Step 6: Physical Properties of Your Protein
Now you have your protein identified and its history charted out, so you must be pretty excited about doing something with it! Here's one more quick site that deserves a mention. Northwestern University Medical School maintains a Basic Sciences web page with a lot of good tools on it. Their Oligonucleotide Properties calculator is very useful for working out primer designs, for instance. The pertinent one here, though, is the Protein Properties Calculator.
- Open the Basic Sciences page.
- Select "Protein Properties Calculator" in the text.
- Cut and paste your FASTA-formatted protein sequence into the window.
- Click "Calculate".
- The page will automatically calculate a molecular weight for you, as well as a volume and an extinction coefficient for determining concentrations with a UV spec (where E(280 nm) = concentration (M) divided by A280).
- Click "HydroPlot" and the page will automatically produce a plot showing the hydrophobic and hydrophilic areas of the sequence as below:
