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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.
A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics

Results of the assignment of 200 detected steps in 10 model(s), can be also downloaded as csv 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
0012kqg-m10_A_DC1_DG2NANNANT01.06BB07
0022kqg-m1_A_DC1_DG2NANNANT00.84IC05
0032kqg-m2_A_DC1_DG2NANNANT00.84IC05
0042kqg-m3_A_DC1_DG2NANNANT00.71IC05
0052kqg-m4_A_DC1_DG2NANNANT00.88BB07
0062kqg-m5_A_DC1_DG2NANNANT01.01BB07
0072kqg-m6_A_DC1_DG2NANNANT00.93BB07
0082kqg-m7_A_DC1_DG2NANNANT00.92IC05
0092kqg-m8_A_DC1_DG2NANNANT00.92IC05
0102kqg-m9_A_DC1_DG2NANNANT00.89IC05
0112kqg-m10_A_DG2_DG3NANNANT00.89AB02
0122kqg-m1_A_DG2_DG3NANNANT01.00BB07
0132kqg-m2_A_DG2_DG3NANNANT00.96BB07
0142kqg-m3_A_DG2_DG3NANNANT00.92AB02
0152kqg-m4_A_DG2_DG3NANNANT00.79AB02
0162kqg-m5_A_DG2_DG3NANNANT00.82AB02
0172kqg-m6_A_DG2_DG3NANNANT00.82AB02
0182kqg-m7_A_DG2_DG3NANNANT00.87BB07
0192kqg-m8_A_DG2_DG3NANNANT00.96AB02
0202kqg-m9_A_DG2_DG3NANNANT00.88BB07
0212kqg-m10_A_DG3_DG4BB2BB07390.39BB07
0222kqg-m1_A_DG3_DG4NANNANT00.67BB08
0232kqg-m2_A_DG3_DG4NANNANT00.54BB07
0242kqg-m3_A_DG3_DG4miBBB12260.53BB12
0252kqg-m4_A_DG3_DG4BB2BB07500.37BB07
0262kqg-m5_A_DG3_DG4BB2BB08470.24BB08
0272kqg-m6_A_DG3_DG4NANNANT00.66BB12
0282kqg-m7_A_DG3_DG4BB2BB07110.48BB07
0292kqg-m8_A_DG3_DG4NANNANT00.66BB08
0302kqg-m9_A_DG3_DG4BB2BB07380.41BB07
0312kqg-m10_A_DG4_DC5NANNANT00.84OP18
0322kqg-m1_A_DG4_DC5NANNANT00.97OP18
0332kqg-m2_A_DG4_DC5NANNANT01.13OP18
0342kqg-m3_A_DG4_DC5NANNANT01.48OP17
0352kqg-m4_A_DG4_DC5NANNANT01.27OP21
0362kqg-m5_A_DG4_DC5NANNANT01.11OP18
0372kqg-m6_A_DG4_DC5NANNANT01.48OP17
0382kqg-m7_A_DG4_DC5NANNANT00.75OP18
0392kqg-m8_A_DG4_DC5NANNANT01.04OP21
0402kqg-m9_A_DG4_DC5NANNANT00.90OP18
0412kqg-m10_A_DC5_DG6NANNANT00.87OP18
0422kqg-m1_A_DC5_DG6NANNANT01.62IC02
0432kqg-m2_A_DC5_DG6NANNANT00.73OP21
0442kqg-m3_A_DC5_DG6OPNOP18100.68OP18
0452kqg-m4_A_DC5_DG6NANNANT00.94OP21
0462kqg-m5_A_DC5_DG6NANNANT02.45OP01
0472kqg-m6_A_DC5_DG6NANNANT01.34OP18
0482kqg-m7_A_DC5_DG6NANNANT01.31OP20
0492kqg-m8_A_DC5_DG6NANNANT00.78OP18
0502kqg-m9_A_DC5_DG6NANNANT00.39OP21
0512kqg-m10_A_DG6_DG7B-ABA05430.57BA05
0522kqg-m1_A_DG6_DG7B-ABA05330.55BA05
0532kqg-m2_A_DG6_DG7B-ABA01420.37BA01
0542kqg-m3_A_DG6_DG7B-ABA05580.26BA05
0552kqg-m4_A_DG6_DG7B-ABA05490.37BA05
0562kqg-m5_A_DG6_DG7NANNANT00.71AB02
0572kqg-m6_A_DG6_DG7B-ABA05480.40BA05
0582kqg-m7_A_DG6_DG7B-ABA05100.69BA05
0592kqg-m8_A_DG6_DG7B-ABA05200.40BA05
0602kqg-m9_A_DG6_DG7B-ABA05570.42BA05
0612kqg-m10_A_DG7_DG8AAAAA02470.48AA02
0622kqg-m1_A_DG7_DG8AAAAA02180.61AA02
0632kqg-m2_A_DG7_DG8AAAAA00170.52AA00
0642kqg-m3_A_DG7_DG8AAAAA02160.70AA02
0652kqg-m4_A_DG7_DG8AAAAA02100.60AA02
0662kqg-m5_A_DG7_DG8B-ABA05280.52BA05
0672kqg-m6_A_DG7_DG8AAAAA02290.52AA02
0682kqg-m7_A_DG7_DG8NANNANT00.49AB02
0692kqg-m8_A_DG7_DG8AAAAA02190.56AA02
0702kqg-m9_A_DG7_DG8AAAAA02300.58AA02
0712kqg-m10_A_DG8_DC9NANNANT01.20OP19
0722kqg-m1_A_DG8_DC9NANNANT01.65BB12
0732kqg-m2_A_DG8_DC9NANNANT01.57ZZ1S
0742kqg-m3_A_DG8_DC9NANNANT01.30OP08
0752kqg-m4_A_DG8_DC9NANNANT01.50ZZ1S
0762kqg-m5_A_DG8_DC9NANNANT01.72AB02
0772kqg-m6_A_DG8_DC9NANNANT01.75AB02
0782kqg-m7_A_DG8_DC9NANNANT01.32OP19
0792kqg-m8_A_DG8_DC9NANNANT01.92AA01
0802kqg-m9_A_DG8_DC9NANNANT01.43ZZ1S
0812kqg-m10_A_DC9_DA10NANNANT01.01BB2S
0822kqg-m1_A_DC9_DA10NANNANT00.94BB2S
0832kqg-m2_A_DC9_DA10NANNANT01.17BB13
0842kqg-m3_A_DC9_DA10NANNANT00.67BBS1
0852kqg-m4_A_DC9_DA10NANNANT00.78BB03
0862kqg-m5_A_DC9_DA10NANNANT01.28AB02
0872kqg-m6_A_DC9_DA10NANNANT01.14AB02
0882kqg-m7_A_DC9_DA10NANNANT01.28BB08
0892kqg-m8_A_DC9_DA10NANNANT00.90BB02
0902kqg-m9_A_DC9_DA10NANNANT01.44ZZ2S
0912kqg-m10_A_DA10_DC11NANNANT01.84ZZS2
0922kqg-m1_A_DA10_DC11SYNBBS1900.20BBS1
0932kqg-m2_A_DA10_DC11B-ABA05290.35BA05
0942kqg-m3_A_DA10_DC11NANNANT00.96BA17
0952kqg-m4_A_DA10_DC11NANNANT01.25BB08
0962kqg-m5_A_DA10_DC11BB2BB07140.51BB07
0972kqg-m6_A_DA10_DC11NANNANT00.54BB07
0982kqg-m7_A_DA10_DC11NANNANT00.98IC05
0992kqg-m8_A_DA10_DC11NANNANT00.79BB20
1002kqg-m9_A_DA10_DC11NANNANT01.69ZZS2
1012kqg-m10_A_DC11_DG12NANNANT01.70OP05
1022kqg-m1_A_DC11_DG12NANNANT01.26OP18
1032kqg-m2_A_DC11_DG12NANNANT00.68OP09
1042kqg-m3_A_DC11_DG12NANNANT01.72IC02
1052kqg-m4_A_DC11_DG12NANNANT00.99OP09
1062kqg-m5_A_DC11_DG12NANNANT01.44BB1S
1072kqg-m6_A_DC11_DG12NANNANT01.79IC02
1082kqg-m7_A_DC11_DG12NANNANT01.59BB1S
1092kqg-m8_A_DC11_DG12NANNANT01.29OP03
1102kqg-m9_A_DC11_DG12NANNANT01.50OP09
1112kqg-m10_A_DG12_DA13NANNANT01.34IC04
1122kqg-m1_A_DG12_DA13NANNANT01.40BB17
1132kqg-m2_A_DG12_DA13NANNANT01.85OP10
1142kqg-m3_A_DG12_DA13NANNANT01.75IC03
1152kqg-m4_A_DG12_DA13NANNANT02.24OP10
1162kqg-m5_A_DG12_DA13NANNANT01.65OP13
1172kqg-m6_A_DG12_DA13NANNANT01.24OP13
1182kqg-m7_A_DG12_DA13NANNANT01.96OP14
1192kqg-m8_A_DG12_DA13NANNANT02.08OP16
1202kqg-m9_A_DG12_DA13NANNANT01.46OP19
1212kqg-m10_A_DA13_DG14NANNANT01.82BB15
1222kqg-m1_A_DA13_DG14NANNANT00.83BB20
1232kqg-m2_A_DA13_DG14NANNANT00.92OP18
1242kqg-m3_A_DA13_DG14NANNANT01.80OP06
1252kqg-m4_A_DA13_DG14NANNANT01.11OP21
1262kqg-m5_A_DA13_DG14NANNANT01.78OP19
1272kqg-m6_A_DA13_DG14NANNANT01.56OP21
1282kqg-m7_A_DA13_DG14NANNANT01.05OP09
1292kqg-m8_A_DA13_DG14NANNANT01.40OP11
1302kqg-m9_A_DA13_DG14NANNANT01.87OP06
1312kqg-m10_A_DG14_DG15miBBB12570.40BB12
1322kqg-m1_A_DG14_DG15miBBB12340.51BB12
1332kqg-m2_A_DG14_DG15miBBB12450.43BB12
1342kqg-m3_A_DG14_DG15B-ABA05320.43BA05
1352kqg-m4_A_DG14_DG15miBBB12700.37BB12
1362kqg-m5_A_DG14_DG15NANNANT00.65BA09
1372kqg-m6_A_DG14_DG15miBBB12700.17BB12
1382kqg-m7_A_DG14_DG15miBBB12630.37BB12
1392kqg-m8_A_DG14_DG15B-ABA05750.22BA05
1402kqg-m9_A_DG14_DG15miBBB12790.24BB12
1412kqg-m10_A_DG15_DG16NANNANT00.57BB16
1422kqg-m1_A_DG15_DG16NANNANT00.38BB16
1432kqg-m2_A_DG15_DG16BB1BB16540.41BB16
1442kqg-m3_A_DG15_DG16NANNANT00.55BB16
1452kqg-m4_A_DG15_DG16NANNANT00.44BB16
1462kqg-m5_A_DG15_DG16NANNANT00.51BB16
1472kqg-m6_A_DG15_DG16NANNANT00.87BB17
1482kqg-m7_A_DG15_DG16NANNANT00.55BB16
1492kqg-m8_A_DG15_DG16A-BAB01730.40AB01
1502kqg-m9_A_DG15_DG16NANNANT00.50BB16
1512kqg-m10_A_DG16_DA17NANNANT01.74OP18
1522kqg-m1_A_DG16_DA17NANNANT01.68OP18
1532kqg-m2_A_DG16_DA17NANNANT01.69BB08
1542kqg-m3_A_DG16_DA17NANNANT01.79OP18
1552kqg-m4_A_DG16_DA17NANNANT01.69OP18
1562kqg-m5_A_DG16_DA17NANNANT01.73OP18
1572kqg-m6_A_DG16_DA17NANNANT01.69OP18
1582kqg-m7_A_DG16_DA17NANNANT01.78OP18
1592kqg-m8_A_DG16_DA17NANNANT01.62BB07
1602kqg-m9_A_DG16_DA17NANNANT01.83BB07
1612kqg-m10_A_DA17_DG18NANNANT00.88OP09
1622kqg-m1_A_DA17_DG18NANNANT00.89OP09
1632kqg-m2_A_DA17_DG18NANNANT00.59OP04
1642kqg-m3_A_DA17_DG18NANNANT00.49OP04
1652kqg-m4_A_DA17_DG18NANNANT00.98OP09
1662kqg-m5_A_DA17_DG18NANNANT01.02OP09
1672kqg-m6_A_DA17_DG18NANNANT00.92OP09
1682kqg-m7_A_DA17_DG18NANNANT00.99OP09
1692kqg-m8_A_DA17_DG18NANNANT00.62OP04
1702kqg-m9_A_DA17_DG18NANNANT00.99OP09
1712kqg-m10_A_DG18_DG19NANNANT00.52BB16
1722kqg-m1_A_DG18_DG19BB1BB16520.33BB16
1732kqg-m2_A_DG18_DG19NANNANT00.58AA09
1742kqg-m3_A_DG18_DG19BB1BB16360.35BB16
1752kqg-m4_A_DG18_DG19NANNANT00.84BB03
1762kqg-m5_A_DG18_DG19BB1BB16470.35BB16
1772kqg-m6_A_DG18_DG19NANNANT00.56BB16
1782kqg-m7_A_DG18_DG19NANNANT00.65BB16
1792kqg-m8_A_DG18_DG19BB1BB16580.40BB16
1802kqg-m9_A_DG18_DG19BB1BB16460.37BB16
1812kqg-m10_A_DG19_DG20NANNANT00.41BB08
1822kqg-m1_A_DG19_DG20NANNANT00.55BB02
1832kqg-m2_A_DG19_DG20NANNANT00.64AB03
1842kqg-m3_A_DG19_DG20NANNANT00.44BA09
1852kqg-m4_A_DG19_DG20NANNANT00.47BB02
1862kqg-m5_A_DG19_DG20NANNANT00.61BB07
1872kqg-m6_A_DG19_DG20NANNANT00.36BB08
1882kqg-m7_A_DG19_DG20NANNANT00.40BB08
1892kqg-m8_A_DG19_DG20NANNANT00.41BB02
1902kqg-m9_A_DG19_DG20BB2BB08410.25BB08
1912kqg-m10_A_DG20_DT21BBBBB00300.63BB00
1922kqg-m1_A_DG20_DT21B-ABA05510.34BA05
1932kqg-m2_A_DG20_DT21NANNANT01.80ZZ01
1942kqg-m3_A_DG20_DT21A-BAB05720.35AB05
1952kqg-m4_A_DG20_DT21B-ABA05590.37BA05
1962kqg-m5_A_DG20_DT21BB1BB16130.88BB16
1972kqg-m6_A_DG20_DT21BBBBB00560.48BB00
1982kqg-m7_A_DG20_DT21BBBBB00500.56BB00
1992kqg-m8_A_DG20_DT21B-ABA05820.31BA05
2002kqg-m9_A_DG20_DT21BBBBB00600.51BB00

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.

© Jiří Černý & Bohdan Schneider

Definition of torsion angles
step:
Table of conformers

δεζα1β1γ1δ1χχ1NCCNNNCC
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

Drag the plot for panning, scroll to zoom, click a point to show superposition in JSmol.

Download

Results (as csv)
Restraints (default edits file)
Best NtC fitted to input structure.

Definition of the conformers as torsion averages (csv) and their esd values (csv) or as their Cartesian coordinates of the 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).

Show



Color by conformation group (pyramids)

group
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Color by NtC (balls)

A

A-B

B-A

B

IC

OPN

Z

N