CYANA Command: angles ramachandran

Ramachandran plot analysis

Parameters

selection=string

(default: none)

Description

Command that analyzes the PHI/PSI distribution of amino acid residues. Only non-terminal amino acid residues with a selected PHI, PSI, OMEGA and CHI1 torsion angle are analyzed, i.e. Pro and Gly are excluded. By default, the selection made in the most recent angles select command is used, or all angles if no selection has been made so far.

The PHI/PSI torsion angle value pairs are classified as lying in the most favored, additionally allowed, generously allowed, or disallowed regions of the Ramachandran plot, as defined by the program Procheck (Laskowski et al., J. Biomol. NMR 8, 477-486, 1996). The percentage of residues in each of these four classes is reported.

Amino acid residues for which the PHI/PSI pair of at least one selected conformer lies in the generously allowed or disallowed regions of the Ramachandran plot are reported in a table. The Ramachandran plot regions are marked by blank, ., + and * for the most favored, additionally allowed, generously allowed, and disallowed regions, respectively.

For example:

    Ramachandran: # 1   5   10   15   20
    SER     3     4 *.....  *. +.+ ....

In this example, Ser 3 is in the disallowed region of the Ramachandran plot in conformers 1 and 9, in the generously allowed region in conformers 12 and 14, in the additionally allowed region in 11 conformers, and in the most favoured region in the remaining 5 conformers. The # column reports the number of conformers in which this residue is in an unfavourable, i.e., disallowed or generously allowed region of the Ramachandran plot.

The angles ramachandran command can be complemented with the ramaplot macro that produces a Ramachandran plot. The angles ramachandran command is included in the detailed overview produced by the overview macro.

See also

• ramaplot
• overview