Yes, use Jmol software, You can import crystal structure coordinates and measure distances. http://jmol.sourceforge.net/#Features

Dear Alice,

Your question is imprecise and has at least two layers. I am assuming that you went through at least several classes that described stereochemistry of proteins, so I am assuming that you are not asking about how neighboring amino acids are far apart, or what the protein folding means. I am assuming that you are using the question about the physical distance between amino acids that are remote in sequence.

First aspect is the internal and coordinated motions. Individual amino acids, especially at the surface of the protein undergo significant motions. These motions can be almost random, coupled to the thermal behavior of the solvent or coordinated which means coupled to the larger solvent-protein rearrangements. These latter motions can have functional implications and people developed experimental as well as modeling tools to measure them up. Most of the crystal structures do not represent well the extent of these motions. Most of the contacts will be temporary and change in time so the single structure representation does not give the justice to what is biologically important.

Second aspect is protein folding and its ambiguity. The same protein can be represented in many different globally distinct conformational states. So focusing on a single conformer present in an individual crystal structure is usually pointless unless you are asking questions about residues essential for folding.

So in essence even if you want to use the existing structures you need to be careful about how you formulate the question and what your answer really mean. Your question is formulated in a dry technical language of how to reach a measuring tool which is present in almost any software for molecular modeling. There are a multitude of these software tools available. In this context answer by Andrei should do the trick. To the most popular tools belong Jmol, Pymol, Rasmol, Chimera. In crystallography Coot dominates the market, but any other integrated package will do the job. Many web sites give enumerated list of tools with links. For instance:

https://www.bioinformatics.org/wiki/Molecular_visualization

https://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Protein/proteinlast.html

https://www.rcsb.org/pages/thirdparty/molecular_graphics

Particular the last one provides wealth of resources that should be accessible and easy to use.

Good Luck.

Bog

Boguslaw Stec's answer is very comprehensive, and I usually use Pymol and Coot to solve similar problems in the analysis of protein crystal structure. If you need more comprehensive technical support, you can consult Creative Biostructure, which I know is a very professional supplier of protein structure biotechnology.

All the best!

Thank you very much for your answers! I will try the different approaches and will get back to you.