saro.motif: Search for S-Aromatic Motifs

In ptm: Analyses of Protein Post-Translational Modifications

Search for S-Aromatic Motifs

Description

Searches for S-aromatic motifs in proteins.

Usage

saro.motif(pdb, threshold = 7, onlySaro = TRUE)

Arguments

pdb	either the path to the PDB file of interest or the 4-letters identifier.
threshold	distance in ångströms, between the S atom and the aromatic ring centroid, used as threshold.
onlySaro	logical, if FALSE the output includes information about Met residues that are not involved in S-aromatic motifs.

Details

For each methionyl residue taking place in a S-aromatic motif, this function computes the aromatic residues involved, the distance between the delta sulfur and the aromatic ring's centroid, as well as the angle between the sulfur-aromatic vector and the normal vector of the plane containing the aromatic ring.

Value

The function returns a dataframe reporting the S-aromatic motifs found for the protein of interest.

Author(s)

Juan Carlos Aledo

References

Reid, Lindley & Thornton, FEBS Lett. 1985, 190, 209-213.

See Also

saro.dist(), saro.geometry()

Examples

## Not run: saro.motif('1CLL')

ptm documentation built on Aug. 7, 2022, 5:05 p.m.