Report for PDB Structure 8j8f

3D viewer
Data explorer

Color by:

Residues

SSE

Chain

Download structure file

Rotate: drag + left click Translate: drag + right click Zoom: scroll

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.

model:

dna entity:

protein chains:

DNA Moieties:

Maj. Groove

Min. Groove

Base

Sugar

Phosphate

Interaction Options

SSE Types:

Helix

Strand/Sheet

Loop/Turn

Marker Size Represents:

residue #

BASA

hbond #

nuc. interaction #

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.

Interaction Criteria:

default

custom

Match on:

all criteria

any criteria

Include Weak Interactions:

yes

Maj. Groove Min. Groove Base Sugar Phosphate

BASA

Hbonds

VdW

Minimum CoM MNN

Distance

Interaction Geometry:

pseudo stacking

pseudo pairing

other

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.

Nucleotides:

Residues:

SSEs:

Controls
Label options
Color options

Residue contact map controls

Layout type:

Radial

Circular

Force-directed layout:

Off

Indicate hydrogen bonds:

Yes

Indicate water-mediated hydrogen bonds:

Yes

Rotate labels:

Scale labels:

Shape Overlay Plot Controls

Select helix:

Select shape parameter:

axis limits:

min

max

reverse sequence

scale labels:

Helical Contact Map Controls

select a helix:

scale labels:

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 chains same colors:

Yes

Helix Strand/Sheet Loop/Turn

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.

Download data

Residue contact map
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)
Helical contact map
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.
Helical shape overlay
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.
RNAscape visualization

DNA moiety selection: Protein SST selection: Interaction criteria:

Mapping algorithm:

Rotate plot:

RNAscape Secondary structure Circular layout

SVG PNG

Translate or reposition: drag + left click View info: hover Highlight: left click

:

Select a DNA-Protein Interface

Interaction Options

Interaction Criteria

Exclude Componenents

Residue contact map controls

Shape Overlay Plot Controls

Helical Contact Map Controls

Customize labels

Nucleotide labels

Residue labels

SSE labels

Protein secondary structure colors

Data explorer

DNA moiety selection: Protein SST selection: Interaction criteria:

Mapping algorithm:

Information

Protein Chain Information

Protein Chain Segments

Protein Entities

DNA Entities

DNA Strands

DNA Helices

DNA-protein Interfaces