torsion.pdb {bio3d}

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.

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.

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.

Note

For the protein backbone, or main-chain atoms, the partial double-bond character of the peptide bond between ‘C=N’ atoms severely restricts internal rotations. In contrast, internal rotations around the single bonds between ‘N-CA’ and ‘CA-C’ are only restricted by potential steric collisions. Thus, to a good approximation, the backbone conformation of each residue in a given polypeptide chain can be characterised by the two angles phi and psi.

Sidechain conformations can also be described by angles of internal rotation denoted chi1 up to chi5 moving out along the sidechain.

Author(s)

Barry Grant

References

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

See Also

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

Examples

# 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")