ptm (version 0.2.2)

saro.motif: 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 <U+00E5>ngstr<U+00F6>ms, 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.

Value

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

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.

References

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

See Also

saro.dist(), saro.geometry()

Examples

# NOT RUN {
saro.motif('1CLL')
# }