Quick hummus recipe

File name: 1gts_old.pdb

Date and time: Wed Nov 8 20:52:02 2023

Number of base-pairs: 28

Number of atoms: 6004

****************************************************************************

HEADER LIGASE/RNA 15-SEP-93 1GTS

TITLE STRUCTURAL BASIS FOR TRANSFER RNA AMINOACEYLATION BY ESCHERICHIA COLI

TITLE 2 GLUTAMINYL-TRNA SYNTHETASE

COMPND MOL_ID: 1;

COMPND 2 MOLECULE: TRNAGLN;

COMPND 3 CHAIN: B;

COMPND 4 MOL_ID: 2;

COMPND 5 MOLECULE: PROTEIN (GLUTAMINYL-TRNA SYNTHETASE (E.C.6.1.1.18));

COMPND 6 CHAIN: A

SOURCE MOL_ID: 1;

SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;

SOURCE 3 ORGANISM_TAXID: 562;

SOURCE 4 MOL_ID: 2;

SOURCE 5 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;

SOURCE 6 ORGANISM_TAXID: 562

KEYWDS PROTEIN-RNA COMPLEX, LIGASE-RNA COMPLEX

EXPDTA X-RAY DIFFRACTION

AUTHOR J.J.PERONA,T.A.STEITZ,M.A.ROULD

REVDAT 5 15-FEB-17 1GTS 1 AUTHOR VERSN

REVDAT 4 24-FEB-09 1GTS 1 VERSN

REVDAT 3 01-APR-03 1GTS 1 JRNL

REVDAT 2 21-SEP-01 1GTS 5

REVDAT 1 07-FEB-95 1GTS 0

JRNL AUTH J.J.PERONA,M.A.ROULD,T.A.STEITZ

JRNL TITL STRUCTURAL BASIS FOR TRANSFER RNA AMINOACYLATION BY

JRNL TITL 2 ESCHERICHIA COLI GLUTAMINYL-TRNA SYNTHETASE.

JRNL REF BIOCHEMISTRY V. 32 8758 1993

JRNL REFN ISSN 0006-2960

JRNL PMID 8364025

JRNL DOI 10.1021/BI00085A006

HELIX 1 1 PHE A 10 SER A 21 1 12

HELIX 2 2 ILE A 41 ASP A 56 1 16

HELIX 3 3 PRO A 70 LYS A 72 5 3

HELIX 4 4 ILE A 75 TRP A 87 1 13

HELIX 5 5 SER A 99 ASN A 115 5 17

HELIX 6 6 PRO A 126 ARG A 133 1 8

HELIX 7 7 VAL A 150 ARG A 161 1 12

HELIX 8 8 ILE A 183 MET A 185 5 3

HELIX 9 9 TYR A 211 GLU A 222 1 12

HELIX 10 10 LEU A 231 PHE A 233 5 3

HELIX 11 11 ASN A 236 ASP A 245 5 10

HELIX 12 12 LYS A 270 THR A 278 1 9

HELIX 13 13 ILE A 293 ARG A 299 1 7

HELIX 14 14 ALA A 303 ILE A 313 1 11

HELIX 15 15 MET A 324 ASN A 338 1 15

HELIX 16 16 PRO A 372 MET A 374 5 3

HELIX 17 17 ARG A 389 ASP A 391 5 3

HELIX 18 18 ALA A 461 HIS A 463 5 3

HELIX 19 19 PRO A 481 ALA A 483 5 3

HELIX 20 20 PHE A 487 VAL A 490 5 4

HELIX 21 21 PRO A 505 ASP A 509 5 5

SHEET 1 A 2 HIS A 28 PHE A 31 0

SHEET 2 A 2 GLN A 60 LEU A 63 1 N GLN A 60 O THR A 29

SHEET 1 B 2 ALA A 119 ASP A 122 0

SHEET 2 B 2 CYS A 171 ALA A 174 -1 N ARG A 173 O TYR A 120

SHEET 1 C 2 TYR A 191 ILE A 193 0

SHEET 2 C 2 ILE A 207 PRO A 209 -1 N TYR A 208 O ARG A 192

SHEET 1 D 2 HIS A 226 THR A 230 0

SHEET 2 D 2 ARG A 254 PHE A 258 1 N ARG A 254 O SER A 227

SHEET 1 E 6 GLU A 408 ARG A 410 0

SHEET 2 E 6 VAL A 416 GLU A 423 -1 N ILE A 417 O VAL A 409

SHEET 3 E 6 THR A 432 TYR A 437 -1 N THR A 436 O LYS A 418

SHEET 4 E 6 PRO A 348 ILE A 353 1 N LYS A 350 O ILE A 433

SHEET 5 E 6 GLU A 384 ASP A 388 -1 N ILE A 387 O VAL A 349

SHEET 6 E 6 TRP A 458 SER A 460 -1 N VAL A 459 O TRP A 386

SHEET 1 F 2 MET A 362 PRO A 366 0

SHEET 2 F 2 SER A 376 PRO A 380 -1 N VAL A 379 O VAL A 363

SHEET 1 G 4 LEU A 496 GLU A 504 0

SHEET 2 G 4 ALA A 464 TYR A 472 -1 N LEU A 471 O VAL A 497

SHEET 3 G 4 PRO A 536 GLY A 543 1 N PRO A 536 O GLU A 468

SHEET 4 G 4 GLY A 522 LEU A 526 -1 N CYS A 525 O ASN A 539

****************************************************************************

RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

Strand I Strand II Helix

1 (0.015) ....>B:...2_:[..G]G-----C[..C]:..71_:B<.... (0.014) |

2 (0.012) ....>B:...3_:[..G]G-----C[..C]:..70_:B<.... (0.005) |

3 (0.017) ....>B:...4_:[..G]G-----C[..C]:..69_:B<.... (0.010) |

4 (0.012) ....>B:...5_:[..G]G-----C[..C]:..68_:B<.... (0.008) |

5 (0.020) ....>B:...6_:[..U]U-----A[..A]:..67_:B<.... (0.011) |

6 (0.011) ....>B:...7_:[..A]A-----U[..U]:..66_:B<.... (0.014) |

7 (0.017) ....>B:..49_:[..C]C-----G[..G]:..65_:B<.... (0.010) |

8 (0.021) ....>B:..50_:[..G]G-----C[..C]:..64_:B<.... (0.008) |

9 (0.009) ....>B:..51_:[..A]A-----U[..U]:..63_:B<.... (0.017) |

10 (0.012) ....>B:..52_:[..G]G-----C[..C]:..62_:B<.... (0.012) |

11 (0.010) ....>B:..53_:[..G]G-----C[..C]:..61_:B<.... (0.007) |

12 (0.009) ....>B:..54_:[..U]U-**--A[..A]:..58_:B<.... (0.011) |

13 (0.015) ....>B:..55_:[..U]U-**+-G[..G]:..18_:B<.... (0.014) x

14 (0.010) ....>B:..37_:[..A]A-**--U[..U]:..33_:B<.... (0.017) |

15 (0.018) ....>B:..38_:[..U]U-*---U[..U]:..32_:B<.... (0.019) |

16 (0.014) ....>B:..39_:[..U]U-----A[..A]:..31_:B<.... (0.011) |

17 (0.011) ....>B:..40_:[..C]C-----G[..G]:..30_:B<.... (0.008) |

18 (0.010) ....>B:..41_:[..C]C-----G[..G]:..29_:B<.... (0.012) |

19 (0.008) ....>B:..42_:[..G]G-----C[..C]:..28_:B<.... (0.009) |

20 (0.010) ....>B:..43_:[..G]G-----C[..C]:..27_:B<.... (0.008) |

21 (0.012) ....>B:..44_:[..C]C-**--A[..A]:..26_:B<.... (0.014) |

22 (0.014) ....>B:..10_:[..G]G-----C[..C]:..25_:B<.... (0.008) |

23 (0.009) ....>B:..11_:[..C]C-----G[..G]:..24_:B<.... (0.016) |

24 (0.010) ....>B:..12_:[..C]C-----G[..G]:..23_:B<.... (0.015) |

25 (0.010) ....>B:..13_:[..A]A-**+-A[..A]:..45_:B<.... (0.012) |

26 (0.013) ....>B:..14_:[..A]A-**--U[..U]:...8_:B<.... (0.030) |

27 (0.013) ....>B:..15_:[..G]G-**+-C[..C]:..48_:B<.... (0.011) x

28 (0.015) ....>B:..19_:[..G]G-----C[..C]:..56_:B<.... (0.009) +

Note: This structure contains 8[7] non-Watson-Crick base-pairs.

****************************************************************************

Detailed H-bond information: atom-name pair and length [ O N]

1 G-----C [3] O6 - N4 2.85 N1 - N3 3.02 N2 - O2 2.97

2 G-----C [3] O6 - N4 2.94 N1 - N3 2.86 N2 - O2 2.67

3 G-----C [3] O6 - N4 3.08 N1 - N3 3.02 N2 - O2 2.86

4 G-----C [3] O6 - N4 2.85 N1 - N3 2.86 N2 - O2 2.84

5 U-----A [2] N3 - N1 2.89 O4 - N6 3.15

6 A-----U [2] N6 - O4 2.70 N1 - N3 2.87

7 C-----G [3] O2 - N2 2.72 N3 - N1 2.70 N4 - O6 2.65

8 G-----C [3] O6 - N4 2.95 N1 - N3 2.81 N2 - O2 2.62

9 A-----U [2] N6 - O4 2.72 N1 - N3 2.62

10 G-----C [3] O6 - N4 2.60 N1 - N3 2.70 N2 - O2 2.69

11 G-----C [3] O6 - N4 2.68 N1 - N3 2.76 N2 - O2 2.73

12 U-**--A [2] O2 - N6 2.80 N3 - N7 2.87

13 U-**+-G [1] O2 - N1 2.67

14 A-**--U [1] N6 - O2 3.20

15 U-*---U [1] O4 - N3 3.12

16 U-----A [2] N3 - N1 2.78 O4 - N6 2.65

17 C-----G [3] O2 - N2 2.76 N3 - N1 2.86 N4 - O6 2.78

18 C-----G [3] O2 - N2 2.72 N3 - N1 2.73 N4 - O6 2.72

19 G-----C [3] O6 - N4 2.66 N1 - N3 2.73 N2 - O2 2.72

20 G-----C [3] O6 - N4 2.66 N1 - N3 2.68 N2 - O2 2.70

21 C-**--A [1] N3 - N6 3.42

22 G-----C [3] O6 - N4 2.71 N1 - N3 2.68 N2 - O2 2.72

23 C-----G [3] O2 - N2 2.78 N3 - N1 2.89 N4 - O6 2.89

24 C-----G [3] O2 - N2 2.68 N3 - N1 2.75 N4 - O6 2.75

25 A-**+-A [2] N6 - N1 2.95 N1 - N6 2.80

26 A-**--U [2] N7 - N3 2.79 N6 - O2 2.59

27 G-**+-C [2] N1 - O2 2.78 N2 - N3 2.87

28 G-----C [3] O6 - N4 2.74 N1 - N3 2.75 N2 - O2 2.68

****************************************************************************

Overlap area in Angstrom^2 between polygons defined by atoms on successive

bases. Polygons projected in the mean plane of the designed base-pair step.

Values in parentheses measure the overlap of base ring atoms only. Those

outside parentheses include exocyclic atoms on the ring. Intra- and

inter-strand overlap is designated according to the following diagram:

i2 3' 5' j2

/|\ |

| |

Strand I | | II

| |

| \|/

i1 5' 3' j1

step i1-i2 i1-j2 j1-i2 j1-j2 sum

1 GG/CC 3.94( 2.63) 0.00( 0.00) 0.11( 0.00) 0.45( 0.00) 4.50( 2.63)

2 GG/CC 3.47( 2.13) 0.00( 0.00) 0.32( 0.00) 0.06( 0.00) 3.85( 2.13)

3 GG/CC 4.03( 2.40) 0.00( 0.00) 0.43( 0.00) 0.00( 0.00) 4.46( 2.40)

4 GU/AC 6.72( 4.06) 0.00( 0.00) 0.00( 0.00) 3.98( 2.46) 10.69( 6.52)

5 UA/UA 0.57( 0.00) 0.00( 0.00) 0.99( 0.81) 0.27( 0.00) 1.83( 0.81)

6 AC/GU 3.17( 1.94) 0.00( 0.00) 0.00( 0.00) 6.23( 3.27) 9.40( 5.21)

7 CG/CG 0.00( 0.00) 0.00( 0.00) 5.38( 2.44) 0.00( 0.00) 5.38( 2.44)

8 GA/UC 4.81( 3.25) 0.00( 0.00) 0.00( 0.00) 2.38( 0.36) 7.19( 3.62)

9 AG/CU 2.80( 2.62) 0.00( 0.00) 0.43( 0.00) 0.16( 0.00) 3.38( 2.62)

10 GG/CC 3.44( 1.90) 0.00( 0.00) 1.26( 0.00) 0.00( 0.00) 4.70( 1.90)

11 GU/AC 6.64( 3.76) 0.00( 0.00) 0.00( 0.00) 4.74( 1.88) 11.38( 5.63)

12 UU/GA 4.64( 1.93) 0.00( 0.00) 0.00( 0.00) 6.32( 3.38) 10.96( 5.31)

13 UA/UG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)

14 AU/UU 4.44( 0.95) 0.00( 0.00) 0.00( 0.00) 4.06( 2.00) 8.49( 2.95)

15 UU/AU 1.18( 0.28) 0.00( 0.00) 0.00( 0.00) 6.21( 3.83) 7.39( 4.11)

16 UC/GA 0.00( 0.00) 0.00( 0.00) 0.02( 0.00) 2.71( 1.21) 2.73( 1.21)

17 CC/GG 0.31( 0.00) 0.00( 0.00) 0.45( 0.00) 3.81( 2.49) 4.57( 2.49)

18 CG/CG 0.00( 0.00) 0.00( 0.00) 5.89( 2.70) 0.00( 0.00) 5.89( 2.70)

19 GG/CC 3.71( 2.31) 0.00( 0.00) 0.60( 0.00) 0.06( 0.00) 4.37( 2.31)

20 GC/AC 6.71( 3.74) 0.00( 0.00) 0.00( 0.00) 4.45( 2.11) 11.16( 5.85)

21 CG/CA 0.00( 0.00) 0.00( 0.00) 0.87( 0.03) 0.87( 0.41) 1.74( 0.44)

22 GC/GC 4.62( 1.70) 0.00( 0.00) 0.00( 0.00) 5.86( 2.85) 10.47( 4.54)

23 CC/GG 0.06( 0.00) 0.00( 0.00) 0.34( 0.00) 2.63( 1.12) 3.03( 1.12)

24 CA/AG 2.12( 1.05) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 2.12( 1.05)

25 AA/UA 0.00( 0.00) 2.55( 0.10) 0.00( 0.00) 0.00( 0.00) 2.55( 0.10)

26 AG/CU 3.78( 1.42) 0.00( 0.00) 0.04( 0.00) 0.00( 0.00) 3.82( 1.42)

27 GG/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)

****************************************************************************

Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in

the coordinate system of the given structure

bp Ox Oy Oz Nx Ny Nz

1 G-C 43.763 40.695 33.941 -0.936 -0.059 -0.347

2 G-C 41.076 38.942 32.800 -0.983 -0.054 -0.176

3 G-C 38.000 37.053 32.495 -0.991 -0.069 -0.118

4 G-C 34.342 35.382 34.257 -0.990 -0.118 0.078

5 U-A 31.340 35.049 35.938 -0.993 -0.022 0.119

6 A-U 28.615 35.067 37.679 -0.971 0.130 0.200

7 C-G 26.011 36.602 39.821 -0.952 0.119 0.283

8 G-C 22.941 38.959 41.259 -0.987 0.156 0.042

9 A-U 19.804 40.241 41.103 -0.994 0.111 0.026

10 G-C 16.510 41.557 39.450 -0.994 0.067 -0.091

11 G-C 13.455 41.442 36.723 -0.977 -0.107 -0.183

12 U-A 11.171 40.875 32.847 -0.969 -0.073 -0.238

13 U+G 7.435 39.279 34.718 -0.987 -0.126 -0.104

14 A-U 21.395 -7.307 19.139 -0.487 0.871 0.068

15 U-U 17.893 -5.574 18.734 -0.481 0.838 0.258

16 U-A 15.177 -3.648 21.093 -0.323 0.900 0.292

17 C-G 14.038 -0.884 24.101 -0.115 0.954 0.278

18 C-G 13.990 1.661 26.690 -0.033 0.966 0.256

19 G-C 15.451 4.564 28.929 0.121 0.989 0.088

20 G-C 17.610 7.924 29.673 0.147 0.989 0.034

21 C-A 19.879 10.986 29.329 0.230 0.968 -0.098

22 G-C 24.155 13.662 29.518 0.089 0.960 -0.264

23 C-G 24.047 16.372 26.932 0.073 0.965 -0.252

24 C-G 21.946 19.322 25.298 -0.079 0.978 -0.193

25 A+A 19.718 22.575 29.089 -0.202 0.979 0.034

26 A-U 17.809 25.518 26.160 -0.161 0.986 -0.036

27 G+C 16.280 28.220 29.546 -0.123 0.986 0.111

28 G-C 1.736 39.189 28.402 -0.899 0.012 -0.439

****************************************************************************

Local base-pair parameters

bp Shear Stretch Stagger Buckle Propeller Opening

1 G-C -0.34 -0.06 -0.36 -15.60 -2.53 -3.53

2 G-C -0.41 -0.22 0.29 -1.46 -12.94 0.37

3 G-C -0.29 -0.04 0.34 -3.20 -19.31 -0.14

4 G-C -0.41 -0.20 -0.14 -18.80 -19.35 -2.04

5 U-A 0.26 -0.03 0.34 -11.10 -8.90 4.60

6 A-U -0.03 -0.17 -0.13 2.94 -3.09 -7.45

7 C-G 0.31 -0.39 -0.31 11.75 -13.60 -2.26

8 G-C -0.95 -0.45 -0.13 -0.69 -10.13 2.18

9 A-U 0.04 -0.34 0.14 -0.19 -14.53 -1.21

10 G-C -0.37 -0.43 -0.26 -5.06 -9.58 -3.11

11 G-C -0.30 -0.29 -0.24 -15.39 -7.72 -2.48

12 U-A 4.25 -2.18 0.08 -1.08 8.07 -95.53

13 U+G 0.57 -5.40 0.33 23.66 8.45 -93.72

14 A-U -6.34 -4.62 0.26 -5.85 10.56 -38.73

15 U-U -2.73 -0.97 -1.35 12.66 -10.24 -31.73

16 U-A -0.12 -0.26 -0.80 15.28 -2.49 -7.58

17 C-G 0.86 -0.42 -0.01 1.74 -2.47 -1.45

18 C-G 0.74 -0.49 -0.01 5.72 -18.35 -1.83

19 G-C -0.54 -0.44 0.16 -1.36 -15.32 -3.22

20 G-C 0.02 -0.34 0.04 -10.38 -17.38 -2.93

21 C-A 3.74 -0.25 -0.23 -8.27 -9.72 -19.76

22 G-C 0.04 -0.33 -0.25 -5.26 -5.33 -2.24

23 C-G 0.37 -0.17 -0.10 -2.28 -3.86 0.52

24 C-G 0.26 -0.33 -0.16 -1.00 -5.14 -1.32

25 A+A 1.40 0.95 0.13 -8.28 13.19 -176.72

26 A-U -4.24 -2.52 0.10 1.23 6.77 -91.68

27 G+C 0.08 3.78 -0.04 5.37 14.64 158.54

28 G-C -0.38 -0.29 -0.02 -17.87 -13.53 -1.58

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

ave. -0.16 -0.60 -0.08 -1.88 -5.85 -15.21

s.d. 1.95 1.61 0.36 10.00 10.04 54.20

****************************************************************************

Local base-pair step parameters

step Shift Slide Rise Tilt Roll Twist

1 GG/CC 0.50 -1.55 2.99 -5.69 8.49 30.75

2 GG/CC 0.14 -1.70 3.20 0.92 3.33 33.12

3 GG/CC 0.86 -2.09 3.76 8.35 8.07 28.87

4 GU/AC 0.50 -1.29 3.17 -0.34 5.96 34.29

5 UA/UA -0.30 -1.25 2.97 5.87 8.05 31.50

6 AC/GU -0.09 -1.84 3.21 3.26 -3.69 37.87

7 CG/CG -0.37 -2.06 3.56 -1.68 14.04 26.93

8 GA/UC 0.00 -0.89 3.27 -2.23 1.71 36.54

9 AG/CU 0.25 -1.83 3.45 3.37 6.30 26.16

10 GG/CC 0.47 -2.23 3.40 3.41 10.82 33.72

11 GU/AC -2.34 -2.35 3.09 0.53 -3.70 88.33

12 UU/GA 1.78 -2.14 3.50 5.88 5.88 38.59

13 UA/UG ---- ---- ---- ---- ---- ----

14 AU/UU 0.04 -2.38 3.12 -3.92 10.40 52.16

15 UU/AU 0.70 -2.10 3.43 -8.15 5.67 39.52

16 UC/GA 0.36 -2.06 3.69 -5.59 11.03 41.18

17 CC/GG -0.30 -1.80 3.14 -0.12 4.91 28.67

18 CG/CG -0.06 -2.15 3.31 -1.94 12.98 18.83

19 GG/CC 0.15 -1.76 3.66 0.18 3.47 36.46

20 GC/AC -0.23 -1.65 3.44 6.77 5.92 39.22

21 CG/CA -3.74 -0.99 3.25 5.15 11.41 55.05

22 GC/GC -0.33 -1.80 3.27 -0.35 1.12 38.06

23 CC/GG 0.50 -2.24 3.25 4.94 7.99 24.65

24 CA/AG 1.52 -4.15 3.22 14.32 3.89 138.98

25 AA/UA -0.97 3.07 3.24 -3.70 2.84 -38.41

26 AG/CU 1.74 -2.99 3.02 3.90 7.79 -74.12

27 GG/CC ---- ---- ---- ---- ---- ----

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

ave. 0.03 -1.77 3.30 1.33 6.19 33.88

s.d. 1.15 1.20 0.22 5.07 4.52 36.72

****************************************************************************

Local base-pair helical parameters

step X-disp Y-disp h-Rise Incl. Tip h-Twist

1 GG/CC -4.05 -1.75 2.36 15.49 10.38 32.37

2 GG/CC -3.49 -0.10 3.02 5.81 -1.61 33.29

3 GG/CC -5.62 0.17 3.20 15.42 -15.97 31.07

4 GU/AC -3.00 -0.88 2.91 10.01 0.58 34.79

5 UA/UA -3.37 1.38 2.48 14.38 -10.49 33.00

6 AC/GU -2.34 0.55 3.35 -5.66 -4.99 38.18

7 CG/CG -6.60 0.38 2.25 27.85 3.33 30.35

8 GA/UC -1.65 -0.31 3.22 2.72 3.56 36.65

9 AG/CU -5.49 0.31 2.95 13.60 -7.27 27.10

10 GG/CC -5.15 -0.31 2.62 18.03 -5.68 35.52

11 GU/AC -1.61 1.69 3.16 -2.65 -0.38 88.39

12 UU/GA -3.91 -1.90 3.37 8.78 -8.78 39.45

13 UA/UG ---- ---- ---- ---- ---- ----

14 AU/UU -3.24 -0.27 2.63 11.68 4.41 53.25

15 UU/AU -3.64 -1.89 2.92 8.23 11.82 40.70

16 UC/GA -3.96 -1.08 3.00 15.27 7.75 42.92

17 CC/GG -4.56 0.58 2.80 9.83 0.23 29.08

18 CG/CG -9.15 -0.42 1.52 34.74 5.19 22.92

19 GG/CC -3.33 -0.22 3.48 5.53 -0.29 36.62

20 GC/AC -3.08 1.11 3.09 8.69 -9.92 40.20

21 CG/CA -1.64 4.22 2.68 12.17 -5.49 56.34

22 GC/GC -2.91 0.46 3.22 1.72 0.53 38.08

23 CC/GG -6.84 0.11 2.46 17.90 -11.07 26.35

24 CA/AG -2.24 -0.73 3.24 2.08 -7.64 139.34

25 AA/UA -4.96 -1.90 2.91 -4.30 -5.60 -38.68

26 AG/CU 2.24 1.55 3.19 -6.44 3.23 -74.56

27 GG/CC ---- ---- ---- ---- ---- ----

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

ave. -3.74 0.03 2.88 9.63 -1.77 34.91

s.d. 2.18 1.36 0.44 9.77 7.09 36.80

****************************************************************************

The 'simple' parameters are intuitive for non-Watson-Crick base pairs

and associated base-pair steps (where the above corresponding 3DNA

parameters often appear cryptic). Note that they are for structural

*description* only, not to be fed into the 'rebuild' program. See URL

http://x3dna.org/highlights/details-on-the-simple-base-pair-parameters

and related blogposts on the 3DNA home page for details.

This structure contains 8 non-Watson-Crick (with leading *) base pair(s)

----------------------------------------------------------------------------

Simple base-pair parameters based on RC8--YC6 vectors

bp Shear Stretch Stagger Buckle Propeller Opening

1 G-C -0.34 -0.05 -0.36 -15.67 -2.10 -3.56

2 G-C -0.41 -0.20 0.29 -1.93 -12.88 0.37

3 G-C -0.29 -0.03 0.34 -3.68 -19.23 -0.14

4 G-C -0.41 -0.19 -0.14 -19.23 -18.92 -2.04

5 U-A 0.26 -0.02 0.34 -10.89 -9.16 4.61

6 A-U -0.03 -0.17 -0.13 2.95 -3.09 -7.45

7 C-G 0.32 -0.38 -0.31 12.04 -13.34 -2.25

8 G-C -0.99 -0.36 -0.13 -1.62 -10.02 2.17

9 A-U 0.05 -0.34 0.14 -0.04 -14.53 -1.20

10 G-C -0.38 -0.42 -0.26 -5.36 -9.42 -3.10

11 G-C -0.30 -0.29 -0.24 -15.54 -7.42 -2.50

* 12 U-A 4.58 1.37 0.08 -6.36 5.08 -95.40

* 13 U+G 4.16 3.48 0.33 -20.18 14.97 -94.79

* 14 A-U -7.50 2.31 0.26 4.96 11.01 -38.62

* 15 U-U -2.90 -0.10 -1.35 8.99 -13.58 -31.79

16 U-A -0.12 -0.26 -0.80 15.23 -2.80 -7.64

17 C-G 0.90 -0.34 -0.01 1.94 -2.31 -1.45

18 C-G 0.77 -0.44 -0.01 6.99 -17.91 -1.81

19 G-C -0.56 -0.42 0.16 -2.16 -15.23 -3.19

20 G-C 0.02 -0.34 0.04 -10.18 -17.50 -2.91

* 21 C-A 3.57 1.14 -0.23 -4.14 -12.07 -19.74

22 G-C 0.04 -0.33 -0.25 -5.20 -5.38 -2.24

23 C-G 0.38 -0.15 -0.10 -2.15 -3.93 0.52

24 C-G 0.27 -0.32 -0.16 -0.88 -5.16 -1.32

* 25 A+A -0.84 1.47 0.13 -13.79 -7.25 -176.71

* 26 A-U -4.79 1.15 0.10 5.60 3.99 -91.58

* 27 G+C 3.56 1.28 -0.04 15.59 0.26 158.39

28 G-C -0.39 -0.28 -0.02 -18.17 -13.11 -1.59

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

ave. -0.05 0.24 -0.08 -2.96 -7.18 -15.25

s.d. 2.40 0.98 0.36 10.04 8.75 54.22

----------------------------------------------------------------------------

Simple base-pair step parameters based on consecutive C1'-C1' vectors

step Shift Slide Rise Tilt Roll Twist

1 GG/CC 0.45 -1.57 2.99 -5.40 8.68 31.24

2 GG/CC 0.08 -1.70 3.20 1.03 3.29 32.48

3 GG/CC 0.80 -2.12 3.76 8.57 7.84 28.88

4 GU/AC 0.50 -1.29 3.17 -0.35 5.96 30.97

5 UA/UA -0.28 -1.26 2.97 5.77 8.12 33.50

6 AC/GU -0.07 -1.84 3.21 3.29 -3.66 36.26

7 CG/CG -0.43 -2.05 3.56 -1.23 14.09 33.28

8 GA/UC -0.04 -0.89 3.27 -2.16 1.80 31.53

9 AG/CU 0.22 -1.83 3.45 3.48 6.24 28.22

10 GG/CC 0.40 -2.24 3.40 3.74 10.71 33.19

* 11 GU/AC -1.79 -2.79 3.09 1.29 -3.51 61.04

* 12 UU/GA 2.71 0.66 3.50 -2.70 7.87 -37.68

* 13 UA/UG ---- ---- ---- ---- ---- ----

* 14 AU/UU -1.09 -2.12 3.12 1.46 11.02 25.02

* 15 UU/AU 0.41 -2.18 3.43 -7.32 6.70 25.51

16 UC/GA 0.44 -2.04 3.69 -5.99 10.82 35.78

17 CC/GG -0.17 -1.81 3.14 -0.49 4.89 29.56

18 CG/CG -0.04 -2.15 3.31 -2.03 12.97 25.83

19 GG/CC 0.11 -1.77 3.66 0.27 3.47 33.26

* 20 GC/AC 0.05 -1.67 3.44 5.72 6.94 20.74

* 21 CG/CA -3.53 -1.58 3.25 3.22 12.10 73.45

22 GC/GC -0.30 -1.81 3.27 -0.37 1.11 36.19

23 CC/GG 0.57 -2.22 3.25 4.68 8.14 24.99

* 24 CA/AG 3.51 -2.68 3.22 9.97 10.99 77.24

* 25 AA/UA -1.90 2.60 3.24 -4.41 1.51 51.10

* 26 AG/CU -1.78 -2.97 3.02 8.71 0.35 -3.99

* 27 GG/CC ---- ---- ---- ---- ---- ----

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

ave. -0.05 -1.65 3.30 1.15 6.34 31.90

s.d. 1.38 1.13 0.22 4.62 4.83 21.91

****************************************************************************

Structure classification:

This structure contains more than one helical regions

This is a right-handed nucleic acid structure

****************************************************************************

lambda: virtual angle between C1'-YN1 or C1'-RN9 glycosidic bonds and the

base-pair C1'-C1' line

C1'-C1': distance between C1' atoms for each base-pair

RN9-YN1: distance between RN9-YN1 atoms for each base-pair

RC8-YC6: distance between RC8-YC6 atoms for each base-pair

bp lambda(I) lambda(II) C1'-C1' RN9-YN1 RC8-YC6

1 G-C 51.1 53.7 10.9 9.1 9.9

2 G-C 52.8 56.3 10.6 8.9 9.8

3 G-C 53.9 54.0 10.8 9.1 10.0

4 G-C 52.8 53.3 10.6 8.8 9.7

5 U-A 60.4 56.8 10.4 8.9 9.9

6 A-U 52.5 50.8 10.8 9.0 9.8

7 C-G 52.7 51.9 10.6 8.7 9.6

8 G-C 48.6 59.8 10.4 8.7 9.6

9 A-U 55.5 51.9 10.5 8.7 9.6

10 G-C 50.6 52.4 10.6 8.8 9.6

11 G-C 53.7 53.6 10.6 8.8 9.6

12 U-A 33.8 18.6 9.7 7.2 6.3

13 U+G 104.3 26.2 8.9 8.2 9.6

14 A-U 5.2 77.8 9.6 7.9 8.0

15 U-U 26.1 53.5 11.2 8.9 9.2

16 U-A 50.1 51.7 10.8 8.9 9.6

17 C-G 57.8 51.3 10.5 8.8 9.6

18 C-G 56.0 49.1 10.5 8.7 9.5

19 G-C 51.6 54.7 10.5 8.7 9.6

20 G-C 55.6 50.5 10.6 8.8 9.6

21 C-A 61.1 25.9 11.9 9.8 10.2

22 G-C 53.0 52.2 10.6 8.8 9.7

23 C-G 57.0 54.1 10.6 8.9 9.9

24 C-G 54.2 52.0 10.6 8.8 9.7

25 A+A 32.5 29.1 13.3 10.9 11.1

26 A-U 17.1 37.5 9.5 7.0 6.2

27 G+C 38.8 57.5 10.6 8.9 10.4

28 G-C 54.0 53.0 10.5 8.8 9.6

****************************************************************************

Classification of each dinucleotide step in a right-handed nucleic acid

structure: A-like; B-like; TA-like, or other cases.

step Xp Yp Zp XpH YpH ZpH Form

1 GG/CC -1.36 8.30 2.28 -5.26 7.43 4.34 A

2 GG/CC -1.57 8.16 2.70 -4.90 7.86 3.48 A

3 GG/CC -1.90 8.41 2.30 -7.01 7.57 4.14 A

4 GU/AC -1.58 8.38 2.24 -4.46 7.90 3.60 A

5 UA/UA -1.48 8.36 2.07 -4.57 7.63 3.95 A

6 AC/GU -1.60 7.85 2.98 -3.89 8.10 2.24 A

7 CG/CG -1.66 8.13 2.43 -8.01 6.13 5.87 A

8 GA/UC -1.72 8.37 2.11 -3.29 8.27 2.47 A

9 AG/CU -2.09 8.16 2.23 -7.39 7.43 4.04 A

10 GG/CC -2.08 7.69 2.54 -6.92 6.60 4.68 A

11 GU/AC -0.59 7.11 3.01 -1.74 7.21 2.79

12 UU/GA 3.88 4.51 0.09 -0.16 4.41 1.21

13 UA/UG --- --- --- --- --- --- ---

14 AU/UU 1.27 6.88 2.33 -1.58 6.32 3.71

15 UU/AU -0.16 7.89 2.18 -3.35 7.51 3.33

16 UC/GA -1.35 7.82 2.65 -4.94 6.93 4.44 A

17 CC/GG -2.11 7.59 2.58 -6.53 7.06 3.80 A

18 CG/CG -2.25 8.51 2.25 -11.20 5.77 6.63 A

19 GG/CC -1.80 8.14 2.33 -4.96 7.89 3.07 A

20 GC/AC -1.25 8.61 2.10 -3.97 8.22 3.37

21 CG/CA -3.05 7.18 3.49 -4.51 6.41 4.65

22 GC/GC -1.85 8.09 2.39 -4.60 8.02 2.62 A

23 CC/GG -1.55 8.28 2.46 -8.09 7.16 4.82 A

24 CA/AG -2.20 4.66 2.33 -2.97 4.62 2.69

25 AA/UA -0.30 5.65 4.47 -4.74 5.98 4.64

26 AG/CU 2.41 1.66 1.69 4.21 1.81 1.84

27 GG/CC --- --- --- --- --- --- ---

****************************************************************************

Minor and major groove widths: direct P-P distances and refined P-P distances

which take into account the directions of the sugar-phosphate backbones

(Subtract 5.8 Angstrom from the values to take account of the vdw radii

of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of

Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.

Minor Groove Major Groove

P-P Refined P-P Refined

1 GG/CC --- --- --- ---

2 GG/CC --- --- --- ---

3 GG/CC 16.4 --- 16.5 ---

4 GU/AC 17.4 15.7 16.9 14.9

5 UA/UA 17.4 15.8 18.2 17.6

6 AC/GU 16.1 14.8 18.3 17.8

7 CG/CG 16.1 14.8 17.8 17.3

8 GA/UC 16.6 15.4 15.0 11.2

9 AG/CU 16.4 14.9 15.5 12.5

10 GG/CC 16.0 --- 15.1 ---

11 GU/AC --- --- --- ---

12 UU/GA --- --- --- ---

13 UA/UG --- --- --- ---

14 AU/UU --- --- --- ---

15 UU/AU --- --- --- ---

16 UC/GA 16.7 --- 15.4 ---

17 CC/GG 16.6 14.8 16.4 11.2

18 CG/CG 16.6 15.2 17.0 11.4

19 GG/CC 17.6 14.4 16.8 12.3

20 GC/AC 17.9 13.7 15.6 13.4

21 CG/CA 16.8 14.2 12.8 11.6

22 GC/GC 16.7 14.9 11.1 9.7

23 CC/GG 16.8 15.1 9.9 3.4

24 CA/AG 16.5 --- 9.2 ---

25 AA/UA --- --- --- ---

26 AG/CU --- --- --- ---

27 GG/CC --- --- --- ---

****************************************************************************

Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs

Deviation from regular linear helix: 0.06(3.41)

****************************************************************************

Main chain and chi torsion angles:

Note: alpha: O3'(i-1)-P-O5'-C5'

beta: P-O5'-C5'-C4'

gamma: O5'-C5'-C4'-C3'

delta: C5'-C4'-C3'-O3'

epsilon: C4'-C3'-O3'-P(i+1)

zeta: C3'-O3'-P(i+1)-O5'(i+1)

chi for pyrimidines(Y): O4'-C1'-N1-C2

chi for purines(R): O4'-C1'-N9-C4

Strand I

base alpha beta gamma delta epsilon zeta chi

1 G --- 128.7 67.6 77.8 -149.5 -76.7 -171.1

2 G -60.0 159.7 59.2 77.5 -155.8 -79.7 -167.8

3 G -70.2 172.5 64.4 88.2 -145.7 -79.6 -164.3

4 G 171.8 -172.1 172.4 81.2 -131.2 -73.7 -176.5

5 U -73.0 178.2 62.7 83.4 -176.0 -81.9 -154.1

6 A 171.1 -167.9 -179.2 159.1 -88.4 -56.4 -136.8

7 C 45.4 165.4 49.1 82.0 -144.1 -80.6 -164.6

8 G -63.1 176.6 55.2 79.4 -159.0 -74.8 -156.8

9 A -61.8 155.6 61.6 80.5 -159.0 -119.2 -163.2

10 G 159.8 -101.0 151.5 71.8 -145.8 -76.6 -179.9

11 G -63.3 145.9 67.6 75.4 -158.0 -71.4 -175.4

12 U -65.1 170.0 57.5 83.6 -124.8 -77.3 -156.0

13 U -62.2 162.9 60.1 77.0 -135.0 -59.2 -153.2

14 A -67.9 176.1 61.0 77.9 -140.7 -68.2 -177.5

15 U -65.5 169.4 60.9 81.4 -151.9 -56.4 -165.3

16 U -71.7 162.9 59.7 80.4 -145.5 -72.5 -168.4

17 C -70.3 172.7 56.0 84.4 -168.6 -110.0 -169.5

18 C 172.9 -76.6 96.1 70.1 -138.4 -88.7 -162.5

19 G -51.0 134.6 65.1 73.5 -155.6 -79.9 -173.3

20 G -67.8 167.9 60.5 76.1 -142.8 -89.4 -163.5

21 C 50.8 -57.8 -166.8 89.3 -0.3 171.5 -178.6

22 G -173.2 138.3 57.5 86.1 -135.9 -83.1 174.3

23 C -83.8 -170.8 63.1 80.4 -148.4 -66.7 -158.4

24 C -65.0 155.8 66.4 73.4 -166.6 -55.5 -166.3

25 A -69.9 175.3 59.3 82.8 165.7 -64.3 -157.9

26 A -66.3 158.6 63.1 78.6 -150.1 -75.8 -169.8

27 G -36.5 123.7 52.1 76.9 59.8 112.5 -150.5

28 G -83.2 -145.6 58.7 159.6 -109.1 99.5 -70.8

Strand II

base alpha beta gamma delta epsilon zeta chi

1 C -88.9 -152.2 62.0 80.5 178.4 -57.7 -135.0

2 C -84.4 -175.5 60.8 82.0 -158.6 -80.3 -162.2

3 C -68.0 166.8 58.2 82.4 -147.2 -75.7 -169.4

4 C -74.3 171.9 63.9 83.1 -162.6 -76.1 -153.6

5 A -81.2 -178.3 64.7 84.3 -147.1 -78.5 -156.5

6 U -70.1 167.7 63.6 82.7 -151.5 -83.8 -166.6

7 G 159.6 -155.0 172.0 91.6 -117.1 -81.8 176.0

8 C -66.2 143.0 58.2 76.7 -146.9 -102.8 -162.8

9 U -118.7 76.8 148.9 98.6 -84.2 -94.6 175.4

10 C 55.9 86.7 40.2 80.4 -146.0 -46.5 -167.8

11 C -99.0 -168.5 55.2 78.9 179.3 -127.0 -169.0

12 A -68.2 -130.2 69.3 146.1 -84.6 -178.2 -74.6

13 G 177.7 168.1 -62.8 153.4 -131.0 -151.0 -101.4

14 U -52.6 152.9 61.5 84.7 -96.5 -124.2 -157.6

15 U 172.7 -67.3 92.6 66.4 -166.6 -76.6 -158.0

16 A -76.8 -175.8 54.1 77.4 -168.4 -107.4 -166.5

17 G 50.5 63.1 44.4 70.5 180.0 -79.5 -170.4

18 G -124.3 77.8 145.8 88.0 -116.5 -145.3 174.7

19 C -53.2 156.4 59.4 85.1 -150.0 -30.4 -161.6

20 C -59.8 164.5 59.7 75.9 -161.2 -77.2 -163.4

21 A -64.6 161.4 58.1 78.2 -152.2 -64.1 -165.6

22 C -74.1 173.2 57.9 81.2 -154.1 -65.9 -160.4

23 G -56.1 151.8 58.6 79.4 -151.6 -64.8 -172.1

24 G -65.6 162.2 55.0 80.5 -163.7 -78.6 -165.5

25 A -161.3 -115.1 72.1 81.4 42.6 137.3 -89.9

26 U -59.2 -162.5 56.9 84.5 -140.1 -133.1 -151.9

27 C -83.8 -167.0 64.7 152.4 -149.4 79.4 -125.9

28 C -177.9 137.4 56.8 82.3 -129.1 -73.9 -174.0

****************************************************************************

Sugar conformational parameters:

Note: v0: C4'-O4'-C1'-C2'

v1: O4'-C1'-C2'-C3'

v2: C1'-C2'-C3'-C4'

v3: C2'-C3'-C4'-O4'

v4: C3'-C4'-O4'-C1'

tm: the amplitude of pucker

P: the phase angle of pseudorotation

Strand I

base v0 v1 v2 v3 v4 tm P Puckering

1 G -0.3 -28.2 44.5 -47.0 29.0 47.1 19.4 C3'-endo

2 G -1.4 -29.0 46.4 -49.2 31.7 49.5 20.5 C3'-endo

3 G 2.4 -23.3 35.5 -34.6 19.8 36.7 14.7 C3'-endo

4 G 4.3 -29.6 43.3 -42.6 23.7 44.5 13.7 C3'-endo

5 U 4.3 -28.8 41.0 -40.1 22.0 42.1 12.9 C3'-endo

6 A -9.9 31.5 -40.3 35.8 -16.2 40.5 184.9 C3'-exo

7 C 5.2 -30.3 43.0 -41.4 22.2 43.9 12.0 C3'-endo

8 G -5.2 -22.0 40.2 -44.1 30.0 44.3 24.9 C3'-endo

9 A 5.6 -29.2 41.9 -40.1 20.9 42.8 11.5 C3'-endo

10 G -9.9 -20.5 41.7 -49.5 36.2 48.3 30.3 C3'-endo

11 G -3.1 -26.3 44.6 -48.8 31.6 48.3 22.6 C3'-endo

12 U 4.3 -26.7 38.5 -37.6 20.2 39.5 12.8 C3'-endo

13 U -3.8 -23.2 40.6 -43.9 29.8 44.2 23.5 C3'-endo

14 A 4.3 -30.9 45.2 -43.7 24.6 46.5 13.4 C3'-endo

15 U 2.5 -25.9 38.7 -39.1 22.5 40.2 15.6 C3'-endo

16 U 3.0 -26.9 40.0 -40.0 22.7 41.4 14.9 C3'-endo

17 C 6.1 -29.1 40.0 -37.1 19.5 40.6 9.9 C3'-endo

18 C -17.5 -12.5 37.0 -48.2 40.4 47.9 39.4 C4'-exo

19 G -21.0 -9.6 35.2 -48.8 43.3 48.7 43.7 C4'-exo

20 G -4.7 -22.6 40.6 -45.2 30.3 44.7 24.8 C3'-endo

21 C 20.2 -39.5 42.7 -32.0 7.3 43.2 351.2 C2'-exo

22 G 1.3 -23.8 37.2 -38.0 21.8 38.8 16.9 C3'-endo

23 C 5.9 -30.8 43.9 -42.5 22.2 44.9 11.7 C3'-endo

24 C -9.0 -25.3 48.3 -54.2 40.4 54.6 27.8 C3'-endo

25 A -2.7 -21.6 36.8 -38.7 26.3 39.8 22.1 C3'-endo

26 A -17.7 -12.9 36.0 -48.5 41.6 47.4 40.6 C4'-exo

27 G -24.2 -5.3 30.8 -45.6 43.5 46.7 48.8 C4'-exo

28 G -12.6 33.9 -42.1 35.4 -14.0 42.1 181.3 C3'-exo

Strand II

base v0 v1 v2 v3 v4 tm P Puckering

1 C -4.8 -19.9 35.8 -39.6 28.4 39.7 25.6 C3'-endo

2 C 0.6 -25.6 40.0 -39.9 25.1 41.9 17.5 C3'-endo

3 C 3.7 -27.0 39.9 -38.5 21.6 41.0 13.5 C3'-endo

4 C 3.0 -29.2 42.6 -41.7 24.3 43.9 14.4 C3'-endo

5 A 8.4 -31.3 41.8 -37.5 18.3 42.2 7.1 C3'-endo

6 U -5.0 -21.6 39.1 -42.5 29.5 43.0 24.7 C3'-endo

7 G 10.9 -28.8 35.3 -30.4 11.9 35.4 1.4 C3'-endo

8 C -5.9 -21.6 40.0 -45.2 31.2 44.6 26.3 C3'-endo

9 U 23.1 -35.1 35.1 -22.4 -1.0 37.1 341.2 C2'-exo

10 C -20.3 -6.9 29.8 -42.7 38.8 42.8 46.0 C4'-exo

11 C -4.6 -21.8 39.2 -42.5 29.2 43.1 24.3 C3'-endo

12 A -22.2 36.8 -36.2 23.5 -0.7 37.9 162.7 C2'-endo

13 G -29.6 45.8 -43.6 27.5 1.5 46.5 159.8 C2'-endo

14 U 4.9 -28.9 41.0 -39.1 21.1 41.9 11.8 C3'-endo

15 U -16.6 -16.8 43.1 -54.4 43.3 53.5 36.3 C4'-exo

16 A 7.3 -34.5 48.9 -45.2 23.4 49.7 10.1 C3'-endo

17 G -23.6 -12.3 40.7 -56.5 49.8 55.8 43.2 C4'-exo

18 G 20.5 -39.0 42.5 -32.1 6.8 43.0 351.1 C2'-exo

19 C -0.5 -23.2 37.6 -38.9 24.2 39.9 19.3 C3'-endo

20 C -2.3 -24.2 41.9 -44.3 28.3 45.0 21.5 C3'-endo

21 A -6.1 -23.9 44.7 -47.4 33.2 49.2 24.5 C3'-endo

22 C -7.0 -19.9 37.9 -43.9 30.6 42.8 27.9 C3'-endo

23 G -5.5 -19.2 37.1 -40.9 28.1 41.2 25.8 C3'-endo

24 G 1.4 -26.5 40.5 -41.1 24.6 42.3 16.9 C3'-endo

25 A -30.0 2.3 23.9 -42.8 44.9 45.7 58.5 C4'-exo

26 U 4.0 -29.3 43.0 -40.6 23.0 44.1 12.9 C3'-endo

27 C -17.1 35.2 -39.4 30.1 -8.2 39.7 173.4 C2'-endo

28 C -6.0 -20.1 37.5 -41.9 29.5 41.9 26.4 C3'-endo

****************************************************************************

Same strand P--P and C1'--C1' virtual bond distances

Strand I Strand II

step P--P C1'--C1' step P--P C1'--C1'

1 G/G 6.14 5.47 1 C/C 5.66 6.04

2 G/G 5.83 5.31 2 C/C 5.73 5.53

3 G/G 5.89 5.46 3 C/C 6.09 5.58

4 G/U 6.39 5.72 4 C/A 5.65 5.20

5 U/A 6.12 5.74 5 A/U 5.94 5.61

6 A/C 9.00 6.00 6 U/G 6.39 5.58

7 C/G 5.40 6.06 7 G/C 5.70 5.23

8 G/A 5.59 5.05 8 C/U 5.73 5.33

9 A/G 5.99 5.18 9 U/C 5.41 5.22

10 G/G 6.21 5.81 10 C/C 5.71 5.66

11 G/U 6.24 6.05 11 C/A 13.52 7.75

12 U/U 5.25 5.48 12 A/G 14.39 6.57

13 U/A --- --- 13 G/U --- ---

14 A/U 5.41 5.50 14 U/U 5.24 5.86

15 U/U 5.66 5.59 15 U/A 5.71 5.30

16 U/C 5.66 5.84 16 A/G 5.68 6.12

17 C/C 6.00 5.16 17 G/G 6.35 5.67

18 C/G 4.95 5.14 18 G/C 5.95 5.21

19 G/G 6.11 5.44 19 C/C 5.85 5.70

20 G/C 5.42 5.03 20 C/A 5.75 5.47

21 C/G 14.64 12.12 21 A/C 5.77 5.29

22 G/C 5.72 6.15 22 C/G 5.83 5.62

23 C/C 5.41 5.49 23 G/G 6.00 5.50

24 C/A 6.39 5.46 24 G/A 11.52 13.80

25 A/A 6.25 5.86 25 A/U 16.28 8.15

26 A/G 6.03 5.15 26 U/C 11.91 4.49

27 G/G --- --- 27 C/C --- ---

****************************************************************************

Helix radius (radial displacement of P, O4', and C1' atoms in local helix

frame of each dimer)

Strand I Strand II

step P O4' C1' P O4' C1'

1 GG/CC 7.57 7.86 7.45 10.70 10.24 9.42

2 GG/CC 9.24 8.81 8.07 9.30 8.73 7.94

3 GG/CC 11.98 10.38 9.81 8.66 9.54 9.02

4 GU/AC 8.72 7.77 7.10 9.43 9.04 8.19

5 UA/UA 10.83 9.63 8.79 6.97 7.45 6.83

6 AC/GU 9.00 8.13 7.39 8.97 7.42 6.67

7 CG/CG 10.17 10.78 10.47 10.01 10.36 10.02

8 GA/UC 8.46 7.42 6.57 9.33 7.77 6.78

9 AG/CU 10.77 10.27 9.70 10.19 9.54 9.12

10 GG/CC 10.15 9.64 9.13 8.97 9.48 8.94

11 GU/AC 9.89 8.37 7.32 7.06 4.88 4.17

12 UU/GA 3.84 2.51 2.06 7.39 9.25 8.65

13 UA/UG ---- ---- ---- ---- ---- ----

14 AU/UU 6.89 7.83 7.59 7.08 6.18 5.06

15 UU/AU 6.50 7.01 6.69 10.10 9.57 8.59

16 UC/GA 7.01 7.68 7.14 10.02 9.93 9.06

17 CC/GG 9.62 9.48 8.74 9.68 9.30 8.70

18 CG/CG 12.07 12.18 12.01 13.12 12.89 12.69

19 GG/CC 9.62 8.46 7.69 9.04 8.56 7.80

20 GC/AC 10.53 8.79 7.83 7.81 7.72 7.22

21 CG/CA 11.43 11.29 10.16 4.29 4.64 4.58

22 GC/GC 9.38 8.61 7.81 9.11 8.03 7.28

23 CC/GG 11.60 11.05 10.61 10.02 10.96 10.50

24 CA/AG 7.66 6.32 5.38 9.69 8.79 8.27

25 AA/UA 3.89 3.63 3.52 13.69 9.45 9.06

26 AG/CU 8.74 6.28 5.08 12.01 8.41 7.34

27 GG/CC ---- ---- ---- ---- ---- ----

****************************************************************************

Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)

for each dinucleotide step

step Px Py Pz Hx Hy Hz

1 GG/CC 41.12 39.21 37.36 -0.93 0.25 -0.26

2 GG/CC 39.14 38.12 35.97 -0.99 0.04 -0.12

3 GG/CC 37.22 38.81 38.01 -0.96 0.27 0.07

4 GU/AC 32.80 38.16 35.60 -1.00 -0.01 -0.06

5 UA/UA 30.55 38.40 37.67 -0.98 0.19 -0.10

6 AC/GU 27.51 37.78 37.60 -0.94 0.25 0.25

7 CG/CG 23.24 39.79 34.61 -0.94 -0.32 0.09

8 GA/UC 21.15 38.88 39.78 -0.99 0.11 0.10

9 AG/CU 18.53 37.11 36.52 -0.99 -0.16 0.06

10 GG/CC 15.72 36.68 37.47 -0.98 -0.17 0.14

11 GU/AC 12.48 39.50 34.93 -0.97 -0.12 -0.23

12 UU/GA 9.32 43.17 36.46 -0.99 0.09 -0.10

13 UA/UG ---- ---- ---- ---- ---- ----

14 AU/UU 18.97 -7.16 21.67 -0.31 0.94 0.17

15 UU/AU 19.35 -3.59 22.33 -0.38 0.93 0.05

16 UC/GA 18.27 -1.34 23.13 -0.25 0.97 0.01

17 CC/GG 18.40 0.98 24.89 -0.12 0.99 0.11

18 CG/CG 21.31 4.40 21.85 -0.38 0.89 -0.23

19 GG/CC 17.54 6.26 26.30 0.05 1.00 0.02

20 GC/AC 18.90 9.00 26.46 0.01 0.99 -0.15

21 CG/CA 22.32 12.12 25.45 0.00 1.00 -0.05

22 GC/GC 21.40 15.43 28.77 0.10 0.97 -0.24

23 CC/GG 18.87 17.80 31.34 0.13 0.99 0.11

24 CA/AG 21.56 21.04 27.54 -0.10 0.99 -0.06

25 AA/UA 23.16 24.55 25.26 -0.08 0.99 0.06

26 AG/CU 15.00 26.40 27.30 -0.24 0.97 0.06

27 GG/CC ---- ---- ---- ---- ---- ----