Question: Ionic Interactions In A Protein Structure
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gravatar for Pals
8.5 years ago by
Pals1.3k
Finland
Pals1.3k wrote:

Hi, I would like to get an overview of ionic bonds in a given protein structure. Are there any programs that can calculate the distance among Glutamate/Aspartate and Arginine? Otherwise, could anyone help with the codes (R, Python) to generate distance among aforementioned residues within a structure (is it feasible?). Would really appreciate your ideas. Thanks!

• 2.0k views
ADD COMMENTlink modified 8.5 years ago by Alastair Kerr5.2k • written 8.5 years ago by Pals1.3k
1
gravatar for Neilfws
8.5 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

To get it done quickly, I usually recommend the WHATIF server (which is a little slow for me as I write this, but is generally reliable).

Choose "Atomic Contacts" from the menu and scroll down to "Salt bridges".

ADD COMMENTlink written 8.5 years ago by Neilfws48k

Probably the only alternative I should opt. Thanks!

ADD REPLYlink written 8.5 years ago by Pals1.3k
0
gravatar for Alastair Kerr
8.5 years ago by
Alastair Kerr5.2k
Manchester/UK/Cancer Biomarker Centre at CRUK-MI
Alastair Kerr5.2k wrote:

I assume you mean peptide bonds rather than ionic? (ionic is metal->metal) [edit: obviously not, see comment below]

For 3D structural algorithms have a look at BALL (Biochemical Algorithms Library), it won best talk at this years bioinformatics open source conference [BOSC]. The function I think you should look at is under 'analytical geometry', BALL::GetDistance. However as I have not used it you should check the documentation.

ADD COMMENTlink modified 8.5 years ago • written 8.5 years ago by Alastair Kerr5.2k
2

Ionic is actually cation->anion, where the cation often is a metal, in chemistry. But "ionic interaction" is often used when discussing protein structure, usually to mean "salt bridge".

ADD REPLYlink written 8.5 years ago by Neilfws48k

Thanks, I've never heard ionic used instead of salt bridge but it makes sense.

ADD REPLYlink written 8.5 years ago by Alastair Kerr5.2k
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