ID code: 1EM0, DD0027 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 17 May 24 * *********************************** ************** FILE : duplex.pdb lis : dna : axin : axout: daf : pdb : acc : 0.000 wid : 0.750 maxn : 500 ior : 0 ibond: 0 splin: 3 break: -1 NLEVE: 0 NBAC : 7 ends : F supp : T COMB : T dinu : F mini : T rest : F LINE : F zaxe : F FIT : T test : F GRV : F old : T axonl: F Least squares fitting of standard bases ... Str Pos Base Rms (ang) 1 : 1) C+A 1 0.051 1 : 2) CA 2 0.098 1 : 3) TA 3 0.030 1 : 4) AA 4 0.060 1 : 5) GA 5 0.080 1 : 6) GA 6 0.055 2 : 1) GB 12 0.083 2 : 2) GB 11 0.043 2 : 3) AB 10 0.062 2 : 4) TB 9 0.049 2 : 5) CB 8 0.040 2 : 6) C+B 7 0.093 Strand: 1 Unit: 6 (GA 6) linkage from atom C3' ( 106) to C4' absent Strand: 2 Unit: 5 (CB 8) linkage from atom C4' ( 142) to C5' absent Strand: 2 Unit: 6 (C+B 7) linkage from atom C2' ( 127) to C3' absent Strand= 2 Nucleo= 12 Atoms = 240 Units = 12 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 6 levels ... Strand 1 has 6 bases (5'-3'): CCTAGG Strand 2 has 6 bases (3'-5'): GGATCC FIRST SUM= 21.608 CPTS: 5.249 0.270 2.445 13.644 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 24 STEP 1 SUM= 21.608 DEL= 0.000E+00 STEP 2 SUM= 14.791 DEL= -0.682E+01 STEP 3 SUM= 44.666 DEL= 0.299E+02 STEP 4 SUM= 13.723 DEL= -0.309E+02 STEP 5 SUM= 13.034 DEL= -0.690E+00 STEP 6 SUM= 12.200 DEL= -0.833E+00 STEP 7 SUM= 11.442 DEL= -0.758E+00 STEP 8 SUM= 11.007 DEL= -0.435E+00 STEP 9 SUM= 10.976 DEL= -0.316E-01 STEP 10 SUM= 10.782 DEL= -0.194E+00 STEP 11 SUM= 10.478 DEL= -0.305E+00 STEP 12 SUM= 10.137 DEL= -0.341E+00 STEP 13 SUM= 12.889 DEL= 0.275E+01 STEP 14 SUM= 10.103 DEL= -0.279E+01 STEP 15 SUM= 10.068 DEL= -0.349E-01 STEP 16 SUM= 10.007 DEL= -0.610E-01 STEP 17 SUM= 9.929 DEL= -0.781E-01 STEP 18 SUM= 9.921 DEL= -0.771E-02 STEP 19 SUM= 9.857 DEL= -0.638E-01 STEP 20 SUM= 9.788 DEL= -0.688E-01 STEP 21 SUM= 9.751 DEL= -0.374E-01 STEP 22 SUM= 9.721 DEL= -0.299E-01 STEP 23 SUM= 9.687 DEL= -0.335E-01 STEP 24 SUM= 9.672 DEL= -0.159E-01 STEP 25 SUM= 9.668 DEL= -0.376E-02 STEP 26 SUM= 9.667 DEL= -0.768E-03 STEP 27 SUM= 9.666 DEL= -0.873E-03 STEP 28 SUM= 9.666 DEL= 0.299E-04 STEP 29 SUM= 9.666 DEL= -0.147E-03 STEP 30 SUM= 9.666 DEL= -0.917E-04 STEP 31 SUM= 9.666 DEL= -0.132E-03 STEP 32 SUM= 9.666 DEL= -0.602E-04 STEP 33 SUM= 9.666 DEL= -0.209E-04 STEP 34 SUM= 9.666 DEL= -0.290E-05 STEP 35 SUM= 9.666 DEL= -0.495E-06 STEP 36 SUM= 9.666 DEL= -0.375E-07 STEP 37 SUM= 9.666 DEL= -0.421E-08 STEP 38 SUM= 9.666 DEL= -0.119E-08 STEP 39 SUM= 9.666 DEL= -0.222E-10 STEP 40 SUM= 9.666 DEL= -0.703E-12 STEP 41 SUM= 9.666 DEL= 0.000E+00 STEP 42 SUM= 9.666 DEL= -0.178E-14 STEP 43 SUM= 9.666 DEL= 0.000E+00 FINAL SUM= 9.666 CPTS: 3.670 2.702 1.043 2.251 GRA=-0.11E-10 0.26E-11-0.70E-11-0.68E-14-0.80E-12 0.73E-11-0.27E-11-0.27E-11 GRA=-0.30E-12 0.46E-11 0.67E-11 0.71E-11-0.15E-11 0.14E-10-0.14E-11 0.40E-11 GRA=-0.39E-11 0.54E-11-0.13E-10-0.71E-11 0.39E-11 0.10E-10 0.12E-10-0.28E-11 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: 0.383 0.348 -0.856 P: 9.734 7.780 51.867 D: 0.351 2) U: 0.399 0.357 -0.845 P: 11.279 8.993 48.778 D: 1.035 3) U: 0.392 0.280 -0.876 P: 12.493 10.327 46.104 D: 0.853 4) U: 0.469 0.264 -0.843 P: 13.611 11.304 43.016 D: 4.226 5) U: 0.316 0.303 -0.899 P: 15.777 12.113 40.038 D: 3.201 6) U: 0.322 0.211 -0.923 P: 16.420 13.150 36.885 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) C+A 1 0.64 -1.06 -6.57 -5.47 3 0 2) CA 2 0.66 -1.13 -10.47 -2.63 3 -3 3) TA 3 0.44 -0.97 -0.62 0.64 4 -27 4) AA 4 0.69 -0.88 -3.22 1.53 2 27 5) GA 5 -0.14 -0.73 0.36 4.75 1 3 6) GA 6 0.33 -1.01 3.02 12.66 1 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 12 0.56 1.13 -3.25 -4.11 1 0 2) GB 11 0.76 1.21 4.15 -2.96 1 3 3) AB 10 0.56 0.99 -2.02 -7.51 2 27 4) TB 9 0.81 0.58 -1.10 -2.62 4 -27 5) CB 8 -0.13 0.79 -8.84 -14.94 3 -3 6) C+B 7 0.32 1.09 -13.44 10.36 3 0 -------------------------------------- |C| Global Base pair-Axis Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) C 1-G 12 0.60 -1.09 -4.91 -0.68 3 0 2) C 2-G 11 0.71 -1.17 -3.16 0.17 3 -3 3) T 3-A 10 0.50 -0.98 -1.32 4.08 4 -27 4) A 4-T 9 0.75 -0.73 -2.16 2.07 2 27 5) G 5-C 8 -0.13 -0.76 -4.24 9.84 1 3 6) G 6-C 7 0.32 -1.05 -5.21 1.15 1 0 Average: 0.46 -0.96 -3.50 2.77 --------------------------------- |D| Global Base-Base Parameters | --------------------------------- Strand 1 with strand 2 ... Duplex Shear Stretch Stagger Buckle Propel Opening Bc Tc (Sx) (Sy) (Sz) (kappa) (omega) (sigma) 1) C 1-G 12 0.08 0.07 0.16 -3.32 -9.58 -0.46 3 0 2) C 2-G 11 -0.10 0.08 0.25 -14.61 -5.59 0.97 3 -3 3) T 3-A 10 -0.12 0.02 -0.08 1.40 -6.86 2.29 4 -27 4) A 4-T 9 -0.12 -0.30 -0.11 -2.12 -1.09 12.42 2 27 5) G 5-C 8 -0.01 0.06 0.29 9.20 -10.19 -4.24 1 3 6) G 6-C 7 0.01 0.08 0.15 16.46 23.01 -4.87 1 0 Average: -0.04 0.00 0.11 1.17 -1.72 1.02 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/C 2 0.10 -0.19 3.70 -2.83 2.25 42.92 -1 3) C 2/T 3 -0.49 0.36 3.04 11.54 7.72 22.29 -3 4) T 3/A 4 0.59 0.28 3.39 0.05 -3.28 51.12 10 5) A 4/G 5 -1.62 0.12 3.90 4.06 12.85 22.39 3 6) G 5/G 6 0.91 -0.45 3.28 6.63 4.15 27.26 1 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 12/G 11 0.27 0.20 3.61 8.46 1.74 41.49 1 3) G 11/A 10 -0.46 -0.41 3.38 -4.48 -8.99 20.97 3 4) A 10/T 9 0.59 -0.60 3.42 3.57 9.05 41.00 10 5) T 9/C 8 -1.73 0.23 3.50 -7.26 -21.95 39.05 -3 6) C 8/C 7 0.88 0.47 3.42 -0.63 29.06 27.89 -1 --------------------------------------- |F| Global Inter-Base pair Parameters | --------------------------------------- Strand 1 with strand 2 ... Duplex Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/C 2 0.19 -0.19 3.66 2.81 0.26 42.21 -1 3) C 2/T 3 -0.47 0.39 3.21 3.53 8.35 21.63 -3 4) T 3/A 4 0.59 0.44 3.41 1.81 -6.17 46.06 10 5) A 4/G 5 -1.68 -0.05 3.70 -1.60 17.40 30.72 3 6) G 5/G 6 0.90 -0.46 3.35 3.00 -12.45 27.57 1 Average: -0.10 0.02 3.47 1.91 1.48 33.64 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/C 2 1.18 -0.25 3.61 0.37 -4.15 42.44 -1 3) C 2/T 3 -0.07 0.27 3.03 11.82 5.43 22.54 -3 4) T 3/A 4 1.35 0.62 3.43 -0.90 -5.19 50.93 10 5) A 4/G 5 -1.51 0.14 3.78 3.12 12.20 22.90 3 6) G 5/G 6 0.79 -0.35 3.40 2.53 4.87 28.08 1 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 12/G 11 0.80 0.32 3.68 5.46 -1.33 41.99 1 3) G 11/A 10 -0.33 0.68 3.29 -6.35 9.31 20.46 3 4) A 10/T 9 0.81 1.04 3.53 0.23 -9.66 41.17 10 5) T 9/C 8 -1.63 -0.43 3.28 -13.32 17.73 38.75 -3 6) C 8/C 7 1.23 -0.88 3.47 -1.86 -33.77 27.72 -1 -------------------------------------- |H| Local Inter-Base pair Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/C 2 0.99 0.03 3.66 2.93 -2.77 42.28 -1 3) C 2/T 3 -0.19 0.47 3.16 2.78 7.52 21.54 -3 4) T 3/A 4 1.09 0.84 3.49 -0.48 -7.44 46.06 10 5) A 4/G 5 -1.59 -0.15 3.53 -4.95 15.35 30.67 3 6) G 5/G 6 1.02 -0.60 3.40 0.97 -14.56 29.69 1 Average: 0.26 0.12 3.45 0.25 -0.38 34.05 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/C 2 0.08 -0.12 1.06 -0.59 0.14 1.22 3.66 -1 3) C 2/T 3 -0.26 0.20 1.69 4.44 0.33 4.75 3.23 -3 4) T 3/A 4 0.34 0.18 2.65 -4.17 0.39 4.94 3.43 10 5) A 4/G 5 -0.79 -0.02 0.48 9.63 0.79 9.64 3.77 3 6) G 5/G 6 0.44 -0.18 3.98 -3.76 0.47 5.47 3.38 1 Overall axis bend ... UU= 9.44 PP= 14.33 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) C 2 0.17 38.16 3) T 3 0.47 -25.08 4) A 4 0.35 -108.80 5) G 5 0.70 -29.45 6) G 6 0.00 0.00 Path length= 17.46 End-to-end= 17.26 Shortening= 1.15 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)C+A 1 26.57 -34.67 184.41 34.85 C3'-exo 105.6 103.7 103.6 2)CA 2 24.95 -7.70 104.59 32.10 O1'-endo 107.4 105.9 102.3 3)TA 3 48.63 -39.14 146.20 48.36 C2'-endo 103.3 98.9 103.3 4)AA 4 -5.05 26.23 48.43 40.22 C4'-exo 107.4 103.1 101.4 5)GA 5 29.11 -28.89 165.72 30.77 C2'-endo 104.6 104.6 100.5 6)GA 6 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)C+A 1 -97.52 170.60 147.95 179.15 -95.70 -63.02 173.40 2)CA 2 -118.92 57.95 107.38 -167.69 -86.94 -67.19 169.40 3)TA 3 -85.83 48.91 143.17 -97.51 174.21 -76.71 133.02 4)AA 4 -130.26 43.40 87.05 178.21 -84.46 -55.03 179.94 5)GA 5 -105.80 58.76 141.95 -171.19 -82.38 -72.32 170.63 6)GA 6 -108.40 ...... ...... ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 12 30.60 -33.31 174.26 34.61 C2'-endo 108.4 102.4 102.4 2)GB 11 44.37 -31.56 136.51 44.90 C1'-exo 103.4 101.3 103.8 3)AB 10 27.75 -28.23 163.05 29.78 C2'-endo 106.8 102.2 105.8 4)TB 9 42.53 -43.83 168.91 45.73 C2'-endo 105.2 101.4 101.4 5)CB 8 -17.72 28.94 20.22 31.31 C3'-endo 109.9 103.3 103.8 6)C+B 7 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 12 -95.33 36.64 150.45 ...... ...... ...... ...... 2)GB 11 -84.79 49.68 136.19 -85.50 148.24 -77.36 159.90 3)AB 10 -102.02 50.52 130.74 -157.78 -84.11 -68.61 159.16 4)TB 9 -99.43 54.34 151.47 -107.77 -175.37 -70.46 149.77 5)CB 8 -154.80 ...... ...... -150.61 -70.59 -53.33 174.20 6)C+B 7 -113.51 ...... ...... ...... ...... ...... ......