SSE Backbone Hydrogen Bonding

Usage

sse.bridges(sse, type="helix", hbond=TRUE, energy.cut=-1.0)

Arguments

sse
an sse object as obtained with dssp.
type
character string specifying ‘helix’ or ‘sheet’.
hbond
use hbond records in the dssp output.
energy.cut
cutoff for the dssp hbond energy.

Description

Determine backbone C=O to N-H hydrogen bonding in secondary structure elements.

Details

Simple functionality to parse the ‘BP’ and ‘hbond’ records of the DSSP output.

Requires input from function dssp with arguments resno=FALSE and full=TRUE.

Value

Returns a numeric matrix of two columns containing the residue ids of the paired residues.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples

# Read a PDB file pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") ) sse <- dssp(pdb, resno=FALSE, full=TRUE) sse.bridges(sse, type="helix")
[,1] [,2] [1,] 5 9 [2,] 6 10 [3,] 7 11 [4,] 8 12 [5,] 9 13 [6,] 10 14 [7,] 25 29 [8,] 26 30 [9,] 27 31 [10,] 28 32 [11,] 29 33 [12,] 30 34 [13,] 31 35 [14,] 32 36 [15,] 89 93 [16,] 90 94 [17,] 91 95 [18,] 92 96 [19,] 93 97 [20,] 94 98 [21,] 95 99 [22,] 109 113 [23,] 110 114

See also

read.pdb, dssp

Author

Lars Skjaerven