PepPlot plots measures of protein secondary structure and hydrophobicity in parallel panels of the same plot.
PepPlot shows several common measures of protein secondary structure together on one coordinated plot. Most of the curves are the average, sum, or product of some residue-specific attribute within a window. In a few cases, the attribute is both specific to the residue and dependent on its position in the window. Throughout the plot, the blue curves are for beta-sheets and the red curves are for alpha-helices; black is used for turns and hydropathy. If your plotter does not have four colors, then dashed lines are for alpha-helix and solid lines are for beta-structures.
This document is only a description of what PepPlot does. You may want to read some of the articles cited below to help you interpret what the curves really mean.
There are ten different panels that can be plotted in any combination and in any order. In the descriptions below they are referred to from top to bottom as if you had plotted them all in the default order as in the example session and figure.
The first part of the plot shows the sequence itself. This panel is extremely crowded if you use a density of more than 100 residues per page.
The second part of the plot shows a schematic representation of the sequence. Each residue is represented by a line at the position where it occurs in the sequence. The lengths and colors of the lines are used to indicate chemically similar groups of amino acids as follows.
Color Category
Green hydrophilic, charged
down = acidic
up = basic
Red hydrophilic, uncharged
short = amides
long = alcohols
Blue hydrophobic
short = aliphatic
long = aromatic
Black Proline
Unmarked Alanine, Glycine, Cysteine
The third panel is a display of the residues that are beta-sheet forming and breaking as defined by Chou and Fasman (Adv. Enz. 47; 45-147 (1978)). To nucleate beta-structures, there should be at least three beta-forming residues and not more than one breaking residue within a window of five.
The fourth panel of the plot shows the Chou and Fasman (1978 cited above) propensity measures for alpha-helix and beta-sheet. As each curve rises past the threshold for its color, it satisfies one criterion for propagation of an alpha-helix or beta-sheet structure. If the curves for alpha and beta propagation drop below the black threshold (at value of the 1.00 level) and if there is at least one breaking residue in four, then the structure may terminate. Both curves are the average of a residue-specific attribute over a window of four.
The fifth panel shows the residues that are alpha-helix forming and breaking, as defined by Chou and Fasman (1978 cited above). For alpha-helices to nucleate, there should be four or more alpha-forming residues and not more than one breaking residue within six residues.
The sixth panel shows regions of the sequence that resemble sequences typically found at the amino end of alpha-helices and beta-structures (Chou and Fasman, 1978 cited above). The curves plot the probabilities for a window of six that the first three residues in the window precede the end of the structure and the last three residues are within the structure. There are two different residue-specific attributes used, one for each half of the product.
The seventh panel shows regions of the sequence typically found at the carboxyl end of alpha-helices and beta-structures (Chou and Fasman, 1978 cited above). The two curves show the probability for a window of six that the first three residues in the window are within the structure and the last three residues are outside the structure. Two different residue-specific attributes are used, one for each half of the product.
The eighth panel shows regions of the sequence typically found in turns (Chou and Fasman, 1978 cited above). The curve is the product of a residue-specific, position-dependent attribute (probability) multiplied across a window of four. The calculated values are multiplied by 10,000 for plotting.
The ninth panel shows the helical hydrophobic moment at each position of the sequence. These curves rise when the molecule forms either an alpha-helix or a beta-sheet at the interface between the solvent and the interior of the molecule. Said another way, the moment statistic is the probability that the sequence at each position is amphiphilic, that is, it appears to have hydrophobic residues on one side and hydrophilic residues on the other. The hydrophobic moment is calculated as described by Eisenberg et al. (Proc. Natl. Acad. Sci. USA 81; 140-144 (1984)), except that we have normalized the hydrophobic moment for the local hydrophobicity of the amino acids in the window where the moment is being determined. This makes the method equivalent to that described by Finer-Moore and Stroud (Proc. Natl. Acad. Sci. USA, 81; 155-159 (1984)).
In a typical alpha-helix, each residue is oriented about 100 degrees from the preceding residue. The alpha moment that we plot in this panel is the maximum for all inter-residue angles between 95 and 105 degrees The alpha moment curve is calculated for a window of eight residues.
Typical beta-strands have 160 degrees of rotation between adjacent residues. The beta hydrophobic moment curve is the maximum for all inter-residue angles between 159 to 161 degrees calculated over a window of six residues.
The tenth panel has two curves based on the average hydrophobicity. The black curve is the Kyte and Doolittle hydropathy measure (J. Mol. Biol. 157; 105-132 (1982)). This curve is the average of a residue-specific hydrophobicity index over a window of nine residues. When the line is in the upper half of the frame, it indicates a hydrophobic region, and when it is in the lower half, a hydrophilic region. You can set the Kyte-Doolittle window to a number other than nine using -HWINdow=n.
The green curve in the tenth panel is the Goldman, Engelman, and Steitz (GES) curve for identifying nonpolar transbilayer helices (reviewed in Ann. Rev. Biophys. Biophys. Chem. 15; 321-353 (1986)). The curve is the average of a residue-specific hydrophobicity scale (the GES scale) over a window of 20 residues. When the line is in the upper half of the frame, it indicates a hydrophobic region and when it is in the lower half, a hydrophilic region. You can suppress the GES curve in this panel with -NOGES. You can set the GES window to a number other than 20 with -GESWindow=n.
Using -GARnier, secondary structure prediction using the method of Garnier, et al. (J. Mol. Biol. 120; 97-120 (1978)) can also be calculated by PepPlot and written into a file.
PepPlot uses dashed lines when four-color plotting is not available. Alpha curves are red when color is available, dashed in black and white. Beta curves are blue in color, solid in black in white. In the hydrophilicity panel, the GES curve is green if color is available and dashed otherwise. In the residue schematic, hydrophilic and charged residues are red and green in the color plot and dashed in black and white. Hydrophobic residues are blue in color and solid in black and white.
There are three threshold lines across the Chou-Fasman panel (panel D). From top to bottom, these lines are as follows: the blue line is the threshold for the beginning of a beta-sheet; the red line is the threshold for the beginning of an alpha-helix; and the black line is the breaking line below which either kind of structure is no longer predicted. In black and white these lines are solid, short dashed, and long dashed, respectively.
PepPlot was written by Drs. Michael Gribskov and John Devereux of the Genetics Computer Group. It was first described in Nucl. Acids Res. 14(1); 327-334 (1986). The original code was revised by John Devereux to support command-line control for Version 5 and to support plotting the panels independently for Version 6.
You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.