If a Protein Design result is open, the Details panel contains the following information:
Title
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The name of the Protein Design job. |
Summary
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- Structure – The name of the parent structure.
- Chain and Position – The names of the parent chains and residue ranges (for structures).
- Type – The component type.
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2D Structure
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The chemical structure of the new amino acid residue. If more than one residue has been changed, this section shows the number of changed residues, the specific changes and their positions. |
Biophysical Properties
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Displays the physical properties of a continuous selection, including:
- MW [g/mol] – The molecular weight of the selected region.
- Net charge – The pH-dependent sum of charges in a population of molecules. Protean 3D calculates the net charge for the selected 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 – The absorbance (optical density) for the residue, which 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.
Note: For aliphatic index, absorbance and extinction coefficient, see Gasteiger et al. (2005)|topic=Research References. In all three calculations, the sequence is treated as independent residues. There is no algorithmic dependence on length.
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Structural Properties
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For structures, displays the structural properties of a continuous selection, including:
- φ and ψ – The “phi” and “psi” dihedral angles in the backbones of the protein.
- Median B-factor – Reflects the fluctuation of atoms about their average positions, which is related to protein dynamics.
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Feature Details
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- experiment – Reports the tool and version, “predicted by Protein Design ($VERSION).
- delta_energy – The change in energy calculated between a variant and wild-type.
- potential – The energy function used to evaluate sequence perturbations, currently DFIRE-A (reference).
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Actions
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Click the links to:
- Export selection details to file – To save details related to the current selection.
- Copy 2D structure to clipboard – To copy the image in the 2D Structure section to the clipboard.
- Show [residue name] in Ligand Expo – To view the entry for the substitute residue on the Protein Data Bank (PDB) Ligand Expo website.
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