I'm recently studying on the tableaux representation of secondary structure elements of proteins. But I don't know how to get the orientations between them from DSSP file. The DSSP file assign helix or strand of sheet to each redisue. Besides, it give some angles such as TCO KAPPA ALPHA PHI PSI. I don't know how to calculate the angle between them. Anyone knows how to do it?
Calculating orientations between secondary structures could be done, very simply, by assigning a vector to the midpoints of the backbone of the residues of each secondary structure and then calculating their angle. For example, if you have two helices (residues 1-10 and 12-20) you could make two vectors out of them and then calculate the angle between these two vectors.
As for the TCO/KAPPA/etc definitions (taken from the DSSP 'manual'):
cosine of angle between C=O of residue i and C=O of residue i-1. For alpha-helices, TCO is near +1, for beta-sheets TCO is near -1. Not used for structure definition.
virtual bond angle (bend angle) defined by the three C-alpha atoms of residues i-2,i,i+2. Used to define bend (structure code 'S').
virtual torsion angle (dihedral angle) defined by the four C-alpha atoms of residues i-1,i,i+1,i+2.Used to define chirality (structure code '+' or '-').
IUPAC peptide backbone torsion angles