I have modeled a protein that has 71% similarity and 60% identity to the template but when I visualized and compared I got slight change in interactions although the residue is same and occupies same place in space but have lost hydrogen bond in my model protein. e.g in template Arg201 has 2 bonds whereas in my model Arg102 has one bond (one H2 bond is lost) although both arginine are aligned in MSA.