sse.bridges. bio3d 2.3-0

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

Author

Lars Skjaerven

SSE Backbone Hydrogen Bonding