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Protein backbone

Where CA is the alpha carbon, C(-1) is the C before the current carbon, etc.

Structure of data files for protein backbone:

Angle First atom Second Third Fourth
[math]\displaystyle{ \phi }[/math] C-1 N CA C
[math]\displaystyle{ \psi }[/math] N CA C N+1
[math]\displaystyle{ \omega }[/math] CA C N+1 CA+1

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.

Build order

N terminus to C terminus, with increasing i

  • Within the residue, calculate proper dihedrals, take improper dihedrals from a table