Where CA is the alpha carbon, C(-1) is the C before the current carbon, etc.
Structure of data files for protein backbone:
Now we want to add other stuff.
|Atom||First atom||Second||Third||Fourth||Dihedral angle|
|Amide hydrgeon (NH)||CA-1||C||N||NH||dihNH|
|Alpha carbon hydrogen (H1)||C-1||N||CA||H1||dihH1|
|First carbon on R-group (CB)||C-1||N||CA||CB||dihCB|
Cool. But do we always need to calculate stuff from the inputs? Not for the so-called "improper dihedrals", such as the C-CA-N-NH dihedral, or the C-CA-N-NH dihedral, because these are always the same. The "proper" dihedrals (N, CA, C) must be calculated from inputs, but the "improper" dihedrals can be taken from a table.
N terminus to C terminus, with increasing i
- Within the residue, calculate proper dihedrals, take improper dihedrals from a table