contacts" help by using command "help contacts" or view the copy at our website here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>

We call these lines "pseudobonds":
<https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>

If you wanted hydrogen bonds specifically, then use the "hbonds" command instead.  The "hbonds" command also has a "saltOnly" option if you want to find only the subset of H-bonds that are salt bridges.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html>

A disulfide bond is a covalent bond, whereas these commands (contacts, hbonds) only look for noncovalent interactions.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Mar 1, 2023, at 8:29 PM, stomp.pumped0g--- via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear UCSF ChimeraX team,
> I hope this email finds you well. I am writing to inquire about the bond type generated by the "contacts" command with all default settings in UCSF ChimeraX for a protein structure that was generated using AlphaFold.
> 
> I am particularly interested in understanding the nature of the blue line that is generated after running this command. As a reminder, my protein structure was generated using AlphaFold, and I would like to know if the bond type is a hydrogen bond, salt bridge, disulfide bond, or another type of bonding.
> 
> Any information or insight you could provide on this matter would be greatly appreciated. Thank you for your time and assistance.
> Best regards,
> James
> <image0.png>