Dear All,
I have built a homology model of my protein using a single template sharing 38% sequence identity. Some of the functionally important residues of target protein are conserved in the template. These residues are well aligned in the input sequence alignment file. In the top most model so obtained, I found difference in side chain dihedral angles of such identical residues. Since both target as well as template contain a few identical residues, their secondary structure is also same, then why these conserved residues in the model adopt rotamers different from those of the template.
Following is comparison of side chain dihedrals of arginine conserved in both target as well as template.
chi1 chi2 chi3 chi4 chi5 template 169 -100 179 -80 0 model 65 81 75 -96 0
Here, chi1, chi2 and chi3 are drastically different
Can anybody please explain why this is so?
Thanks
Ruchi