Please, read before you upload coordinates of your DNA or RNA:
The dinucleotide steps are identified based on atom names as defined by the PDB format, version 3.1 or above (sugar atoms as O4' not O4* - we are trying to convert the naming but using the correct format is preferred).
Steps with non-standard or missing atoms that define torsions δ ... δ+1, χ, and χ+1 are not considered in the assignment process.
Conformers are assigned for modified residues that contain standard names for atoms defining the step torsions between δ and δ+1 and χ and χ+1.
The front page of DNATCO:
Select a locally stored PDB file and press SUBMIT button to upload (left hand side)
Enter a 4-characters PDB ID, choose if the coordinates are downloaded from wwPDB or PDB-REDO and press SUBMIT button (middle)
Click on the SEARCH button to search in already assigned results from wwPDB deposited structures (right hand side)
Analysis of results and Expert mode:
Click a row of the table (or click a step in JSmol applet (2)) to display the assigned step details; Hovering over a row shows the description.
Selected step is shown in ball and sticks representation in the interactive JSmol applet. The behavior of the applet can be changed above to center on the analyzed step or the whole molecule.
Bellow is a short help explaining the applet controls.
Step backbone torsion angles are plotted (black line graph) and compared to the distribution of the manually curated data. (the controls are shown or hidden by clicking the Expert button (3)):
- Violin plot shows the distribution of torsion angles for the NtC data.
- Black bar inside indicates 1st and 3rd quartile.
- Mean values are indicated as white points.
- "Error bars" show the minimum and maximum values satisfying the assignment algorithm.
- The thumbnail can be used as a reference for definition of backbone torsion angles.
- The table bellow summarizes the angular values.
Download the results as CSV file containing the complete numerical results, definition of parameters and relevant papers:
- The resulting CSV file contains comma separated step_ID, assigned NtC and CANA, 12 torsion parameters of the step (δ to χ1, NN, CC, NCCN),
angular distances from the assigned or nearest NtC class average values, and confal scores for each parameter and whole step (by default as a harmonic mean of values).
- The result version string "_v30C34A21" decodes as DNATCO version 3.0 with conformers (NtC) version 3.4 and structural alphabet (CANA) version 2.1
- Browse the reference table of conformers and download definition of the conformers as torsion averages (csv) and their esd values (csv)
or as their Cartesian oordinates of all 84 conformer classes.
Changing colors and displayed structures:
Shows coloring options. Color of "pyramids" in the position of phosphates in the structure refer to groups of conformers:
- "A" refers to A-like DNA/RNA
- "BI" to BI-like DNA/RNA
- "BII" to BII-like
- "miB" contains minor B classes
- "Z" is Z-like DNA/RNA
- "IC" refers to classes with intercalated bases
- "OPN" to opened bases
- "SYN" refers to a base in syn orientation and
- "N" shows unassigned (NANT) steps.
Each group can be turned on (default) or off separately by clicking the checkbox bellow
The color of the BII-like DNA was changed from original yellow to magenta which made BII-like conformers more visible within the 1kx3 structure.
- D - "Default colors" - after changing colors by user this button changes colors back to default
- Q - "Toggle quality" - improve quality of the structure to make better figures
- T - "Transparent" - makes pyramids transparent to see also phosphate atoms (otherwise hidden by the pyramids)
- Expert - go to expert mode
- P - "Protein" - show also protein atoms available for particular PDB ID (histone protein in gray)
- H - "Hetero atoms" - show also hetero atoms like ions, ligands...
- W - "Water" - show also water molecules
Comparison of NtC classes:
Center view (after selecting a step in the table of steps) center the view on on the selected step or the whole structure.
Reference - show the green step (best representative of a conformational class) overlaid over the selected step:
- By default the green step is the average of the class to which the selected step is assigned, it can be turned off or changed for comparison to different class.
- Changing the reference class also updates the Expert mode part:
The violin plot shows the distributions for the selected class, while the black line still shows the parameters of step.
Values in the table below the plot are recalculated for the selected class. (see the next Figure)
Model - select a model if more models are available
Example of changing the reference class
The Figure shows a comparison between the BB00 and BB18 NtC classes for the selected 1bna_B_DA17_DA18 step.