:

Download Structure File

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.


Information

Current model selection:

Protein Chain Information


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
abcdefghijklmnopqrstuvwxyz0123456789
Customize Label
DNAproDB is maintained by The Rohs Lab @ University of Southern California. It is free to use by anyone, including commercial users.