saro.dist {ptm}

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 ångströms, 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.

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.

Value

The function returns a dataframe with as many rows as methionyl residues are found in the protein. The distances in ångströms 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.

Author(s)

Juan Carlos Aledo

References

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

See Also

saro.motif(), saro.geometry()

Examples

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