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Table 1 Physicochemical properties used by the FEATURE algorithm

From: The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications

Atom – based Residue – based Secondary structure – based
ATOM-TYPE-IS-C RESIDUE_NAME_IS_ALA SECONDARY_STRUCTURE1_IS_3HELIX
ATOM-TYPE-IS-CT RESIDUE_NAME_IS_ARG SECONDARY_STRUCTURE1_IS_4HELIX
ATOM-TYPE-IS-Ca RESIDUE_NAME_IS_ASN SECONDARY_STRUCTURE1_IS_5HELIX
ATOM-TYPE-IS-N RESIDUE_NAME_IS_ASP SECONDARY_STRUCTURE1_IS_BRIDGE
ATOM-TYPE-IS-N2 RESIDUE_NAME_IS_CYS SECONDARY_STRUCTURE1_IS_STRAND
ATOM-TYPE-IS-N3 RESIDUE_NAME_IS_GLN SECONDARY_STRUCTURE1_IS_TURN
ATOM-TYPE-IS-Na RESIDUE_NAME_IS_GLU SECONDARY_STRUCTURE1_IS_BEND
ATOM-TYPE-IS-O RESIDUE_NAME_IS_GLY SECONDARY_STRUCTURE1_IS_COIL
ATOM-TYPE-IS-O2 RESIDUE_NAME_IS_HIS SECONDARY_STRUCTURE1_IS_HET
ATOM-TYPE-IS-OH RESIDUE_NAME_IS_ILE SECONDARY_STRUCTURE1_IS_UNKNOWN
ATOM-TYPE-IS-S RESIDUE_NAME_IS_LEU SECONDARY_STRUCTURE2_IS_HELIX
ATOM-TYPE-IS-SH RESIDUE_NAME_IS_LYS SECONDARY_STRUCTURE2_IS_BETA
ATOM-TYPE-IS-OTHER RESIDUE_NAME_IS_MET SECONDARY_STRUCTURE2_IS_COIL
ATOM-NAME-IS-ANY RESIDUE_NAME_IS_PHE SECONDARY_STRUCTURE2_IS_HET
ATOM-NAME-IS-C RESIDUE_NAME_IS_PRO SECONDARY_STRUCTURE2_IS_UNKNOWN
ATOM-NAME-IS-N RESIDUE_NAME_IS_SER  
ATOM-NAME-IS-O RESIDUE_NAME_IS_THR  
ATOM-NAME-IS-S RESIDUE_NAME_IS_TRP  
ATOM-NAME-IS-OTHER RESIDUE_NAME_IS_TYR  
HYDROXYL RESIDUE_NAME_IS_VAL  
AMIDE RESIDUE_NAME_IS_HOH  
AMINE RESIDUE_NAME_IS_OTHER  
CARBONYL CLASS1_IS_HYDROPHOBIC  
RING-SYSTEM CLASS1_IS_CHARGED  
PEPTIDE CLASS1_IS_POLAR  
  CLASS1_IS_UNKNOWN  
  CLASS2_IS_NONPOLAR  
  CLASS2_IS_POLAR  
  CLASS2_IS_BASIC  
  CLASS2_IS_ACIDIC  
  CLASS2_IS_UNKNOWN  
  PARTIAL-CHARGE  
  VDW-VOLUME  
  CHARGE  
  CHARGE-WITH-HIS  
  NEG-CHARGE  
  POS-CHARGE  
  HYDROPHOBICITY  
  MOBILITY  
  SOLVENT-ACCESSIBILITY  
  1. In order to represent a local microenvironment, FEATURE determines the value of physicochemical properties in each of six concentric, spherical shells centered on the site of interest. Properties include those at the atom level, residue level, and secondary structure level.