R: Calculate Mainchain and Sidechain Torsion/Dihedral Angles

torsion.pdb {bio3d} | R Documentation

## 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")

[Package bio3d version 2.4-0 Index]