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Select a DNA-Protein Interface

Use the inputs below to select a particular DNA-protein interface to visualize. By default, only interactions with the DNA major groove, minor groove or bases are shown. To turn on backbone contacts, select specific secondary structure interactions, and set custom interaction criteria, click the show advanced options button below.


Interaction Options

Interaction Criteria

You may apply custom cut-off values to use for deciding which interactions to draw if you choose "custom" Interaction Criteria below. A nucleotide-residue interaction will be included if it meets the chosen criteria. To ignore a criteria, set it to zero or leave it blank. We reccomend using the default criteria for generic use cases.


Exclude Componenents

Use the lists below to select individual residues, nucleotides or SSEs you wish to exclude from the current visualizations. Note: nucleotides will still be drawn, but any interactions with exlcuded nucleotides will be ignored, this may remove additional residues.


Residue Contact Map Controls


Shape Overlay Plot Controls

min
max

Helical Contact Map Controls


Customize Labels

You can apply custom label formats to individual chains below, or to all DNA or Protein chains. Blank fields are ignored. To change the labels of individual nucleotides, residues or SSEs, simply double-click a label in the visualization charts.

Nucleotide Labels
Residue Labels
SSE Labels

Protein Secondary Structure Colors

You can apply custom color schemes to each individual protein chain in the structure, or apply a new secondary structure color scheme to all chains using the inputs below.


All chain colors:

Data Explorer

Below you can explore the DNAproDB data file for this structure. Click on the items below to expand them and reveal further items. Explanations of these features are available from the documentation page. Click the download button to download the data file or use the select box to find and view a particular data item.


The Residue Contact Map shows individual nucleotide-residue interactions, DNA secondary structure, protein secondary structure and DNA interaction moieties. The DNA is displayed as a graph, with nucleotides being nodes and edges between them indicating backbone links, base pairing or base stacking. Different base pairing geometries are indicated via the base-pair edges, and other structural features such as backbone breaks, missing phosphates, and the DNA strand sense are represented. Protein residues are displayed as small nodes with the node shape and color representing residue secondary structur. Edges between residue and nucleotide nodes represent an interaction between the two and which DNA moiety(s) the interaction involves.

Use the chart controls at the top left to modify labels, change the color scheme, rotate the plot, export it as a PNG file and more. You can also

  • Click to select individual residues or nucleotides and highlight them in the 3D view (hold SHIFT for multiple selections)
  • Double Click on labels to re-name them
  • Drag components to reposition them
  • Scroll to zoom in or out on the plot
  • Hover above residues, nucleotides or interaction lines to display additional information (can be toggled off in chart controls)

The Helical Contact Map plots protein secondary structural elements (SSE) interactions along the helical axis for a selected DNA helix. Interactions of SSEs with different DNA moieties are represented in concentric annuli and the position of each plotted SSE is given in helicoidal coordinates; a curvilinear coordinate system defined by the axis of a helical DNA segment.

Use the chart controls at the top left to modify labels, change the color scheme, rotate the plot, export it as a PNG file and more. You can also

  • Click to select individual residues or SSE and highlight them in the 3D view (hold SHIFT for multiple selections)
  • Double Click on labels to re-name them
  • Hover above a SSE to display additional information
  • Drag text labels to reposition them.

The Helical Shape Plot plots DNA shape parameters (such as major and minor groove width, or helical parameters) for a selected helix along the sequence of the helix. In addition, DNA-protein residue interactions are plotted showing approximately where each residue in the interface interacts along the DNA sequence and the secondary structure of that residue. Protein residue interactions can be toggled off if only DNA shape parameters are desired, or they can be displayed to indicate possible DNA shape readout, such as the presence of positively charged residues in regions of narrow minor groove width.

Use the chart controls at the top left to modify labels, change the color scheme, rotate the plot, export it as a PNG file and more. You can also

  • Click to select individual residues and highlight them in the 3D view (hold SHIFT for multiple selections)
  • Double Click on labels to re-name them
  • Hover above residues to display additional information
  • Drag text labels to reposition them.


Current model selection:

Protein Chain Information

Chain ID A.U. ID Uniprot ID(s) CATH ID(s) Molecular
Function
Biological
Process
Cellular
Component
Protein
Name(s)
Source
Organism
Sequence Sequence
Length
Secondary
Structure
Chain
Segments

Protein Chain Segments

Segment ID Length N-terminal
Residue
C-terminal
Residue

Protein Entities

Entity ID # Residues # Segments Chain
Segments

DNA Entities

Entity ID Type Nucleotides Base Pairs Strands Helices Single-Stranded
Segments

DNA Strands

Parent
Entity
Strand ID Length 5' Nucleotide 3' Nucleotide Sequence GC Content Protein Bound

DNA Helices

Parent
Entity
Helix ID Sequence Length Conformation A-tracts? Mismatches? Non-WC
Basepairs?
GC
Content
Mean
Radius
Axis
Curvature
Axis
Length [Å]

DNA-protein Interfaces

DNA Entity ID Pro. Chain ID Pro. Chain
Segments
Nuc-Res
Interactions
Weak Nuc-Res
Interactions
Total BASA [Ų] Total Hbonds Total vdW Hydrophobicity
Score (SAP)
Secondary Structure
Composition
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Customize Label