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

`SeqAA`	Amino acid sequence. Enter any of the following: Character vector or string containing 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`
`PropertyTitleValue`	Character vector or string that specifies the property to plot. Default is `Hydrophobicity (Kyte & Doolittle)`. To display a list of properties to plot, enter an empty character vector or empty string for `PropertyTitleValue`. For example, type: proteinpropplot(sequence, 'propertytitle', '') Tip To access references for the properties, view the `proteinpropplot` file.
`StartatValue`	Integer that specifies the starting point for the plot from the N-terminal end of the amino acid sequence `SeqAA`. Default is `1`.
`EndatValue`	Integer that specifies the ending point for the plot from the N-terminal end of the amino acid sequence `SeqAA`. Default is `length(SeqAA)`.
`SmoothingValue`	Character vector or string the specifies the smoothing method. Choices are: `linear` (default) `exponential` `lowess`
`EdgeWeightValue`	Value 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`.
`WindowLengthValue`	Integer 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 character vector or empty string for PropertyTitleValue. For example, type:

proteinpropplot(sequence, 'propertytitle', '')

Tip

To access references for the properties, view the proteinpropplot file.

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

Example 24. Plotting Hydrophobicity

Use the getpdb function to retrieve a protein sequence.
```
prion = getpdb('1HJM', 'SEQUENCEONLY', true);
```
Plot the hydrophobicity (Kyte and Doolittle, 1982) of the residues in the sequence.
```
proteinpropplot(prion)
```

Example 25. Plotting Parallel Beta Strand

Use the getgenpept function to retrieve a protein sequence.
```
s = getgenpept('aad50640');
```
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.

Version History

Introduced in R2007a