The Protein Utilities palette consists of the common tools and options that are used with all of the Protein applications and utilities. When Protein Design, Protein MODELER, Protein Health or Profile Analysis are activated from the QUANTA Applications menu, the Protein Utilities palette is displayed.
D. Eisenberg, R.M. Weiss, T.C. Terwilliger, Nature 299, 371-374 (1982)
D. Eisenberg, R.M. Weiss, T.C. Terwilliger, Faraday Symp Chem Soc. 17, 109-120 (1982)
The Smoothed Ca Trace, Secondary Structure and Hydrophobic Moment tools on the Protein Utility palette are simplified representation of proteins which should help you to visualize the overall protein structure.
The vectors which are displayed by the Secondary Structure tool and used in several of the Protein Design utilities show the direction of a secondary structure element. The vectors are derived from the positions of the Ca atoms of all the residues in that secondary structure elment.The vector direction is the principle moment of the Ca atom coordinates and the vector is positioned so that it goes through the average position of the Ca atoms. The ends of the vector are the projection of the terminal Ca atoms onto the vector.
It is usually observed that the side chains of hydrophobic residues are oriented towards the interior of a protein. The hydrophobic moment of a residue is a vector whose length is proportional to the hydrophobicity of the residue and whose direction is dependent on the side chain orientation. The hydrophobic moment will generally point to the interior of the protein. The hydrophobic moments of several side chains can be summed to give some indication of the preferred orientation of the region of protein.
The hydrophobic moment vector of a residue is defined as having its origin at the position of the Ca atom. The vector length is proportional to the hydrophobicity of the residue (as taken from standard amino acid hydrophobicity scales). The direction of the hydrophobic vector is found by averaging the vectors from the Ca atom to all the non-hydrogen atoms in the side chain. If the residue hydrophobicity is negative (i.e., the residue is hydrophilic) the vector will point in the opposite direction to the side chain. Some hydrophobicity scales have all positive values, to use one of these for plotting hydrophobic moments the scale is adjusted by subtracting the average hydrophobicity value from the value for each individual amino acid.
The hydrophobic moment of a secondary structure element is defined as the sum of the hydrophobic moments for all residues in the element and the vector origin is the center of the secondary structure vector (i.e., the line you see drawn by the Secondary Structure tool).
The Protein Utilities palette contains tools that are used during various functions in Protein Design, Protein MODELER, Protein Health, and Profile Analysis.
This tool displays the Pick Range palette, you should pick the first and last residue of the required range on either the molecule or the sequence viewer. The selected range remains active, and the tool highlighted, until you pick the tool again.
This tool removes all atom identification labels that are displayed after picking atoms in the viewing area.
This tool prints information about a selected atom in the textport, such as atom name, atom number, and residue number.
This tool places the next picked atom at the center of the viewing area. The atom becomes the center of rotation for subsequent operations.
This tool calculates and changes the geometric center of displayed atoms and places the molecule in the center of the viewing area.
This tool resets the display so that all active and visible structures are completely viewable.
This tool displays the distance between two atoms picked in the viewing area.
This tool displays the angle between three atoms picked in the viewing area.
This tool displays the dihedral angle of four atoms picked in the viewing area.
This tool displays the labels from the geometry tools.
This tool removes the labels resulting from the distance, bond angle, and dihedral tools.
This tool toggles the display of the color legend in the viewing area that is located in the lower right corner of the viewing area.
This tool displays a smooth Ca trace through averaged coordinates from which the general fold of a protein is easily discerned. The color of the trace is taken from the current color of the Ca atoms.
This tool displays the general protein structure and vectors for only active molecules. Color 4 (yellow) is used for strands; color 8 (purple) is used for helixes.
This tool displays hydrophobic moment vectors for active molecules. Residue vectors for hydrophobic residues are color 14 (pink); hydrophilic residues are color 12 (pale blue); secondary structures are color 3 (red).
This tool displays the Torsion Table which list the torsion angles of all the active structures.
This option displays the Protein Utilities Options dialog box for changing variables for smooth Ca trace, secondary structure vectors, and hydrophobic moment and scales options.
This dialog box offers some protein-specific coloring and display schemes. The color schemes apply one color to each residue and have the same color for that residue in the structure and in the Sequence Viewer. The coloring on the molecule structure can be applied to every atom in the residue or to just the carbon atoms with the other atoms having their usual element color. This option can be toggled by checking the Color non-carbon atoms by element color type button.
If the current coloring or display was not set up via this utility then the Color File or Display File buttons are checked.
There are two different sets of coloring options for structures and sequences since most of the coloring schemes for structure are not applicable to sequences. Molecules can be colored by structural properties: the secondary structure, structural domain, solvent accessibility and residue environment and there is an option to color protein structures by the Sequence Classification. These structure property coloring schemes are explained in the chapters describing the analysis of the properties (the residue environment coloring scheme is explained in the Profile Analysis chapter). If the secondary structure coloring mode is selected for a protein whose secondary structure is not known, then it will be derived. However, the other properties take significantly longer to calculate and the appropriate utility should be used to calculate the property before using the coloring mode. If information is not available for a particular coloring scheme, the structure will be given a neutral color.
The sequence coloring modes of Hydrophobicity and Size color a residue according to a classification of amino acids types. The classification scheme is stored in the file $HYD_LIB/protein_param.dat under the keyword CLASS. Users can amend the classification or add new schemes by editing this file - see the Protein Parameter File Appendix for further information.
The homology coloring scheme is useful to show on the molecule structures and sequence viewer the regions of high and low homology. This complements the Match Residue tool in Align and Superpose, which highlights the homologous residues on the Sequence Viewer with vertical yellow bands. The criteria for homology is the same as is currently set in Align and Superpose by the Match Residues tool. The color scheme and the minimal score required for a residue to be colored as homologous can be changed in the Align and Superpose utility by selecting Homology Color from the Options dialog box.