bio3d (version 2.1-3)

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)

Arguments

pdb

a PDB structure object as obtained from function read.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.

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

##-- 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")