ramachandran

Ramachandran plot for Protein Data Bank (PDB) data

Syntax

info = ramachandran(pdbID)

info = ramachandran(file)

info = ramachandran(pdbData)

info = ramachandran(___,Name=Value)

Description

info = ramachandran(pdbID) draws the Ramachandran plot for the protein specified by the Protein Data Bank (PDB) database identifier pdbID.

info = ramachandran(file) draws the Ramachandran plot for the protein stored in the PDB-formatted file specified by file.

info = ramachandran(pdbData) draws the Ramachandran plot for the protein stored in the PDB-formatted data specified by MATLAB^® structure pdbData.

info = ramachandran(___,Name=Value) specifies options using one or more name-value arguments in addition to the input arguments in previous syntaxes. For example, to compute and plot torsion angles for all chains, set Chain to "all".

Examples

Draw Ramachandran Plot

Draw the Ramachandran plot for the human serum albumin complexed with octadecanoic acid, which has a PDB database identifier of 1E7I.

ramachandran("1E7I");

Draw Ramachandran Plot for Specific Chain

To retrieve protein structure data for the human growth hormone from the PDB database, use the getpdb function. Save the information to a file.

pbd1a22 = getpdb("1a22",ToFile="1a22.pdb");

Compute the torsion angles and draw the Ramachandran plot for chain A of the human growth hormone, which is represented in the PDB file 1a22.pdb.

pbd1a22ChainA = ramachandran("1a22.pdb",Chain="A")

pbd1a22ChainA = struct with fields:
         Angles: [191×3 double]
     ResidueNum: [191×1 double]
    ResidueName: {191×1 cell}
          Chain: 'A'
        HPoints: [1×1 Line]

Draw Ramachandran Plots with Highlighted Glycine Residues and Ramachandran Regions

To retrieve protein structure data for the human growth hormone from the PDB database and store the information in a structure, use the getpdb function.

struct1a22 = getpdb("1a22");

Draw a combined Ramachandran plot for all chains of the human growth hormone represented in the PDB structure struct1a22. Highlight the glycine residues with a circle. Draw the reference Ramachandran regions in the plot.

ramachandran(struct1a22,Chain="all",...
    Glycine=true,Regions=true);

To display a data tip with information about the residue, click a data point. To display a data tip defining a region, click the region. To display multiple data tips, press and hold the Alt key.

Draw a separate Ramachandran plot for each chain of the human growth hormone represented in the PDB structure struct1a22. Highlight the glycine residues with a circle. Draw the reference Ramachandran regions in the plot.

ramachandran(struct1a22,Chain="all",Plot="separate",...
    Glycine=true,Regions=true);

Write Tab-Delimited Report File from Ramachandran Structure

Create an array of two structures containing torsion angles for chains A and D in the Calcium/Calmodulin-dependent protein kinase, which has a PDB database identifier of 1hkx.

a = ramachandran("1hkx",Chain=["A","D"])

a=1×2 struct array with fields:
    Angles
    ResidueNum
    ResidueName
    Chain
    HPoints

Write a tab-delimited report file containing torsion angles phi (Φ) and psi (Ψ) for chains A and D in the Calcium/Calmodulin-dependent protein kinase.

fid = fopen("rama_1hkx_report.txt","wt");
for c = 1:numel(a)
    for i = 1:length(a(c).Angles)
        if ~all(isnan(a(c).Angles(i,:)))
            fprintf(fid,"%s\t%d\t%s\t%f\t%f\n",a(c).Chain,...
                a(c).ResidueNum(i),a(c).ResidueName{i},...
                a(c).Angles(i,1:2));
        end
    end
end
fclose(fid);

Open the file you created.

edit rama_1hkx_report.txt

Input Arguments

pdbID — Unique identifier for protein structure record in PDB database

character vector | string scalar

Unique identifier for protein structure record in PDB database, specified as a character vector or string scalar.

Each structure in the PDB database is represented by a four-character alphanumeric identifier. For example, the identifier for hemoglobin is 4hhb.

file — Filename with or without path

character vector | string scalar

Filename with or without path, specified as a character vector or string scalar.

The referenced file is a PDB-formatted file. If you specify only a filename, that file must be on the MATLAB search path or in the MATLAB Current Directory.

pdbData — PDB-formatted data

MATLAB structure

PDB-formatted data, specified as a MATLAB structure.

To get a MATLAB structure that contains PDB-formatted data, use the getpdb or pdbread functions.

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: ramachandran("1a22",Glycine=true,Regions=true);

Chain — Chains

"all" (default) | character vector | cell array of character vectors | string array

Chains, specified as "all" or a character vector, cell array of character vectors, or string array.

To compute and plot the torsion angles for all chains, use "all".

To specify one or more case-sensitive chain IDs, use a character vector, cell array of character vectors, or string array.

Plot — How to plot chains

"combined" (default) | "separate" | "none"

How to plot chains, specified as "combined", "separate", or "none".

• "combined" — Plot torsion angles for all specified chains in one combined plot.

• "separate" — Plot torsion angles for all specified chains in separate plots.

• "none" — Plot nothing.

Model — Structure model

1 (default) | integer

Structure model to consider, specified as an integer.

Glycine — Highlighting of glycine residues

false (default) | true

Highlighting of glycine residues with a circle in the plot, specified as true or false.

Regions — Drawing of Ramachandran reference regions

false (default) | true

Drawing of Ramachandran reference regions in the plot, specified as true or false.

The default regions are core right-handed alpha, core beta, core left-handed alpha, and allowed. The core regions correspond to data points of preferred values of psi/phi angle pairs. The allowed regions correspond to possible, but disfavored values of psi/phi angle pairs, based on simple energy considerations. The boundaries of these default regions are based on the calculations by Morris et al., 1992.

The default colormap uses red for core regions and yellow for allowed regions.

RegionDef — Custom reference region information

MATLAB structure | array of MATLAB structures

Custom reference region information in a Ramachandran plot, specified as a MATLAB structure or array of structures. Each structure must contain these fields:

• Name — Name of the region, specified as a character vector or string scalar.

• Color — Color of the region in the plot, specified as a character vector, string scalar, or three-element numeric vector of RGB values.

• Patch — Boundary of the region, specified as a 2-by-N matrix of values. The first row of the matrix contains the torsion angle phi (Φ) values. The second row of the matrix contains the torsion angle psi (Ψ) values. N is the number of data points needed to define the region. When you plot the psi/phi angle pairs, the data points specify the boundary of the region.

To specify multiple regions, use an array of structures. When a larger region contains or covers a smaller region, list the structure for the smaller region first in the array so that the smaller region is plotted last and is visible in the plot.

Output Arguments

info — Information about torsion angles, residues, chains, and data points

MATLAB structure | array of MATLAB structures

Information about torsion angles, residues, chains, and data points, returned as a MATLAB structure or array of MATLAB structures. Each structure contains the fields described in this table.

Field	Description
Angles	Three-column matrix containing the torsion angles phi (Φ), psi (Ψ), and omega (ω) for each residue in the sequence, ordered by residue sequence number. The number of rows in the matrix is equal to the number of rows in the ResidueNum column vector, which can be used to determine which residue corresponds to each row in the Angles matrix. The Angles matrix contains a row for each number in the range of residue sequence numbers, including residue sequence numbers missing from the PDB file. Rows corresponding to residue sequence numbers missing from the PDB file contain the value NaN.
ResidueNum	Column vector containing the residue sequence numbers from the PDB file. The ResidueNum vector starts with one of the following: The lowest residue sequence number if the lowest residue sequence number is negative or zero The number 1 if the lowest residue sequence number is positive The ResidueNum vector ends with the highest residue sequence number and includes all numbers in the range, including residue sequence numbers missing from the PDB file. The angles listed in the Angles matrix are in the same order as the residue sequence numbers in the ResidueNum vector. You can use the ResidueNum vector to determine which residue corresponds to each row in the Angles matrix.
ResidueName	Column vector containing the residue names for the protein.
Chain	Character vector or string specifying the chains in the protein.
HPoints	Handle to the data points in the plot.

More About

Ramachandran Plot

A Ramachandran plot is a plot of the torsion angle phi, Φ, (torsion angle between the C-N-CA-C atoms) versus the torsion angle psi, Ψ, (torsion angle between the N-CA-C-N atoms) for each residue of a protein sequence.

References

[1] Morris, A.L., MacArthur, M.W., Hutchinson, E.G., and Thornton, J.M. (1992). Stereochemical Quality of Protein Structure Coordinates. PROTEINS: Structure, Function, and Genetics 12, 345–364.

Version History

Introduced before R2006a