proteinpropplot

Plot properties of amino acid sequence

Syntax

proteinpropplot (SeqAA)

proteinpropplot(SeqAA, ...'PropertyTitle', PropertyTitleValue, ...)
proteinpropplot(SeqAA, ...'Startat', StartatValue, ...)
proteinpropplot(SeqAA, ...'Endat', EndatValue, ...)
proteinpropplot(SeqAA, ...'Smoothing', SmoothingValue, ...)
proteinpropplot(SeqAA, ...'EdgeWeight', EdgeWeightValue, ...)
proteinpropplot(SeqAA, ...'WindowLength', WindowLengthValue, ...)

Arguments

SeqAAAmino acid sequence. Enter any of the following:
  • Character string of letters representing an amino acid

  • Vector of integers representing an amino acid, such as returned by aa2int

  • Structure containing a Sequence field that contains an amino acid sequence, such as returned by getembl, getgenpept, or getpdb

PropertyTitleValueString that specifies the property to plot. Default is Hydrophobicity (Kyte & Doolittle). To display a list of properties to plot, enter a empty string for PropertyTitleValue. For example, type:
proteinpropplot(sequence, 'propertytitle', '')
StartatValueInteger that specifies the starting point for the plot from the N-terminal end of the amino acid sequence SeqAA. Default is 1.
EndatValueInteger that specifies the ending point for the plot from the N-terminal end of the amino acid sequence SeqAA. Default is length(SeqAA).
SmoothingValueString the specifies the smoothing method. Choices are:
  • linear (default)

  • exponential

  • lowess

EdgeWeightValueValue that specifies the edge weight used for linear and exponential smoothing methods. Decreasing this value emphasizes peaks in the plot. Choices are any value ≥0 and ≤1. Default is 1.
WindowLengthValueInteger that specifies the window length for the smoothing method. Increasing this value gives a smoother plot that shows less detail. Default is 11.

Description

proteinpropplot (SeqAA) displays a plot of the hydrophobicity (Kyte and Doolittle, 1982) of the residues in sequence SeqAA.

proteinpropplot(SeqAA, ...'PropertyName', PropertyValue, ...) calls proteinpropplot with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:


proteinpropplot(SeqAA, ...'PropertyTitle', PropertyTitleValue, ...)
specifies a property to plot for the amino acid sequence SeqAA. Default is Hydrophobicity (Kyte & Doolittle). To display a list of possible properties to plot, enter an empty string for PropertyTitleValue. For example, type:

proteinpropplot(sequence, 'propertytitle', '')

proteinpropplot(SeqAA, ...'Startat', StartatValue, ...) specifies the starting point for the plot from the N-terminal end of the amino acid sequence SeqAA. Default is 1.

proteinpropplot(SeqAA, ...'Endat', EndatValue, ...) specifies the ending point for the plot from the N-terminal end of the amino acid sequence SeqAA. Default is length(SeqAA).

proteinpropplot(SeqAA, ...'Smoothing', SmoothingValue, ...) specifies the smoothing method. Choices are:

  • linear (default)

  • exponential

  • lowess

proteinpropplot(SeqAA, ...'EdgeWeight', EdgeWeightValue, ...) specifies the edge weight used for linear and exponential smoothing methods. Decreasing this value emphasizes peaks in the plot. Choices are any value ≥0 and ≤1. Default is 1.

proteinpropplot(SeqAA, ...'WindowLength', WindowLengthValue, ...) specifies the window length for the smoothing method. Increasing this value gives a smoother plot that shows less detail. Default is 11.

Examples

Plotting Hydrophobicity

  1. Use the getpdb function to retrieve a protein sequence.

    prion = getpdb('1HJM', 'SEQUENCEONLY', true);
  2. Plot the hydrophobicity (Kyte and Doolittle, 1982) of the residues in the sequence.

    proteinpropplot(prion)

Plotting Parallel Beta Strand

  1. Use the getgenpept function to retrieve a protein sequence.

    s = getgenpept('aad50640');
  2. Plot the conformational preference for parallel beta strand for the residues in the sequence.

    proteinpropplot(s,'propertytitle','Parallel beta strand')

References

[1] Kyte, J., and Doolittle, R.F. (1982). A simple method for displaying the hydropathic character of a protein. J Mol Biol 157(1), 105–132.

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