bio3d (version 2.4-4)

torsion.pdb: Calculate Mainchain and Sidechain Torsion/Dihedral Angles

Description

Calculate all torsion angles for a given protein PDB structure object.

Usage

torsion.pdb(pdb)

Value

Returns a list object with the following components:

phi

main chain torsion angle for atoms C,N,CA,C.

psi

main chain torsion angle for atoms N,CA,C,N.

omega

main chain torsion angle for atoms CA,C,N,CA.

alpha

virtual torsion angle between consecutive C-alpha atoms.

chi1

side chain torsion angle for atoms N,CA,CB,*G.

chi2

side chain torsion angle for atoms CA,CB,*G,*D.

chi3

side chain torsion angle for atoms CB,*G,*D,*E.

chi4

side chain torsion angle for atoms *G,*D,*E,*Z.

chi5

side chain torsion angle for atoms *D,*E,*Z, NH1.

coords

numeric matrix of ‘justified’ coordinates.

tbl

a numeric matrix of psi, phi and chi torsion angles.

Arguments

pdb

a PDB structure object as obtained from function read.pdb.

Author

Barry Grant

Details

The conformation of a polypeptide chain can be usefully described in terms of angles of internal rotation around its constituent bonds. See the related torsion.xyz function, which is called by this function, for details.

References

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

See Also

torsion.xyz, read.pdb, dssp, stride.

Examples

# \donttest{
# PDB server connection required - testing excluded

##-- PDB torsion analysis
pdb <- read.pdb( "1bg2" )
tor <- torsion.pdb(pdb)
head(tor$tbl)

## basic Ramachandran plot
plot(tor$phi, tor$psi)

## torsion analysis of a single coordinate vector 
#inds <- atom.select(pdb,"calpha")
#tor.ca <- torsion.xyz(pdb$xyz[inds$xyz], atm.inc=1)

##-- Compare two PDBs to highlight interesting residues
aln <- read.fasta(system.file("examples/kif1a.fa",package="bio3d"))
m <- read.fasta.pdb(aln)
a <- torsion.xyz(m$xyz[1,],1)
b <- torsion.xyz(m$xyz[2,],1)
d <- wrap.tor(a-b)
plot(m$resno[1,],d, typ="h")
# }