Chemistry
Life Sciences

Bacteriophage Head-Tail Connector Protein

Visualize and analyze a bacteriophage protein structure

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Install the ProteinVisualization paclet and load the package:

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PacletInstall["WolframChemistry/ProteinVisualization"];Needs["WolframChemistry`ProteinVisualization`"]

Visualize the structure of the bacteriophage head-tail connector protein as a ribbon diagram:

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BiomoleculePlot3D["1IJG",ViewPointAbove]

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Generate a 3D plot of the backbone atoms and bonds of the protein, and color code the atoms by amino acid residues:

In[3]:=

ProteinBackboneAtomPlot["1IJG",PlotTheme"SpaceFilling","ShowSideChains"False,ViewPointAbove]

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Show the α-carbon trace of the protein, color coded by chains:

In[4]:=

AlphaCarbonPathPlot3D["1IJG","BackboneColorRules"{"Chains",Automatic},ViewPointAbove]

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To highlight the planar geometry of peptide bonds, show the amide planes along with the backbone atoms and bonds of the protein:

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AmidePlanePlot["1IJG",PlotTheme"Tubes",ViewPointAbove]

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Highlight the planes that form dihedral angles ϕ and ψ to get residue information and dihedral angle values upon mouse hover:

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DihedralAnglePlot["1IJG",ViewPointAbove]

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Plot the dihedral angles ϕ and ψ on a Ramachandran plot:

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RamachandranPlot["1IJG","ResidueColors"True,ImageSize500,PlotStylePointSize[0.01]]

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Create a contact map displaying residue-residue distances:

In[8]:=

ProteinContactMap["1IJG","ShowResidues"True,ImageSize450]

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Visualize the residue-residue interactions within 8 Angstroms:

In[9]:=

ProteinContactGraphPlot["1IJG","CutOff"Quantity[8,"Angstroms"],"ScaledVertexSize"True,"EdgeColorFunction"True,ImageSize500,VertexSize30]

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External Links

Ramachandran Plot
1IJG

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Citation:
- Simpson, Alan A., et al. "Structure determination of the head–tail connector of bacteriophage ϕ29." Acta Crystallographica Section D: Biological Crystallography 57.9 (2001): 1260-1269.

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Contributed by: Soutick Saha

Wolfram Language Example Repository

Bacteriophage Head-Tail Connector Protein

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