If the active selection consists of one or more molecules, features or regions, the Details panel contains the following information:
Title
![]() |
The name or type of molecule, feature or region. If a region is selected, the text will read "Selected Region." |
Summary
![]() |
- Residues, Ligands, Water – The number of residues, ligands, and water molecules in the selection.
- Structure – The name of the parent structure.
- Chain and Position – The names of the parent chains and residue ranges (for structures).
- Sequence – Sequence name and positions of selected residues (for sequences).
|
Biophysical Properties
![]() |
Displays the physical properties of a continuous selection, including:
- MW [g/mol] – The molecular weight of the selected region.
- 1μg to pmol – The number of picomoles of protein in 1 microgram.
- 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 (GRAVY) – 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). This calculation is available only for amino acid selections and is made using the method of Gasteiger et al. (2005).
- 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).
- 1 mg/mL to A280 – Calculates protein concentration from absorbance, where A280 is the absorbance (optical density) for the residue. This calculation is affected by presence of disulfide bonds, and assumes the disulfide bonds are oxidized (formed). This calculation is made using the method of Gasteiger et al. (2005).
- 1 mg/mL to A280 (red.) – Same as above, but assumes all disulfide bonds have been reduced (broken).
- A280 to 1 mg/mL – Calculates the absorbance of a protein concentration, where A280 is the absorbance (optical density) for the residue. This calculation is affected by presence of disulfide bonds and assumes the disulfide bonds are oxidized (formed). This calculation is made using the method of Gasteiger et al. (2005).
- A280 to 1 mg/mL (red.) – Same as above, but assumes all disulfide bonds have been reduced (broken).
- ε280 [M-¹cm-¹] – The extinction coefficient (amount of light a residue absorbs). This calculation assumes all Cys residues are reduced and all disulfide bonds are oxidized (formed). This calculation is available only for amino acid selections and is made using the method of Gasteiger et al. (2005).
- ε280 [M-¹cm-¹] (red.) – Same as above, but assumes all disulfide bonds have been reduced (broken).
Note: For aliphatic index, absorbance and extinction coefficient, the sequence is treated as independent residues. There is no algorithmic dependence on length.
|
Structural Properties
![]() |
For structures, displays the structural properties of a continuous selection, including:
- Distance - displays the minimum distance in angstroms (Å) between a pair of residues or ligands. The interface displays the two atoms selected for the calculation. Distance is calculated for Model 1 only.
- Surface area in current selection – is displayed only when a surface|topic=The Surfaces Area has been applied to all or part of a selection. The display shows the area, in square Angstroms, for the part of the surface that is contained in the selection.
|
Features in Selection
![]() |
When available, displays a list of features located within the range of the current selection. Available information may include a list of Site names or Disulfide Bond names, and the numbers of Helices or Sheets in the selection. Click on any hyperlink to open details for that feature. |
Actions
![]() |
Click the link to export the data to a file. |
