ptm (version 0.2.2)

stru.part: Partition of Structural Regions

Description

Carries out a partition of the structural regions of a given protein.

Usage

stru.part(pdb, cutoff = 0.25)

Arguments

pdb

is either a PDB id, or the path to a pdb file

cutoff

accessibility below which a residue is considered to be buried.

Value

A dataframe where each residue is assigned to one of the four structural groups considered.

Details

The accessibilities of a residue computed in the complex (ACCc) and in the monomer (ACCm) allow to distinguish four structural regions as follows.

Interior: ACCc < cutoff & (ACCm - ACCc) = 0.

Surface: ACCc > cutoff & (ACCm - ACCc) = 0.

Support: ACCm < cutoff & (ACCm - ACCc) > 0.

Rim: ACCc > cutoff & (ACCm - ACCc) > 0.

Core: ACCm > cutoff & ACCc < cutoff.

References

Levy (2010) J. Mol. Biol. 403: 660-670 (PMID: 20868694).

See Also

atom.dpx(), res.dpx(), acc.dssp()

Examples

# NOT RUN {
stru.part('1u8f')
# }