Get all torsion angles in a nucleic acid structure

In the field of nucleic acid structure analysis, a commonly calculated set of parameters is the torsion angles. Specifically, they include the main chain and chi (χ) torsion angles defined as follows:

• α: O3'(i-1)-P-O5'-C5'
• β: P-O5'-C5'-C4'
• γ: O5'-C5'-C4'-C3'
• δ: C5'-C4'-C3'-O3'
• ε: C4'-C3'-O3'-P(i+1)
• ζ: C3'-O3'-P(i+1)-O5'(i+1)
• χ: for pyrimidines (Y, i.e., T, U, C): O4'-C1'-N1-C2; for purines (R, i.e., A, G): O4'-C1'-N9-C4

A related set of parameters characterizes the sugar conformation:

• ν0: C4'-O4'-C1'-C2'
• ν1: O4'-C1'-C2'-C3'
• ν2: C1'-C2'-C3'-C4'
• ν3: C2'-C3'-C4'-O4'
• ν4: C3'-C4'-O4'-C1'
• tm: amplitude of pseudorotation of the sugar ring
• P: phase angle of pseudorotation of the sugar ring

These torsion angles are clearly defined and are readily available from various informatics programs. Not surprisingly, 3DNA also provides a complete set of DNA/RNA backbone torsions, calculated robustly and efficiently. The key is the "-s" option of find_pair" program, which is nevertheless little used, mostly because it is not the default.

Using the Haloarcula marismortui 50S large ribosomal subunit as an example (1jj2), the output file 1jj2.outs from the following command contains all the above mentioned main chain and sugar conformational parameters:

find_pair -s 1jj2.pdb stdout | analyze

Please see the Jena "Nucleic acid backbone parameters" website for a diagram (based on Saenger's book) defining the various backbone torsion angles.