ID code: 1ICG, AH0015 *********************************** ************** ****** 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) GA 1 0.023 1 : 2) CA 2 0.027 1 : 3) UA 3 0.029 1 : 4) UA 4 0.025 1 : 5) CA 5 0.026 1 : 6) GA 6 0.021 1 : 7) GA 7 0.025 1 : 8) CA 8 0.034 2 : 1) CB 8 0.024 2 : 2) GB 7 0.019 2 : 3) GB 6 0.027 2 : 4) CB 5 0.017 2 : 5) UB 4 0.027 2 : 6) UB 3 0.026 2 : 7) CB 2 0.023 2 : 8) GB 1 0.033 Strand= 2 Nucleo= 16 Atoms = 332 Units = 16 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 8 levels ... Strand 1 has 8 bases (5'-3'): GCUUCGGC Strand 2 has 8 bases (3'-5'): CGGCUUCG FIRST SUM= 177.339 CPTS: 1.530 32.831 2.929 140.049 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 32 STEP 1 SUM= 177.339 DEL= 0.000E+00 STEP 2 SUM= 139.258 DEL= -0.381E+02 STEP 3 SUM= 102.707 DEL= -0.366E+02 STEP 4 SUM= 109.742 DEL= 0.704E+01 STEP 5 SUM= 86.040 DEL= -0.237E+02 STEP 6 SUM= 76.375 DEL= -0.967E+01 STEP 7 SUM= 63.350 DEL= -0.130E+02 STEP 8 SUM= 57.505 DEL= -0.585E+01 STEP 9 SUM= 60.694 DEL= 0.319E+01 STEP 10 SUM= 55.209 DEL= -0.549E+01 STEP 11 SUM= 51.256 DEL= -0.395E+01 STEP 12 SUM= 46.946 DEL= -0.431E+01 STEP 13 SUM= 238.694 DEL= 0.192E+03 STEP 14 SUM= 47.748 DEL= -0.191E+03 STEP 15 SUM= 46.757 DEL= -0.991E+00 STEP 16 SUM= 46.413 DEL= -0.344E+00 STEP 17 SUM= 45.678 DEL= -0.735E+00 STEP 18 SUM= 49.637 DEL= 0.396E+01 STEP 19 SUM= 45.488 DEL= -0.415E+01 STEP 20 SUM= 46.266 DEL= 0.778E+00 STEP 21 SUM= 45.456 DEL= -0.809E+00 STEP 22 SUM= 45.401 DEL= -0.552E-01 STEP 23 SUM= 45.324 DEL= -0.771E-01 STEP 24 SUM= 45.195 DEL= -0.129E+00 STEP 25 SUM= 45.189 DEL= -0.582E-02 STEP 26 SUM= 45.129 DEL= -0.602E-01 STEP 27 SUM= 45.041 DEL= -0.882E-01 STEP 28 SUM= 44.947 DEL= -0.937E-01 STEP 29 SUM= 44.912 DEL= -0.348E-01 STEP 30 SUM= 44.894 DEL= -0.182E-01 STEP 31 SUM= 44.879 DEL= -0.152E-01 STEP 32 SUM= 44.869 DEL= -0.978E-02 STEP 33 SUM= 44.862 DEL= -0.711E-02 STEP 34 SUM= 44.860 DEL= -0.168E-02 STEP 35 SUM= 44.858 DEL= -0.234E-02 STEP 36 SUM= 44.856 DEL= -0.236E-02 STEP 37 SUM= 44.853 DEL= -0.232E-02 STEP 38 SUM= 44.853 DEL= -0.784E-03 STEP 39 SUM= 44.852 DEL= -0.109E-03 STEP 40 SUM= 44.852 DEL= -0.106E-04 STEP 41 SUM= 44.852 DEL= -0.667E-05 STEP 42 SUM= 44.852 DEL= -0.108E-04 STEP 43 SUM= 44.852 DEL= -0.140E-04 STEP 44 SUM= 44.852 DEL= -0.664E-05 STEP 45 SUM= 44.852 DEL= -0.646E-05 STEP 46 SUM= 44.852 DEL= -0.214E-05 STEP 47 SUM= 44.852 DEL= -0.454E-06 STEP 48 SUM= 44.852 DEL= -0.344E-07 STEP 49 SUM= 44.852 DEL= -0.391E-08 STEP 50 SUM= 44.852 DEL= -0.293E-08 STEP 51 SUM= 44.852 DEL= -0.281E-08 STEP 52 SUM= 44.852 DEL= -0.116E-08 STEP 53 SUM= 44.852 DEL= -0.204E-09 STEP 54 SUM= 44.852 DEL= -0.151E-10 STEP 55 SUM= 44.852 DEL= -0.129E-11 STEP 56 SUM= 44.852 DEL= -0.163E-12 STEP 57 SUM= 44.852 DEL= -0.213E-13 STEP 58 SUM= 44.852 DEL= 0.000E+00 FINAL SUM= 44.852 CPTS: 1.836 28.420 2.918 11.678 GRA= 0.29E-09-0.11E-09-0.30E-09-0.73E-09 0.77E-10-0.11E-09-0.20E-09-0.63E-09 GRA=-0.50E-09 0.75E-09 0.11E-09 0.51E-10-0.36E-09-0.71E-09 0.17E-09 0.28E-09 GRA= 0.58E-10-0.68E-10-0.40E-10 0.31E-09 0.88E-10-0.70E-09-0.17E-09 0.35E-09 GRA=-0.13E-09-0.42E-09 0.35E-09-0.46E-09-0.52E-09-0.37E-09 0.81E-09-0.92E-09 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: 0.125 -0.038 -0.991 P: 17.739 -1.169 19.545 D: 0.607 2) U: 0.124 0.060 -0.990 P: 17.981 -1.299 16.487 D: 4.429 3) U: 0.067 0.168 -0.984 P: 18.462 -0.681 13.416 D: 17.024 4) U: 0.187 0.221 -0.957 P: 17.249 -0.362 9.612 D: 2.749 5) U: 0.407 0.233 -0.883 P: 17.895 0.158 7.389 D: 16.157 6) U: 0.584 0.165 -0.795 P: 20.635 -0.016 5.465 D: 3.144 7) U: 0.614 0.112 -0.781 P: 22.787 0.598 2.750 D: 0.742 8) U: 0.634 0.076 -0.770 P: 25.139 0.907 0.368 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 1 -2.61 0.23 -6.20 -0.43 1 0 2) CA 2 -2.74 -0.02 -2.59 1.54 3 -7 3) UA 3 -1.11 -0.18 1.02 6.67 4 -19 4) UA 4 -3.93 -1.69 -0.94 9.53 4 -18 5) CA 5 -3.58 -1.50 8.34 2.25 3 -10 6) GA 6 -3.87 -1.04 1.56 -4.90 1 9 7) GA 7 -3.05 -0.83 -5.46 -3.81 1 5 8) CA 8 -3.09 -1.12 -4.63 2.55 3 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CB 8 -2.59 -0.13 1.31 -9.63 3 0 2) GB 7 -2.67 0.01 -3.37 -12.54 1 5 3) GB 6 -3.59 -0.28 -2.17 -14.54 1 9 4) CB 5 -3.81 -0.45 4.54 -7.56 3 -10 5) UB 4 -4.35 -0.72 -0.69 -3.27 4 -18 6) UB 3 -1.53 0.58 0.59 -5.53 4 -19 7) CB 2 -2.92 0.85 1.50 -9.03 3 -7 8) GB 1 -3.26 1.09 0.70 -5.41 1 0 -------------------------------------- |C| Global Base pair-Axis Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) G 1-C 8 -2.60 0.18 -2.44 4.60 1 0 2) C 2-G 7 -2.70 -0.01 -2.98 7.04 3 -7 3) U 3-G 6 -2.35 0.05 -0.57 10.60 4 -19 4) U 4-C 5 -3.87 -0.62 1.80 8.54 4 -18 5) C 5-U 4 -3.96 -0.39 3.83 2.76 3 -10 6) G 6-U 3 -2.70 -0.81 1.08 0.31 1 9 7) G 7-C 2 -2.99 -0.84 -1.98 2.61 1 5 8) C 8-G 1 -3.18 -1.11 -1.96 3.98 3 0 Average: -3.04 -0.44 -0.40 5.05 --------------------------------- |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) G 1-C 8 -0.02 0.10 -0.27 -7.52 -10.06 2.02 1 0 2) C 2-G 7 -0.07 -0.00 -0.00 0.78 -11.00 0.32 3 -7 3) U 3-G 6 2.48 -0.46 -0.42 3.20 -7.88 -0.85 4 -19 4) U 4-C 5 -0.12 -2.14 0.08 -5.48 1.97 -40.79 4 -18 5) C 5-U 4 0.77 -2.22 -0.25 9.03 -1.01 -42.35 3 -10 6) G 6-U 3 -2.35 -0.46 -0.42 0.97 -10.43 0.67 1 9 7) G 7-C 2 -0.13 0.01 -0.20 -6.96 -12.84 1.10 1 5 8) C 8-G 1 0.17 -0.03 0.10 -5.33 -2.86 -0.41 3 0 Average: 0.09 -0.65 -0.17 -1.41 -6.76 -10.04 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/C 2 -0.28 -0.40 3.20 2.97 7.55 29.95 5 3) C 2/U 3 1.94 -0.13 2.95 9.45 8.98 41.00 -3 4) U 3/U 4 -4.49 -2.01 3.86 -2.73 10.48 -0.33 -4 5) U 4/C 5 0.29 0.21 2.23 10.24 6.05 37.17 -2 6) C 5/G 6 1.28 0.27 2.88 -3.18 4.29 48.43 8 7) G 6/G 7 0.72 0.09 3.62 -6.25 4.59 40.05 1 8) G 7/C 8 -0.13 -0.61 3.49 2.71 7.98 32.03 5 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 8/G 7 -0.22 0.30 2.93 -5.33 -8.48 31.66 5 3) G 7/G 6 -0.61 -0.32 3.37 7.03 -5.86 42.17 1 4) G 6/C 5 -1.89 0.33 3.37 5.95 -0.63 39.60 8 5) C 5/U 4 -0.60 -0.29 2.55 -4.27 -9.04 38.73 -2 6) U 4/U 3 4.39 1.50 3.05 4.88 -13.70 5.41 -4 7) U 3/C 2 -1.49 0.37 3.41 1.67 -7.00 39.62 -3 8) C 2/G 1 -0.44 0.57 3.20 1.08 2.00 33.55 5 --------------------------------------- |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) G 1/C 2 -0.25 -0.35 3.07 -1.18 8.01 30.81 5 3) C 2/U 3 0.67 0.10 3.16 8.24 7.42 41.58 -3 4) U 3/U 4 -3.19 -1.17 3.62 1.61 5.56 19.63 -4 5) U 4/C 5 -0.15 0.25 2.39 2.99 7.54 37.95 -2 6) C 5/G 6 2.84 -0.62 2.97 0.85 8.99 26.92 8 7) G 6/G 7 -0.39 -0.14 3.52 -2.29 5.80 39.84 1 8) G 7/C 8 -0.28 -0.59 3.35 1.89 2.99 32.79 5 Average: -0.11 -0.36 3.15 1.73 6.62 32.79 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/C 2 -0.39 -2.04 3.29 2.62 5.20 30.34 5 3) C 2/U 3 1.65 -1.55 3.19 6.33 8.10 41.74 -3 4) U 3/U 4 -4.92 -2.29 3.57 -4.03 10.21 -0.91 -4 5) U 4/C 5 0.87 -1.95 3.42 1.26 8.22 36.40 -2 6) C 5/G 6 2.47 -2.16 3.71 -3.68 9.37 47.14 8 7) G 6/G 7 1.64 -2.42 3.60 -2.80 3.18 40.51 1 8) G 7/C 8 0.43 -2.64 3.30 3.04 4.94 32.06 5 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 8/G 7 -0.78 -1.80 3.06 -11.19 7.76 30.29 5 3) G 7/G 6 -1.39 -2.14 3.22 -2.91 3.71 42.79 1 4) G 6/C 5 -2.91 -2.39 3.42 -0.60 1.87 39.99 8 5) C 5/U 4 -1.20 -2.25 3.44 -2.84 9.33 38.04 -2 6) U 4/U 3 4.04 -2.08 3.94 6.49 12.84 5.94 -4 7) U 3/C 2 -1.34 -1.85 3.40 -3.35 7.51 39.52 -3 8) C 2/G 1 -0.25 -2.26 3.31 -3.05 -1.20 33.39 5 -------------------------------------- |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) G 1/C 2 -0.60 -1.91 3.18 -4.28 6.56 30.42 5 3) C 2/U 3 0.13 -1.84 3.31 1.71 5.92 42.40 -3 4) U 3/U 4 -3.84 -2.12 3.45 -1.52 6.25 19.61 -4 5) U 4/C 5 -0.10 -2.33 3.43 -0.94 7.49 37.23 -2 6) C 5/G 6 3.20 -1.94 3.69 1.07 11.86 26.59 8 7) G 6/G 7 0.13 -2.12 3.65 -3.07 5.35 40.27 1 8) G 7/C 8 0.08 -2.44 3.32 -0.01 1.87 32.56 5 Average: -0.14 -2.10 3.43 -1.01 6.47 32.73 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G 1/C 2 -0.15 -0.16 -0.64 5.58 0.22 5.61 3.07 5 3) C 2/U 3 0.32 0.03 5.84 3.85 0.32 6.99 3.17 -3 4) U 3/U 4 -1.67 -0.50 -0.77 7.62 1.74 7.66 4.01 -4 5) U 4/C 5 -0.07 0.02 0.96 13.33 0.07 13.36 2.37 -2 6) C 5/G 6 1.57 -0.20 3.60 11.44 1.59 11.99 3.35 8 7) G 6/G 7 -0.10 -0.11 0.77 3.50 0.15 3.58 3.52 1 8) G 7/C 8 -0.10 -0.32 1.88 1.63 0.34 2.48 3.36 5 Overall axis bend ... UU= 32.92 PP= 40.80 Duplex Offset L.Dir ... wrt end-to-end vector 1) G 1 0.00 0.00 2) C 2 0.97 54.81 3) U 3 1.54 34.88 4) U 4 4.03 37.10 5) C 5 4.23 2.14 6) G 6 2.38 -56.32 7) G 7 1.34 -89.95 8) C 8 0.00 0.00 Path length= 22.85 End-to-end= 20.66 Shortening= 9.59 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 1 -22.88 34.09 15.41 35.97 C3'-endo 107.1 102.3 103.0 2)CA 2 -26.10 38.85 15.57 41.08 C3'-endo 106.7 101.3 101.9 3)UA 3 -26.76 37.59 11.21 38.79 C3'-endo 105.7 101.9 102.7 4)UA 4 -29.32 39.73 9.15 40.97 C3'-endo 106.8 101.3 101.9 5)CA 5 -29.56 42.27 12.79 44.26 C3'-endo 107.1 99.3 101.3 6)GA 6 -32.25 42.20 6.09 42.94 C3'-endo 104.9 100.9 101.3 7)GA 7 -25.31 36.65 14.04 38.71 C3'-endo 108.1 100.9 102.8 8)CA 8 -11.21 26.76 35.62 33.45 C3'-endo 108.1 104.3 103.5 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GA 1 -176.55 -115.38 85.41 -132.54 -86.23 -66.88 163.37 2)CA 2 -166.67 60.54 76.41 -141.01 -73.94 -68.90 164.02 3)UA 3 -162.50 60.58 79.55 -173.48 -101.10 -55.59 -179.44 4)UA 4 -164.05 51.86 80.62 -146.79 -68.19 -73.60 177.96 5)CA 5 -162.19 54.29 75.90 -146.61 -68.73 -68.70 172.57 6)GA 6 -172.66 59.09 74.85 -141.70 -75.12 -55.77 165.29 7)GA 7 -173.67 60.28 82.89 -147.86 -65.35 -71.87 -178.38 8)CA 8 -158.44 62.04 87.36 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CB 8 -22.75 38.81 23.33 43.14 C3'-endo 106.8 101.2 101.2 2)GB 7 -29.00 38.09 7.54 39.46 C3'-endo 107.8 100.4 102.3 3)GB 6 -35.00 33.18 337.91 36.42 C2'-exo 104.7 101.2 104.1 4)CB 5 -17.88 30.33 22.55 33.55 C3'-endo 108.3 101.6 104.6 5)UB 4 -30.01 39.06 5.94 39.98 C3'-endo 106.3 101.0 102.4 6)UB 3 -24.46 35.32 14.48 37.34 C3'-endo 107.0 102.6 101.7 7)CB 2 -25.73 40.92 18.76 43.77 C3'-endo 106.1 100.6 101.4 8)GB 1 -26.03 34.22 6.37 34.96 C3'-endo 106.8 102.1 103.8 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CB 8 -152.03 40.93 75.31 ...... ...... ...... ...... 2)GB 7 -169.55 63.21 80.12 -126.47 -88.47 -42.21 153.42 3)GB 6 -174.66 -157.82 95.48 -135.41 -70.60 -69.19 165.80 4)CB 5 -155.19 45.68 84.62 -161.99 -64.75 131.10 -175.45 5)UB 4 -164.25 49.33 84.61 -147.16 -70.05 -56.57 -177.35 6)UB 3 -158.16 55.66 79.19 -168.89 -93.36 -68.30 -175.64 7)CB 2 -166.18 60.52 79.48 -145.09 -72.89 -63.57 169.49 8)GB 1 -176.92 61.15 85.63 -141.08 -74.83 -70.39 176.27