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!
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".
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.