The Biophysical Properties report is an optional type of Report view that can be generated on demand.
To open the Biophysical Properties report, do either of the following:
- Use the Report > Biophysical Properties from Document/Selection command.
- Use the View > Report > Show command or press the Report tab (
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). If the Biophysical Properties report is not current displayed, select it from the drop-down menu in the upper left corner of the Report view. If a Biophysical Properties report is not in the menu list, add it using the Add reports to this view tool (![]()
).
). If the Biophysical Properties report is not current displayed, select it from the drop-down menu in the upper left corner of the Report view. If a Biophysical Properties report is not in the menu list, add it using the Add reports to this view tool (
).An example Biophysical Properties report is shown below:
Each Property in the table is described below:
| Property | Description |
|---|---|
| MW [g/mol] | The molecular weight of the selected region. |
| Net charge [pH=7] | The pH-dependent sum of charges in a population of molecules. Protean 3D calculates the net charge for protein regions and amino acid residues, and assumes a pH of 7. |
| pI | The isoelectric point (the pH at which the residue carries no net electrical charge), calculated from pKa tables from Lehninger et al. (2005) . This calculation is available only for amino acid selections. |
| Average hydropathy | The Kyte-Doolittle hydropathy value, calculated using the method of Kyte, J. and Doolittle, R.F. (1982) . This calculation is available only for amino acid selections. |
| Aliphatic index | The relative volume occupied by aliphatic side chains (alanine, valine, isoleucine and leucine). See note below for reference. This calculation is available only for amino acid selections. |
| A280 (ox.) | The absorbance (optical density) for the residue in an oxidized environment. This value is affected by presence of disulfide bonds. See note below for reference. This calculation is available only for amino acid selections. |
| A280 (red.) | The absorbance (optical density) for the residue in a reduced environment. This value is affected by presence of disulfide bonds. See note below for reference. This calculation is available only for amino acid selections. |
| ε280 [M-¹cm-¹] | The extinction coefficient (amount of light a residue absorbs). Protean 3D assumes all Cys residues are reduced. See note below for reference. This calculation is available only for amino acid selections. |
| Instability index | An estimate of the stability of the protein in a test tube. A protein whose instability index is smaller than 40 is predicted as stable, while a value above 40 predicts that the protein may be unstable. This value is calculated using the method of Guruprasad et al. (1990) . |
For information about the tools available in this view, see Report view.
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