Table 7.20.4.

Predictive Features Used by PolyPhen-2

Feature	Source	Notes
Bond annotation	UniProtKB/Swiss-Prot annotation	Includes annotation codes DISULFID(disulfide bond), CROSSLNK(covalent link between proteins)
Functional site annotation	UniProtKB/Swiss-Prot annotation	Includes annotation codes BINDING(binding site for any chemical group), ACT_SITE(enzyme active site), METAL (binding site for a metal ion), LIPID(lipidated residue), CARBOHYD(glycosylated residue), MOD_RES(other covalent modification), NON_STD(non-standard amino acid), SITE (other interesting site)
Region annotation	UniProtKB/Swiss-Prot annotation	Includes annotation codes TRANSMEM(membrane-crossing region), INTRAMEM(membrane-contained region with no crossing), COMPBIAS(region with compositional bias), REPEAT(repetitive sequence motif or domain), COILED (coiled coil region), SIGNAL(endoplasmic reticulum targeting sequence), PROPEP(sequence cleaved during maturation)
PHAT score	PHAT trans-membrane specific matrix (Ng et al., 2000)	Measures effect of substitutions in trans-membrane regions; only used for positions annotated as trans-membrane.
PSIC score	PSIC software (Sunyaev et al., 1999)	See text for details.
Secondary structure annotation	DSSP database (Joosten et al., 2011)	Only used for sites that map to a 3-D structure.
Solvent-accessible surface area	DSSP database (Joosten et al., 2011)	Value in Å2. Only used for site that map to a 3-D structure.
Phi-psi dihedral angles	DSSP database (Joosten et al., 2011)	Only used for sites that map to a 3-D structure.
Normalized accessible surface area	Calculated by PolyPhen-2	Calculated by dividing the value retrieved from DSSP by the maximal possible surface area. The maximal possible surface area is defined by the 99th percentile of the surface area distribution for this particular amino acid type in PDB. Only used for sites that map to a 3-D structure.
Change in accessible surface propensity	Calculated by PolyPhen-2	Accessible surface propensities (knowledge-based hydrophobic “potentials”) are logarithmic ratios of the likelihood of a given amino acid occurring at a site with a particular accessibility to the likelihood of this amino acid occurring at any site (background frequency). Only used for sites that map to a 3-D structure.
Change in residue side chain volume	Calculated by PolyPhen-2	Value in Å3. Only used for sites that map to a 3-D structure.
Region of the phi-psi map (Ramachandran map)	Calculated by PolyPhen-2	Calculated from the dihedral angles retrieved from DSSP. Only used for sites that map to a 3-D structure.
Normalized B-factor	Calculated by PolyPhen-2	B-factor is used in crystallographic studies of macromolecules to characterize the “mobility” of an atom. It is believed that the values of B-factor of a residue may be correlated with its tolerance to amino acid substitutions (Chasman and Adams, 2001). Only used for sites that map to a 3-D structure.
Ligand contacts	Calculated by PolyPhen-2	Contacts of the query residue with heteroatoms, excluding water and “non-biological” crystallographic ligands that are believed to be related to the structure determination procedure rather than to the biological function of the protein. Only used for sites that map to a 3-D structure.
Interchain contacts	Calculated by PolyPhen-2	Contacts of the query residue with residues from other polypeptide chains present in the PDB file. Only used for sites that map to a 3-D structure.
Functional site contacts	Calculated by PolyPhen-2	Contacts of the query residue with sites annotated as BINDING, ACT_SITE, LIPID, or METALin the site annotation retrieved from UniProtKB. Only used for sites that map to a 3-D structure.