Curates a reference table for the 22 amino acids (20 standard + U + O) used
by pepVet scoring and validation utilities. The molecular_weight column
stores free amino acid monoisotopic masses rather than peptide residue
masses. Subtract the mass of water (18.01056 Da) to get residue-level
masses. The pKa_side_chain column stores conventional reference values for
the ionizable side chains C, D, E, H, K, R, Y, and U. Non-ionizable residues
are recorded as NA.
Format
A tibble with 22 rows and 6 variables:
- amino_acid
Single-letter amino acid code.
- molecular_weight
Free amino acid monoisotopic mass in daltons.
- residue_monoisotopic_mass
Residue monoisotopic mass in daltons, equal to
molecular_weight - 18.01056.- hydrophobicity
Kyte-Doolittle hydrophobicity value.
- pKa_side_chain
Conventional side-chain reference pKa, or
NAfor non-ionizable residues.- is_basic
Logical flag for basic residues H, K, and R.
Source
Hydrophobicity values follow Kyte J, Doolittle RF (1982). "A simple method for displaying the hydropathic character of a protein." Journal of Molecular Biology, 157(1), 105-132. doi:10.1016/0022-2836(82)90515-0 .
Monoisotopic masses follow the free amino acid convention used by ExPASy FindMod: https://web.expasy.org/findmod/findmod_masses.html.
Side-chain pKa values follow conventional reference values summarized by Thurlkill RL, Grimsley GR, Scholtz JM, Pace CN (2006). "pK values of the ionizable groups of proteins." Protein Science, 15(5), 1214-1218. doi:10.1110/ps.051840806 ; and Pace CN, Grimsley GR, Scholtz JM (2009). "Protein ionizable groups: pK values and their contribution to protein stability and solubility." Journal of Biological Chemistry, 284(20), 13285-13289. doi:10.1074/jbc.R800080200 .