Counting Number Of Protein Bonds, From Pdb File

Question

[User 1933]

Whats the best way to measure / count number of

• SS bonds (Disulfide bond)
• hydrogen bonds
• Hydrophobic Bonds
• Ionic Bonds - Salt Bridges

from a pdb file. Is there any tools ?! I run DSSP on my pdb file, but there is always a warning regarding SSbonds, like the following, I played with the optimization parameter, but it didn't regulate the issue.

!!! Additional ssbond found between residues CYS 247 and CYS 253 !!!

Since, I am running DSSP on many pdf file, I need an accurate as well as safe method to count such bonds.

[Michael Schubert]

Is there a bond between Cys247 and Cys253 in your pdb file? What is their distance?

[User 1933]

when I put my pdb file in pymol, apparently there is no bond! but distance is quite short (as the warning states), distance is 2.4A in this case, so I expect to see a bond. Perhaps, energy computation issue and flexibility of residues is in conflict with this ss-bond. I assume that DSSP is not the best software for such job.

Answer 1

[Vladimir Chupakhin]

Try Bio3D.

[User 1933]

a very very big -1

Answer 2

[Neilfws]

You might like to try the WHATIF Server, which has tools to calculate everything you want and lots more.

Also, remember that calculating bonds in PDB files is always an estimate, not an "accurate, safe" method. Interactions are inferred using distance and size and there is uncertainty, depending on the resolution and quality of the structure. Most tools will also require some "tweaking" of parameters but this is more best judgement than optimization.

[User 1933]

I have distance among all Cys, can I define a threshold (say, 8A) and say, if two Cys are closer than 8A there is bond ?! Same way for Hydrogen bond ...

[Neilfws]

That's exactly the point; you have to make a threshold choice, there is no "right answer". Most people would review the structural biology literature and do "what most other people do."