Amino Acid Properties
Reference table for all 20 standard amino acids. These are the exact values used in BenchCalc's peptide analysis tools. Click column headers to sort.
| Amino Acid | 1-Letter | 3-Letter | Residue Mass (Da) | Side Chain pKa | Hydropathy | Category |
|---|
Terminal Group pKa Values
Common Modifications
Data Sources
ℹ️ Frequently Asked Questions
What is residue mass?
Residue mass is the molecular weight of an amino acid minus one water molecule (18.015 Da). When amino acids form peptide bonds, one H₂O is lost per bond. To calculate peptide MW: sum all residue masses + one H₂O for the free termini.
Residue mass = Amino acid MW − H₂O (18.015 Da)
What is the difference between average and monoisotopic residue mass?
Average residue mass uses the weighted average of all naturally occurring isotopes. This is what you measure on lab balances and is appropriate for solution preparation and weighing.
Monoisotopic residue mass uses only the most abundant isotope of each element (¹²C = 12.000, ¹H = 1.00783, ¹⁴N = 14.003, ¹⁶O = 15.995, ³²S = 31.972). This corresponds to the M+0 peak in high-resolution mass spectrometry (LC-MS/MS, MALDI-TOF) and is the standard for peptide identification in proteomics.
Use the Average / Monoisotopic toggle above the table to switch between the two sets. For peptide MW calculation with both modes, see the Peptide Molecular Weight Calculator.
What is the Kyte-Doolittle hydropathy index?
A scale from −4.5 (most hydrophilic, Arg) to +4.5 (most hydrophobic, Ile). The GRAVY (Grand Average of Hydropathy) of a peptide is the mean of all its residue hydropathy values. Positive GRAVY indicates a hydrophobic peptide; negative GRAVY indicates hydrophilic.
Why use the IPC_peptide pKa set instead of textbook values?
The IPC_peptide pKa set was computationally optimized on 16,882 experimental peptide pI measurements using a basin-hopping algorithm. It achieves approximately 60% better accuracy than traditional textbook values (e.g., Lehninger) for peptide pI prediction (RMSD ~0.25 pH units).
Textbook pKa values are measured on isolated amino acids in solution, while the IPC_peptide values are calibrated to reflect the actual behavior of amino acids within peptide chains.
Which amino acids have ionizable side chains?
Seven amino acids have side chains that contribute to charge:
Basic (positive): His (pKa 6.018), Lys (pKa 10.517), Arg (pKa 12.503)
Acidic (negative): Asp (pKa 3.887), Glu (pKa 4.317)
Polar (negative): Cys (pKa 8.297), Tyr (pKa 10.071)
The remaining 13 amino acids have non-ionizable side chains and do not directly contribute to the net charge of the peptide.