Data Item _pdbx_vrpt_instance_intra_plane_outliers.type

General

Item name
_pdbx_vrpt_instance_intra_plane_outliers.type
Category name
pdbx_vrpt_instance_intra_plane_outliers
Attribute name
type
Required in PDB entries
no
Used in currrent PDB entries
No

Item Description

The type of chiral problem that the label_atom_id has. One of: (A) "mainchain": The N label_atom_id of an amino acid residue is expected to be in the same plane as the Calpha, C, and O atoms of the previous residue. If the improper torsion angle of these atoms is more than 10 degrees, this is flagged as a planarity deviation. From mmcif item "_pdbx_validate_main_chain_plane". (B) "peptide": A deviation is flagged if the omega torsion angle of a peptide group differs by more than 30 degrees from the values expected for a proper cis or trans conformation (0 degrees and 180 degrees, respectively). For mmcif item: "_pdbx_validate_peptide_omega". (C) "sidechain": Certain groups of atoms in protein sidechains and nucleotide bases are expected to be in the same plane. An atom's deviation from planarity is calculated by fitting a plane through these atoms and then calculating distance of individual label_atom_id from the plane. Expected value of such distances have been pre-calculated from data analysis (wwPDB, 2012). If an label_atom_id is modelled to be more than six times farther than the pre-calculated value, the residue is flagged to have a sidechain planarity deviation. From mmcif item "_pdbx_validate_planes".

Data Type

Data type code
code
Data type detail
code item types/single words ...
Primitive data type code
char
Regular expression
[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*

Controlled Vocabulary

Allowed Value Details
mainchain
peptide
sidechain

Controlled Vocabulary at Deposition

Allowed Value Details
mainchain
peptide
sidechain

Aliases

Alias Item Name Dictionary Name Dictionary Version
_plane-outlier.type http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd V6.00