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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.