ptm (version 0.2.2)

saro.dist: Compute Distances to the Closest Aromatic Residues

Description

Computes distances to the closest aromatic residues.

Usage

saro.dist(pdb, threshold = 7, rawdata = FALSE)

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.

rawdata

logical to indicate whether we also want the raw distance matrix between delta S and aromatic ring centroids.

Value

The function returns a dataframe with as many rows as methionyl residues are found in the protein. The distances in <U+00E5>ngstr<U+00F6>ms to the closest tyrosine, phenylalanine and triptophan are given in the columns, as well as the number of S-aromatic motifs detected with each of these amino acids. Also a raw distance matrix can be provided.

Details

For each methionyl residue this function computes the distances to the closest aromatic ring from Y, F and W. When that distance is equal or lower to the threshold, it will be computed as a S-aromatic motif.

References

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

See Also

saro.motif(), saro.geometry()

Examples

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