Table 2.

Quantitative physicochemical amino acid properties

Category/Property	Symbol	Reference	Descriptiona
Hydrophobicity
Hydropathy	h	[54]	The hydrophilic and hydrophobic inclinations of a given residue side chain in terms of transfer of free energy.
Surrounding hydrophobicity	Hp	[55]	The average sum of residue hydrophobic indices within an optimum sphere of 8 Å radius around a residue in protein crystals (kcal/mol).
Thermodynamic transfer hydrophobicity	Ht	[56]	The experimental values of Noazaki & Tanford [57] combined with values of Zimmerman et al. [58] adjusted to the same scale (kcal/mol).
Ionization Constants
Equilibrium constant	pK'	[56]	The ionizable character of the carboxyl group (pH units).
Isoelectric point	pHi	[58]	The isoionic point of the free amino acid, including the ionizable character of the entire residue (pH units).
Molecular Size & Composition
Bulkiness	Bl	[58]	The ratio of the side chain volume to length (i.e., the average cross section of the chain) (Å2).
Composition	c	[59]	The atomic weight ratio of the non-carbon elements in the end groups or rings to carbons in the side chain.
Molecular weight	Mw	[60]	The mass of the atoms constituting the residue.
Partial specific volume	V0	[61]	The reciprocal of density (m3 mol-1 × 10-6).
Non-bonded Energy
Long range energy	El	[62]	The energy between two amino acids separated further than 10 residues (i.e., due to electrostatic and Van der Waals forces) (kcal/mol).
Short and medium range energy	Esm	[62]	The sum of the energy between 1) main chain atoms of a residue and its own side chain atoms, and 2) two residues located within 10 residues along the chain (kcal/mol).
Total non-bonded energy	Et	[62]	Sum of average short, medium, and long range non-bonded energies (kcal/mol).
Polarity & Polarizability
Polar requirement	Pr	[63]	The slope of the line regressing log RM and the mol fraction of water in the pyrimidine-water solvent (RM = 1/RF - 1, where RF is the chromatographic index [58]).
Polarity	p	[59]	The average of Pr and PA (PA = 13.66 - 14.85RF).
Refractive index	μ	[55]	The measure of the polarizability of a residue (i.e., the reciprocal measure of its electrical stability under an external field).
Secondary Structure
Alpha-helical tendency	Pα	[64]	The average intrinsic property of a residue to adopt an alpha-helical conformation.
Beta-structure tendency	Pβ	[64]	The average intrinsic property of a residue to adopt a beta-sheet conformation.
Coil tendency	Pc	[65]	A measure of the tendency that a particular residue will be found in a coil secondary structure.
Helical contact area	Ca	[66]	The maximum area loss that could occur in going from an isolated α-helix to a fully buried environment in the complex (Å2).
Turn tendency	Pt	[64]	The average intrinsic property of a residue to adopt a beta-turn conformation.
Solvent Accessibility
Solvent accessibility reduction ratio	Ra	[67]	The ratio of solvent accessibility: the solvent accessibility of a residue in a hypothetically extanded state over its accessibility in a native folded protein.
Tertiary Structure
Average number of surrounding residues	Na	[67]	The average number of residues surrounding a residue within the effective distance of influence.
Buriedness	Br	[61]	The average propensity of a residue to be found in the interior of a protein.
Compressibility	K0	[61]	The relative increase in the volume of the system per unit decrease in pressure (m3 mol-1 Pa-1 × 10-15).
Mean rms fluctuational displacement	F	[68]	The relationship between the average amount of root-mean-square displacement of a residue and its distance from the centroid of the protein (Å).

^a Properties without defined units are dimensionless.

Twenty-five amino acid properties representative of the breadth of amino acid property space.