Yes, we can analyze the DNA protein interaction in Jmol application.
You will have to open the corresponding PDB file in Jmol and check for atomic distances, bond angles, dihedral angles, etc.
I would suggest, the best option for analysis of DNA-protein interactions with the software called UCSF-Chimera. This software has many more features for structure analysis, this includes 3D molecular views, Hydrogen bonds (weak and strong) and non-covalent interactions, change the display, highlight active-sites or amino acids in the structure, etc.
We have spoken tutorials for UCSF-Chimera for self-learning, Below is the link, please check them, you may find them useful for structural analysis of proteins and DNA, RNA other macromolecules