This utility provides tools that assign secondary structures to proteins. By defining the secondary structure of a molecule, the shape of the molecule can be visualized. This is a two-step procedure; hydrogens bonds are calculated and then secondary structures are assigned based on the hydrogen bond patterns.
W. Kabsch and C. Sander, Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features, Biopolymers, 22, 2577 (1983)
Jane S. Richardson, The Anatomy and Taxonomy of Protein Structure, Advances in Protein Chemistry, 34, 167-218 (1981).
Richardson, J.S., Getzoff, D.C., and Richardson, D.C., Proceedings of the National Academy of Science, USA 75, 2574-2578 (1978).
In the method of Kabsch and Sanders hydrogen bonds are determined by an energy calculation. Minimum or maximum energy values for electrostatic interactions among the amide NH and CO are used to assign hydrogen bonds. This calculation requires the coordinates of the amide hydrogen atoms. If these coordinates are missing from the MSF, hydrogen bonds are calculated according to amide N-O cutoff distances and C-O-N angles.
The calculation uses the formula in Kabsch and Sander:1
| Eq. 1 |
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Where the coefficient values are:
| Eq. 2 |
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| Eq. 3 |
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The following conventions are used below in the secondary structure definitions:
Ca torsion for the ith residue is defined by Ca(i-1), Ca(i), Ca(i+1), and Ca(i+2)
hbond(i, j) is a hydrogen bond between the amide O of residue i and the amide N-H of residue j
The following types of secondary structures are recognized:
This utility calculates the secondary structures for the active MSFs. The tools and options in this palette are primarily designed to recalculate the assigned secondary structure using user-specified variables.
This tool calculates the hydrogen bonds between mainchain atoms for active molecules.
This tool toggles the display of hydrogen bonds. It can only be used after the hydrogen bonds have been calculated using Calculate Hydrogen Bonds, or hydrogen bonds have been added using Add Hydrogen Bond.
This tool adds a hydrogen bond between main chain donor or acceptor pairs. It will not add a hydrogen bond where one has already been calculated and is currently displayed, or between wrongly matched pairs of atoms. Two atoms must be picked. The tool remains active until it is deselected.
This tool deletes a hydrogen bond that has been calculated and displayed. Two atoms must be picked. The tool remains active until it is deselected.
This tool recalculates the secondary structures based on changes you may have made. Otherwise the default values are reread.
Sets the mode of action using only the Ca torsion angles in the analysis of the secondary structure.
This tool changes the secondary structure assignments for single residues or range of residues. The mode of the residue selection is determined by the next two tools.
The default for editing secondary structures is to edit single residues. These residues can be picked either from the sequence table or from the display.
This option selects single residues for editing secondary structures. This is the default mode for Assign Secondary Structure.
This option activates the Pick Range palette, which enables a range of residues to be selected for editing.
This tool displays the Secondary Structure Analysis Parameters dialog box for redefining the different cutoff parameters.
The dialog box shows the default options.
This tool displays the Color Secondary Structure dialog box from which you can change the default color designation for secondary structures.
This tool lists the secondary structure information to a file with the name MSFname_secstr.out. The column headings for the output are:
This tool lists the information about the secondary structure assignments to the textport. This information is the same as described in the previous tool.
This tool displays Secondary Structure Title dialog box for saving the secondary structure information to the MSF as extra information.
The dialog prompts for a title and uses the title default for the first analysis. Each change that is saved can be given a title. If you choose to overwrite existing data, the standard MSF Save Option dialog box is displayed.
This tool displays the Secondary Structure Title dialog box from which previously saved secondary structure information can be read. All saved titles are listed.
This tool exits the Analyze Secondary Structure palette.