I'm wondering about the minimal set of parameters necessary to define a protein's structure. My understanding is that the backbone geometry is defined by the phi and psi angles (torsion angles), and then from this template the side-chain rotamers are defined. Is this sufficient to yield a geometric structure, or are there other factors involved?
On a related note, how exactly are two protein structures compared? I often see references to percent similarity, but what does this really mean? In the Protein Data Bank, atomic coordinates are given, but my intuition is that coordinates are only important relative to all the other amino acids in the chain. In other words, absolute coordinate comparison would seem to be uninformative.