Enum: LocalStructuralFeature

Fine-grained local three-dimensional features of protein structures, spanning super-secondary structural motifs, functional sites, and local geometric surface features. This is the curated, ontology-mapped analogue of the learned per-residue feature vocabularies produced by protein language models and their sparse-autoencoder interpretations. Members marked with the ontology_gap annotation have no suitable OBO term and are candidates for new ontology terms.

URI: valuesets:LocalStructuralFeature

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Permissible Values

Value	Title	Meaning	Description	Exact Mappings	Related Mappings	Broad Mappings	Obo Gap	Ontology Gap	Related Edam
POLYPEPTIDE_STRUCTURAL_MOTIF	polypeptide structural motif	SO:0001079	A recurring 3D structural element within the chain that does not form a stable globular unit (the general parent class for local motifs)
BETA_HAIRPIN	beta hairpin		Two adjacent antiparallel beta strands connected by a short loop or turn					true
BETA_BULGE	beta bulge	SO:0001107	A local disruption of beta-sheet hydrogen bonding across three residues
ASX_MOTIF	asx motif	SO:0001106	A five-residue motif nucleated by an Asp/Asn side chain (Asx)
NEST	polypeptide nest motif	SO:0001120	A motif of two consecutive residues forming an anion-binding concavity
COILED_COIL	coiled coil	SO:0001080	Two or more alpha helices wound together like strands of a rope	uniprot_core:Coiled_Coil_Annotation
HELIX_CAP	helix cap		N-cap or C-cap residue terminating an alpha helix					true
CATALYTIC_RESIDUE	catalytic residue	SO:0001104	An amino acid residue directly involved in enzyme catalysis (active site)		uniprot_core:Active_Site_Annotation
PROTEIN_BINDING_SITE	protein binding site	SO:0000410	A site that interacts selectively and non-covalently with polypeptide molecules			uniprot_core:Binding_Site_Annotation
DISULFIDE_BOND	disulfide bond		A covalent S-S bond between two cysteine residues	uniprot_core:Disulfide_Bond_Annotation			true
METAL_BINDING_SITE	metal binding site		A local site coordinating one or more metal ions			uniprot_core:Binding_Site_Annotation	true
POCKET	binding pocket		A concave, solvent-accessible surface depression that can accommodate a ligand					true	EDAM:data_1542
CLEFT	cleft		An elongated surface groove between structural elements or domains					true
CAVITY	interior cavity		An enclosed, solvent-inaccessible internal void within the structure					true	EDAM:data_1542
TUNNEL	tunnel / channel		An elongated, often buried, passage through the structure connecting two regions					true
GROOVE	groove		A surface channel, e.g. a nucleic-acid-binding groove					true
ELBOW	elbow / hinge		A localized bend or hinge between two structural elements or domains					true
KINK	helix kink		A localized bend interrupting the regular geometry of a helix					true
INTERFACE	interaction interface		A surface patch mediating contact with another chain or molecule					true

Slots

Name	Description
local_structural_feature	Local 3D structural feature, motif, site, or geometric feature

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/valuesets

LinkML Source

name: LocalStructuralFeature
instantiates:
- valuesets_meta:ValueSetEnumDefinition
description: Fine-grained local three-dimensional features of protein structures,
  spanning super-secondary structural motifs, functional sites, and local geometric
  surface features. This is the curated, ontology-mapped analogue of the learned per-residue
  feature vocabularies produced by protein language models and their sparse-autoencoder
  interpretations. Members marked with the ``ontology_gap`` annotation have no suitable
  OBO term and are candidates for new ontology terms.
title: Local Structural Feature
from_schema: https://w3id.org/valuesets
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: DRAFT
rank: 1000
permissible_values:
  POLYPEPTIDE_STRUCTURAL_MOTIF:
    text: POLYPEPTIDE_STRUCTURAL_MOTIF
    description: A recurring 3D structural element within the chain that does not
      form a stable globular unit (the general parent class for local motifs)
    meaning: SO:0001079
    title: polypeptide structural motif
  BETA_HAIRPIN:
    text: BETA_HAIRPIN
    description: Two adjacent antiparallel beta strands connected by a short loop
      or turn
    annotations:
      ontology_gap:
        tag: ontology_gap
        value: 'true'
    title: beta hairpin
  BETA_BULGE:
    text: BETA_BULGE
    description: A local disruption of beta-sheet hydrogen bonding across three residues
    meaning: SO:0001107
    title: beta bulge
  ASX_MOTIF:
    text: ASX_MOTIF
    description: A five-residue motif nucleated by an Asp/Asn side chain (Asx)
    meaning: SO:0001106
    title: asx motif
  NEST:
    text: NEST
    description: A motif of two consecutive residues forming an anion-binding concavity
    meaning: SO:0001120
    title: polypeptide nest motif
  COILED_COIL:
    text: COILED_COIL
    description: Two or more alpha helices wound together like strands of a rope
    meaning: SO:0001080
    title: coiled coil
    exact_mappings:
    - uniprot_core:Coiled_Coil_Annotation
  HELIX_CAP:
    text: HELIX_CAP
    description: N-cap or C-cap residue terminating an alpha helix
    annotations:
      ontology_gap:
        tag: ontology_gap
        value: 'true'
    title: helix cap
  CATALYTIC_RESIDUE:
    text: CATALYTIC_RESIDUE
    description: An amino acid residue directly involved in enzyme catalysis (active
      site)
    meaning: SO:0001104
    title: catalytic residue
    related_mappings:
    - uniprot_core:Active_Site_Annotation
  PROTEIN_BINDING_SITE:
    text: PROTEIN_BINDING_SITE
    description: A site that interacts selectively and non-covalently with polypeptide
      molecules
    meaning: SO:0000410
    title: protein binding site
    broad_mappings:
    - uniprot_core:Binding_Site_Annotation
  DISULFIDE_BOND:
    text: DISULFIDE_BOND
    description: A covalent S-S bond between two cysteine residues
    annotations:
      obo_gap:
        tag: obo_gap
        value: 'true'
    title: disulfide bond
    exact_mappings:
    - uniprot_core:Disulfide_Bond_Annotation
  METAL_BINDING_SITE:
    text: METAL_BINDING_SITE
    description: A local site coordinating one or more metal ions
    annotations:
      obo_gap:
        tag: obo_gap
        value: 'true'
    title: metal binding site
    broad_mappings:
    - uniprot_core:Binding_Site_Annotation
  POCKET:
    text: POCKET
    description: A concave, solvent-accessible surface depression that can accommodate
      a ligand
    annotations:
      ontology_gap:
        tag: ontology_gap
        value: 'true'
      related_edam:
        tag: related_edam
        value: EDAM:data_1542
    title: binding pocket
  CLEFT:
    text: CLEFT
    description: An elongated surface groove between structural elements or domains
    annotations:
      ontology_gap:
        tag: ontology_gap
        value: 'true'
    title: cleft
  CAVITY:
    text: CAVITY
    description: An enclosed, solvent-inaccessible internal void within the structure
    annotations:
      ontology_gap:
        tag: ontology_gap
        value: 'true'
      related_edam:
        tag: related_edam
        value: EDAM:data_1542
    title: interior cavity
  TUNNEL:
    text: TUNNEL
    description: An elongated, often buried, passage through the structure connecting
      two regions
    annotations:
      ontology_gap:
        tag: ontology_gap
        value: 'true'
    title: tunnel / channel
  GROOVE:
    text: GROOVE
    description: A surface channel, e.g. a nucleic-acid-binding groove
    annotations:
      ontology_gap:
        tag: ontology_gap
        value: 'true'
    title: groove
  ELBOW:
    text: ELBOW
    description: A localized bend or hinge between two structural elements or domains
    annotations:
      ontology_gap:
        tag: ontology_gap
        value: 'true'
    title: elbow / hinge
  KINK:
    text: KINK
    description: A localized bend interrupting the regular geometry of a helix
    annotations:
      ontology_gap:
        tag: ontology_gap
        value: 'true'
    title: helix kink
  INTERFACE:
    text: INTERFACE
    description: A surface patch mediating contact with another chain or molecule
    annotations:
      ontology_gap:
        tag: ontology_gap
        value: 'true'
    title: interaction interface