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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.

©Jiří Černý & Bohdan Schneider

INFLUENCE OF GROOVE INTERACTIONS ON DNA HOLLIDAY JUNCTION FORMATION

Results of the assignment of 9 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

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Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.
step numberStep nameCANANtCconfalrmsd
11s1k_A_DC1_DC2BBBBB00240.48BB00
21s1k_A_DC2_1AP3BB2BB07500.44BB07
31s1k_A_1AP3_DG4BBBBB00360.26BB00
41s1k_A_DG4_DT5BBBBB00540.31BB00
51s1k_A_DT5_DA6B12BB04210.30BB04
61s1k_A_DA6_DC7BBwBB02460.26BB02
71s1k_A_DC7_DT8miBBB15400.41BB15
81s1k_A_DT8_DG9NANNANT00.39BB15
91s1k_A_DG9_DG10NANNANT00.38BB15

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA

Similarity of step to class averages

Download

Results as csv or json file.
Restraints file for Phenix (steps with RMSD <= 0.5Å)
Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Best NtC fitted to input structure.

Definitions

Average parameters (csv), esd values (csv), and Cartesian coordinates of conformers.

Download the papers

Description of DNATCO server:
Černý et al., Nucleic Acids Research, 44, W284 (2016).
Definition of conformers:
Schneider et al., Acta Cryst D, 74, 52-64 (2018).
Example of application:
Schneider et al., Genes, 8(10), 278, (2017).

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