A selected region or strand - User Guide to Protean 3D - 17.3

If a region or single strand is selected in any of the views, the Details panel contains the following information:

Titles	The strand identifier or the words “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 – The name of the parent chain. Position – The sequence position.
Biophysical Properties	Displays the physical properties of the current selection, and may include: MW [g/mol] – The molecular weight of the selected region. Formal charge – The sum of formal charges in a molecule for a given electronic state. This is shown only for non-amino acid selections. 1μg to pmol – 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). 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)\|topic=Research References. 1 mg/mL to A₂₈₀ – Where A₂₈₀ is the absorbance (optical density) for the residue, which is affected by presence of disulfide bonds. See note below for reference. A₂₈₀ to 1 mg/mL – 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. 1 mg/mL to A₂₈₀ (red.) – A₂₈₀ to 1 mg/mL (red.) – ε₂₈₀ [M^-¹cm-¹] (red.) – Note: For aliphatic index, absorbance and extinction coefficient, see Gasteiger et al.. In all three calculations, the sequence is treated as independent residues. There is no algorithmic dependence on length.
Structural Properties	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.
Features in Selection	Sheet – The number of strands in the selections. Hypervariable – Click on the provided link to view information about the hypervariable region (HVR).
Actions	Click the link to export the data to a file.

Try it! – View details about a structure

A group of structures

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