Table of Contents
Moment makes a contour plot of the helical hydrophobic moment of a peptide sequence.
Hydrophobic moment is the hydrophobicity of a peptide measured for different angles of rotation per residue. Moment helps you to recognize amphiphilic structures by identifying when the residues on one side of the structure are more hydrophobic than on the other. The hydrophobic moment is calculated for all angles of rotation from 0 to 180 degrees.
Hydrophobic moment was described by Eisenberg (Eisenberg et al., Proc. Natl. Acad. Sci. USA 81; 140-144 (1984)). It is a measure of the probability that the peptide at any particular position is located at the interface between the interior of the protein and the surface, or more exactly, that the peptide separates hydrophobic and hydrophilic regions. We have normalized the hydrophobic moment for the local hydrophobicity of the amino acids in the window where the moment is being determined, making the method equivalent to that described by Finer-Moore and Stroud (Proc. Natl. Acad. Sci. USA, 81; 155-159 (1984)).
Moment plots the height of the hydrophobic moment calculated for all possible angles of rotation for a window that you specify. The form of the plot is a set of contours (iso-moments). The contours should help identify peaks of hydrophobic moment at particular positions and angles of rotation.
Each residue in a typical alpha-helix is offset 100 degrees from the preceding residue. Typical beta-structures have 160 degrees between adjacent residues.
Here is a session using Moment to plot the hydrophobic moment for human adenylate kinase (PIR:Kihua):
MOMENT plot of what sequence ? PIR:Kihua
Begin (* 1 *) ?
End (* 194 *) ?
Plot how many contours [1-10](* 2 *) ?
What threshold for contour 1 (* 0.35 *) ?
What threshold for contour 2 (* 0.45 *) ?
What is the window size (* 10 *) ?
How many residues/page (* 194 *) ?
That will take 1 pages. Would you like to:
P)lot the hydrophobic moment
S)elect a different number of residues per page
G)et a different sequence file
Please select one (* P *):
The maximum hydrophobic moment is 0.61
The minimum hydrophobic moment is 0.00
When your LaserWriter attached to tty07 is ready, press <Return>.
If you are reading the Program Manual, the plot from this session is shown in the figure below.
Moment accepts a single protein sequence as input. If Moment rejects your protein sequence, turn to Appendix VI to see how to change or set the type of a sequence.
PepPlot shows the maximum hydrophobic moment for the range from 95 to 105 calculated in a window of 8 residues (alpha-helix) and from 159 to 161 calculated in a window of six residues (beta-sheet). PeptideStructure and PlotStructure together make plots of Chou and Fasman predictions along with measures of hydrophobicity, flexibility, antigenicity, and surface probability. HelicalWheel plots a peptide sequence as a helical wheel to help you recognize amphiphilic regions.
There cannot be more than 1,000 residues per page. There is a small error from recalculation of the window adjacent to the page boundaries. The hydrophobic moment calculation is only defined for protein sequences composed of the 20 standard amino acids shown in Appendix III.
Accelrys GCG (GCG) must be configured for graphics before you run any program with graphics output! If the % setplot command is available in your installation, this is the easiest way to establish your graphics configuration, but you can also use commands like % postscript that correspond to the graphics languages GCG supports. See Section 5, Using Graphics in the User's Guide for more information about configuring your process for graphics.
If you need to stop this program, use <Ctrl>C to reset your terminal and session as gracefully as possible. Searches and comparisons write out the results from the part of the search that is complete when you use <Ctrl>C. The graphics device should stop plotting the current page and start plotting the next page. If the current page is the last page, plotters should put the pen away and graphic terminals should return to interactive mode.
All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional.
Minimal Syntax: % moment [-INfile=]pir:kihua -Default
-BEGin=1 -END=194 sets the range of interest
-WINdow=10 sets the window for averaging
-NCONtours=2 sets the number of contours to plot
-CONTours=0.35,0.45 sets the threshold for each contour
-DENsity=194 sets the density in residues per page
-MENu=p chooses a plot from the menu
Local Data Files: None
All GCG graphics programs accept these and other switches. See the Using
Graphics section of the USERS GUIDE for descriptions.
-FIGure[=filename] stores plot in a file for later input to FIGURE
-FONT=3 draws all text on the plot using font 3
-COLor=1 draws entire plot with pen in stall 1
-SCAle=1.2 enlarges the plot by 20 percent (zoom in)
-XPAN=10.0 moves plot to the right 10 platen units (pan right)
-YPAN=10.0 moves plot up 10 platen units (pan up)
-PORtrait rotates plot 90 degrees
You can set the parameters listed below from the command line.
Sets the size of the sequence window within which the average helical hydrophobic moment is calculated.
Specifies the number of contours to plot.
Sets the maximum threshold for each contour plotted.
Specifies the plot density in units of residues per page.
Draws the plot without first offering you the opportunity to either select a new sequence or change the plot density.
The parameters below apply to all GCG graphics programs. These and many others are described in detail in Section 5, Using Graphics of the User's Guide.
Writes the plot as a text file of plotting instructions suitable for input to the Figure program instead of sending it to the device specified in your graphics configuration.
Draws all text characters on the plot using Font 3 (see Appendix I).
Draws the entire plot with the pen in stall 1.
The parameters below let you expand or reduce the plot (zoom), move it in either direction (pan), or rotate it 90 degrees (rotate).
Expands the plot by 20 percent by resetting the scaling factor (normally 1.0) to 1.2 (zoom in). You can expand the axes independently with -XSCAle and -YSCAle. Numbers less than 1.0 contract the plot (zoom out).
Moves the plot to the right by 30 platen units (pan right).
Moves the plot up by 30 platen units (pan up).
Rotates the plot 90 degrees. Usually, plots are displayed with the horizontal axis longer than the vertical (landscape). Note that plots are reduced or enlarged, depending on the platen size, to fill the page.
Printed: May 27, 2005 13:00
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