Table 1

Physicochemical properties used by the FEATURE algorithm

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


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.

Halperin et al. BMC Genomics 2008 9(Suppl 2):S2   doi:10.1186/1471-2164-9-S2-S2

Open Data