Table 2 Quantitative physicochemical amino acid properties

Hydrophobicity

   Hydropathy

The hydrophilic and hydrophobic inclinations of a given residue side chain in terms of transfer of free energy.

   Surrounding hydrophobicity

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

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

The ionizable character of the carboxyl group (pH units).

   Isoelectric point

The isoionic point of the free amino acid, including the ionizable character of the entire residue (pH units).

Molecular Size & Composition

   Bulkiness

The ratio of the side chain volume to length (i.e., the average cross section of the chain) (Ų).

   Composition

The atomic weight ratio of the non-carbon elements in the end groups or rings to carbons in the side chain.

   Molecular weight

The mass of the atoms constituting the residue.

   Partial specific volume

The reciprocal of density (m³ mol^-1 × 10^-6).

Non-bonded Energy

   Long range energy

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

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

Sum of average short, medium, and long range non-bonded energies (kcal/mol).

Polarity & Polarizability

   Polar requirement

The slope of the line regressing log R _M and the mol fraction of water in the pyrimidine-water solvent (R _M = 1/R _F - 1, where R _F is the chromatographic index [58]).

   Polarity

The average of P _r and P _A (P _A = 13.66 - 14.85R _F ).

   Refractive index

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

The average intrinsic property of a residue to adopt an alpha-helical conformation.

   Beta-structure tendency

The average intrinsic property of a residue to adopt a beta-sheet conformation.

   Coil tendency

A measure of the tendency that a particular residue will be found in a coil secondary structure.

   Helical contact area

The maximum area loss that could occur in going from an isolated α-helix to a fully buried environment in the complex (Ų).

   Turn tendency

The average intrinsic property of a residue to adopt a beta-turn conformation.

Solvent Accessibility

   Solvent accessibility reduction ratio

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

The average number of residues surrounding a residue within the effective distance of influence.

   Buriedness

The average propensity of a residue to be found in the interior of a protein.

   Compressibility

The relative increase in the volume of the system per unit decrease in pressure (m³ mol^-1 P_a^-1 × 10^-15).

   Mean rms fluctuational displacement

The relationship between the average amount of root-mean-square displacement of a residue and its distance from the centroid of the protein (Å).