Protein Properties
A protein's amino acid sequence already determines many measurable properties. They are computed from the sequence alone, so they are quick to get and useful for planning experiments, but they are estimates, not measurements.
The properties
| Property | Meaning and use |
|---|---|
| Molecular weight | The sum of the amino-acid residue masses plus one water, in daltons (kDa = 1,000 Da). Compare it with the band on an SDS-PAGE gel or a mass spectrum. |
| Isoelectric point (pI) | The pH at which the protein has no net charge. Below the pI it is net positive, above it net negative. It guides ion-exchange chromatography and isoelectric focusing, and proteins are least soluble near their pI. |
| Net charge vs pH | The whole curve from pH 0 to 14; the pI is where it crosses zero. Use it to choose a buffer pH that gives the charge you want. |
| GRAVY | Grand average of hydropathy: the mean Kyte–Doolittle value of all residues. Positive means water-avoiding (hydrophobic, often membrane proteins), negative means water-loving. |
| Instability index | A score from the pairs of neighbouring residues (Guruprasad 1990, as in ExPASy). Below 40 is predicted stable, above 40 unstable. It estimates stability in a test tube, not inside a cell. |
| Aliphatic index | The relative volume of the aliphatic side chains Ala, Val, Ile and Leu (Ikai 1980). Higher values are associated with thermostable proteins. |
| Extinction coefficient ε280 | How strongly the protein absorbs light at 280 nm, from its tryptophan, tyrosine and disulfide-bonded cysteine content (5,500 × Trp + 1,490 × Tyr + 125 × cystine). Concentration (M) = A280 ÷ ε280 for a 1 cm path. |
Secondary structure and membrane helices
The Chou–Fasman propensities describe how much each amino acid favours helix or sheet. The tool reports the whole-sequence average, a rough tendency, not a residue-by-residue prediction (the original method is only about 50–60% accurate). Transmembrane helices are candidates where a 19-residue window has an average Kyte–Doolittle hydropathy of at least 1.6; the rule finds some but not all helices (5 of the 7 in bacteriorhodopsin), so confirm with TMHMM or DeepTMHMM. The signal peptide check looks for the typical N-terminal pattern and is only a hint; use SignalP to be sure.
How Aaron's Archive does it
The mass, pI (using the same pK values as ExPASy), charge, GRAVY, instability index and extinction coefficient were compared with Biopython's ProtParam on several hundred proteins and agree. Ubiquitin gives pI 6.56, the ExPASy value.
Pitfalls
Computed properties ignore folding, modifications such as phosphorylation, and cofactors, so real pI, charge and stability can differ. Use them to plan, then measure.
Common questions about protein properties
How is the extinction coefficient calculated?
At 280 nm it is the sum of the contributions of tryptophan (5,500), tyrosine (1,490) and cystine (125) residues, in M-1cm-1. A protein with 3 tyrosines and no tryptophan or cysteine is 3 × 1,490 = 4,470.
What does an instability index above 40 mean?
A rule of thumb from comparing stable and unstable proteins: values above 40 suggest the protein may be unstable in a test tube. It is a prediction, not a measurement.
What is a negative GRAVY?
The average hydropathy of the residues is below zero, so the protein leans hydrophilic. Strongly positive values lean hydrophobic, as in membrane proteins.
Where can I calculate these?
Use the protein property calculator.