ID code: 1JGG, PDT031 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 16 Jul 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) TA 201 0.040 1 : 2) AA 202 0.026 1 : 3) AA 203 0.022 1 : 4) TA 204 0.030 1 : 5) TA 205 0.035 1 : 6) GA 206 0.043 1 : 7) AA 207 0.013 1 : 8) AA 208 0.030 1 : 9) TA 209 0.040 1 : 10) TA 210 0.068 2 : 1) AB 220 0.019 2 : 2) TB 219 0.034 2 : 3) TB 218 0.035 2 : 4) AB 217 0.056 2 : 5) AB 216 0.037 2 : 6) CB 215 0.026 2 : 7) TB 214 0.065 2 : 8) TB 213 0.021 2 : 9) AB 212 0.048 2 : 10) AB 211 0.020 Strand= 2 Nucleo= 20 Atoms = 410 Units = 20 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 10 levels ... Strand 1 has 10 bases (5'-3'): TAATTGAATT Strand 2 has 10 bases (3'-5'): ATTAACTTAA FIRST SUM= 35.178 CPTS: 4.430 4.434 3.829 22.484 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 40 STEP 1 SUM= 35.178 DEL= 0.000E+00 STEP 2 SUM= 24.618 DEL= -0.106E+02 STEP 3 SUM= 60.594 DEL= 0.360E+02 STEP 4 SUM= 22.664 DEL= -0.379E+02 STEP 5 SUM= 21.888 DEL= -0.776E+00 STEP 6 SUM= 20.737 DEL= -0.115E+01 STEP 7 SUM= 19.079 DEL= -0.166E+01 STEP 8 SUM= 18.515 DEL= -0.564E+00 STEP 9 SUM= 18.041 DEL= -0.474E+00 STEP 10 SUM= 17.886 DEL= -0.155E+00 STEP 11 SUM= 17.604 DEL= -0.283E+00 STEP 12 SUM= 16.990 DEL= -0.613E+00 STEP 13 SUM= 18.455 DEL= 0.146E+01 STEP 14 SUM= 16.744 DEL= -0.171E+01 STEP 15 SUM= 16.328 DEL= -0.416E+00 STEP 16 SUM= 16.111 DEL= -0.217E+00 STEP 17 SUM= 15.788 DEL= -0.323E+00 STEP 18 SUM= 16.410 DEL= 0.622E+00 STEP 19 SUM= 15.705 DEL= -0.704E+00 STEP 20 SUM= 15.565 DEL= -0.141E+00 STEP 21 SUM= 15.424 DEL= -0.141E+00 STEP 22 SUM= 15.209 DEL= -0.215E+00 STEP 23 SUM= 16.261 DEL= 0.105E+01 STEP 24 SUM= 15.178 DEL= -0.108E+01 STEP 25 SUM= 15.161 DEL= -0.174E-01 STEP 26 SUM= 15.131 DEL= -0.296E-01 STEP 27 SUM= 15.102 DEL= -0.289E-01 STEP 28 SUM= 15.023 DEL= -0.792E-01 STEP 29 SUM= 14.969 DEL= -0.538E-01 STEP 30 SUM= 14.882 DEL= -0.873E-01 STEP 31 SUM= 14.773 DEL= -0.109E+00 STEP 32 SUM= 14.664 DEL= -0.109E+00 STEP 33 SUM= 14.630 DEL= -0.335E-01 STEP 34 SUM= 14.610 DEL= -0.205E-01 STEP 35 SUM= 14.598 DEL= -0.115E-01 STEP 36 SUM= 14.593 DEL= -0.551E-02 STEP 37 SUM= 14.590 DEL= -0.300E-02 STEP 38 SUM= 14.590 DEL= 0.952E-04 STEP 39 SUM= 14.589 DEL= -0.531E-03 STEP 40 SUM= 14.589 DEL= -0.170E-03 STEP 41 SUM= 14.589 DEL= -0.189E-04 STEP 42 SUM= 14.589 DEL= -0.626E-05 STEP 43 SUM= 14.589 DEL= -0.816E-05 STEP 44 SUM= 14.589 DEL= -0.262E-05 STEP 45 SUM= 14.589 DEL= -0.175E-05 STEP 46 SUM= 14.589 DEL= -0.187E-05 STEP 47 SUM= 14.589 DEL= -0.702E-06 STEP 48 SUM= 14.589 DEL= -0.516E-06 STEP 49 SUM= 14.589 DEL= -0.816E-07 STEP 50 SUM= 14.589 DEL= -0.639E-07 STEP 51 SUM= 14.589 DEL= -0.464E-08 STEP 52 SUM= 14.589 DEL= -0.144E-07 STEP 53 SUM= 14.589 DEL= -0.208E-08 STEP 54 SUM= 14.589 DEL= -0.849E-10 STEP 55 SUM= 14.589 DEL= -0.545E-09 STEP 56 SUM= 14.589 DEL= -0.135E-09 STEP 57 SUM= 14.589 DEL= -0.265E-10 STEP 58 SUM= 14.589 DEL= -0.503E-12 STEP 59 SUM= 14.589 DEL= -0.373E-13 STEP 60 SUM= 14.589 DEL= 0.178E-14 STEP 61 SUM= 14.589 DEL= -0.178E-14 FINAL SUM= 14.589 CPTS: 3.453 6.659 0.440 4.039 GRA=-0.28E-08 0.16E-08-0.11E-08-0.19E-09-0.44E-08-0.26E-09-0.95E-09-0.57E-09 GRA= 0.68E-09-0.18E-08 0.11E-08 0.12E-08-0.72E-08-0.35E-08-0.44E-09-0.73E-10 GRA=-0.27E-08 0.36E-08 0.55E-09-0.58E-09 0.34E-08-0.13E-08 0.23E-09-0.70E-10 GRA=-0.11E-08 0.20E-08 0.88E-09 0.18E-10-0.79E-09-0.37E-08 0.65E-09-0.69E-09 GRA= 0.35E-08 0.15E-08-0.97E-09 0.71E-09-0.18E-08 0.77E-08-0.24E-09 0.97E-09 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.997 -0.053 -0.049 P: 40.581 17.991 40.694 D: 2.305 2) U: -0.996 -0.044 -0.071 P: 36.418 17.494 39.985 D: 2.820 3) U: -0.997 -0.044 -0.068 P: 33.610 17.998 39.633 D: 1.121 4) U: -1.000 -0.025 -0.002 P: 30.064 18.174 39.753 D: 1.194 5) U: -0.998 -0.056 -0.015 P: 26.715 18.412 39.931 D: 3.223 6) U: -0.998 -0.064 0.006 P: 23.506 17.491 39.859 D: 1.757 7) U: -1.000 -0.015 0.025 P: 19.942 17.732 40.257 D: 0.930 8) U: -0.997 -0.072 0.023 P: 16.488 17.255 40.276 D: 0.601 9) U: -0.999 -0.034 0.024 P: 13.156 16.952 40.123 D: 0.639 10) U: -0.992 -0.082 0.096 P: 9.899 16.743 40.315 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) TA 201 -0.35 0.58 18.98 -1.76 4 0 2) AA 202 -0.49 0.76 5.19 -8.57 2 28 3) AA 203 -0.50 0.41 0.93 -3.16 2 24 4) TA 204 -0.32 0.11 0.34 -3.35 4 -24 5) TA 205 -0.59 -0.16 2.73 -11.29 4 -26 6) GA 206 0.26 0.26 7.20 -4.27 1 12 7) AA 207 -0.13 0.64 1.74 -10.60 2 18 8) AA 208 -0.43 0.67 -3.89 -6.20 2 24 9) TA 209 -0.41 0.33 -5.95 -4.72 4 -24 10) TA 210 -0.64 0.23 -0.28 -3.02 4 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) AB 220 0.06 -0.45 12.29 -13.18 2 0 2) TB 219 -0.66 -0.81 15.28 -11.34 4 -28 3) TB 218 -0.05 -0.61 0.07 -2.91 4 -24 4) AB 217 -0.62 -0.32 -0.02 -3.30 2 24 5) AB 216 -0.63 0.12 3.92 -11.58 2 26 6) CB 215 -0.07 -0.25 -0.41 -1.40 3 -12 7) TB 214 -0.65 -0.81 -2.78 -3.48 4 -18 8) TB 213 -0.28 -0.46 -2.65 -6.47 4 -24 9) AB 212 -0.79 -0.52 -4.49 -6.49 2 24 10) AB 211 -0.58 -0.56 -1.55 -9.08 2 0 -------------------------------------- |C| Global Base pair-Axis Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) T201-A220 -0.14 0.52 15.64 5.71 4 0 2) A202-T219 -0.57 0.78 10.23 1.38 2 28 3) A203-T218 -0.28 0.51 0.50 -0.12 2 24 4) T204-A217 -0.47 0.22 0.16 -0.02 4 -24 5) T205-A216 -0.61 -0.14 3.32 0.14 4 -26 6) G206-C215 0.10 0.25 3.40 -1.43 1 12 7) A207-T214 -0.39 0.72 -0.52 -3.56 2 18 8) A208-T213 -0.35 0.57 -3.27 0.13 2 24 9) T209-A212 -0.60 0.42 -5.22 0.89 4 -24 10) T210-A211 -0.61 0.39 -0.91 3.03 4 0 Average: -0.39 0.42 2.33 0.61 --------------------------------- |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) T201-A220 -0.41 0.14 -1.02 6.69 -14.94 13.31 4 0 2) A202-T219 0.17 -0.04 -0.67 -10.09 -19.91 3.31 2 28 3) A203-T218 -0.45 -0.20 0.46 0.86 -6.07 7.31 2 24 4) T204-A217 0.30 -0.21 -0.19 0.37 -6.65 3.63 4 -24 5) T205-A216 0.04 -0.04 -0.42 -1.20 -22.86 3.86 4 -26 6) G206-C215 0.33 0.02 0.34 7.62 -5.67 11.58 1 12 7) A207-T214 0.52 -0.18 0.43 4.51 -14.07 9.44 2 18 8) A208-T213 -0.15 0.21 -0.10 -1.24 -12.67 8.04 2 24 9) T209-A212 0.38 -0.20 0.10 -1.46 -11.21 2.14 4 -24 10) T210-A211 -0.07 -0.34 -0.58 1.26 -12.11 -5.62 4 0 Average: 0.07 -0.08 -0.16 0.73 -12.62 5.70 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) T201/A202 -0.43 0.64 4.40 -15.08 -6.30 38.39 10 3) A202/A203 0.57 -0.62 3.36 -4.08 5.31 34.56 4 4) A203/T204 0.03 -0.65 3.21 1.53 -3.50 34.99 7 5) T204/T205 -0.57 -0.57 3.22 0.95 -6.65 32.43 -4 6) T205/G206 1.47 0.81 3.64 3.23 6.69 43.82 -9 7) G206/A207 -0.75 0.74 3.60 -6.75 -9.04 38.69 2 8) A207/A208 -0.09 -0.22 3.21 -3.49 6.83 30.36 4 9) A208/T209 -0.16 -0.53 3.44 -4.17 0.92 34.48 7 10) T209/T210 -0.24 -0.12 2.94 9.54 4.89 25.41 -4 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) A220/T219 -1.01 -0.82 4.04 1.70 1.33 48.39 10 3) T219/T218 1.20 0.46 2.24 -15.03 8.53 30.55 -4 4) T218/A217 -0.72 0.64 3.86 2.03 2.92 38.68 7 5) A217/A216 -0.32 0.73 3.45 2.51 -9.56 32.20 4 6) A216/C215 1.18 -0.75 2.88 -5.59 10.50 36.10 9 7) C215/T214 -0.94 -0.94 3.52 -3.65 0.63 40.82 -2 8) T214/T213 0.58 0.61 3.74 2.26 -5.43 31.77 -4 9) T213/A212 -0.70 0.13 3.24 -3.94 0.54 40.39 7 10) A212/A211 0.20 -0.02 3.61 6.81 -5.79 33.18 4 --------------------------------------- |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) T201/A202 -0.72 0.73 4.22 -6.69 -3.81 43.39 10 3) A202/A203 0.88 -0.54 2.80 -9.56 -1.61 32.56 4 4) A203/T204 -0.34 -0.65 3.53 1.78 -3.21 36.83 7 5) T204/T205 -0.44 -0.65 3.34 1.73 1.46 32.32 -4 6) T205/G206 1.32 0.78 3.26 -1.18 -1.90 39.96 -9 7) G206/A207 -0.84 0.84 3.56 -5.20 -4.84 39.75 2 8) A207/A208 0.25 -0.41 3.47 -0.61 6.13 31.06 4 9) A208/T209 -0.43 -0.33 3.34 -4.05 0.19 37.44 7 10) T209/T210 -0.02 -0.05 3.27 8.17 5.34 29.30 -4 Average: -0.04 -0.03 3.42 -1.73 -0.25 35.85 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) T201/A202 -0.30 1.31 4.29 -10.89 2.08 38.75 10 3) A202/A203 0.58 -0.80 3.36 -0.40 6.87 34.81 4 4) A203/T204 0.02 -0.85 3.22 3.35 -3.20 34.90 7 5) T204/T205 -0.18 -0.66 3.31 4.98 -5.43 32.05 -4 6) T205/G206 1.79 0.82 3.44 8.70 9.94 43.12 -9 7) G206/A207 -0.50 1.13 3.61 -1.71 -5.57 39.39 2 8) A207/A208 0.07 -0.48 3.26 1.31 5.94 30.57 4 9) A208/T209 -0.14 -1.05 3.37 -0.86 -1.97 34.56 7 10) T209/T210 -0.20 -0.51 2.98 11.05 3.51 24.96 -4 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) A220/T219 -2.24 1.42 3.44 -8.36 9.90 46.31 10 3) T219/T218 0.61 -0.29 2.40 -18.15 -4.07 28.58 -4 4) T218/A217 -1.17 -0.85 3.80 0.13 -2.82 38.73 7 5) A217/A216 -0.82 -1.02 3.41 -1.82 10.27 32.31 4 6) A216/C215 0.81 0.71 2.94 -9.39 -8.95 35.45 9 7) C215/T214 -1.41 0.50 3.47 -4.94 -1.98 40.57 -2 8) T214/T213 -0.08 -1.02 3.73 -0.67 3.98 31.93 -4 9) T213/A212 -1.31 -0.70 3.08 -8.24 -3.09 39.65 7 10) A212/A211 -0.61 -0.58 3.61 2.22 3.89 33.93 4 -------------------------------------- |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) T201/A202 -1.31 1.44 3.95 -9.40 5.91 42.99 10 3) A202/A203 0.56 -0.51 2.87 -9.54 1.81 31.53 4 4) A203/T204 -0.55 -0.82 3.54 1.75 -2.93 36.87 7 5) T204/T205 -0.50 -0.83 3.37 1.85 2.53 32.39 -4 6) T205/G206 1.26 0.80 3.20 -0.98 1.09 39.60 -9 7) G206/A207 -0.99 0.85 3.56 -3.16 -3.64 39.92 2 8) A207/A208 0.00 -0.74 3.49 0.25 5.02 31.49 4 9) A208/T209 -0.73 -0.84 3.27 -4.60 -2.36 37.30 7 10) T209/T210 -0.37 -0.55 3.30 6.66 3.63 29.58 -4 Average: -0.29 -0.13 3.39 -1.91 1.23 35.74 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) T201/A202 -0.29 0.46 -1.29 0.51 0.54 1.38 4.25 10 3) A202/A203 0.59 -0.27 0.18 -0.10 0.65 0.20 2.87 4 4) A203/T204 -0.15 -0.35 2.12 -3.31 0.38 3.93 3.55 7 5) T204/T205 -0.31 -0.29 -1.43 1.29 0.43 1.93 3.36 -4 6) T205/G206 0.62 0.38 -1.25 -0.32 0.73 1.29 3.34 -9 7) G206/A207 -0.36 0.37 -1.29 -2.71 0.51 3.00 3.59 2 8) A207/A208 0.21 -0.26 2.14 2.44 0.33 3.24 3.49 4 9) A208/T209 -0.19 -0.19 -2.10 -0.57 0.26 2.18 3.35 7 10) T209/T210 -0.01 -0.02 3.87 3.19 0.02 5.02 3.27 -4 Overall axis bend ... UU= 8.49 PP= 13.34 Duplex Offset L.Dir ... wrt end-to-end vector 1) T201 0.00 0.00 2) A202 0.73 -87.57 3) A203 1.02 -165.10 4) T204 1.02 139.54 5) T205 1.15 85.13 6) G206 0.65 82.92 7) A207 0.61 -11.06 8) A208 0.27 -32.51 9) T209 0.25 -21.69 10) T210 0.00 0.00 Path length= 31.08 End-to-end= 30.71 Shortening= 1.19 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)TA 201 42.81 -35.13 147.98 42.66 C2'-endo 104.5 100.9 102.6 2)AA 202 28.93 -31.14 172.17 32.35 C2'-endo 107.1 102.8 102.7 3)AA 203 38.79 -34.00 153.50 39.12 C2'-endo 105.0 101.4 102.5 4)TA 204 37.36 -29.58 144.51 37.38 C2'-endo 104.8 102.1 103.4 5)TA 205 37.58 -27.04 137.19 38.00 C1'-exo 105.2 101.7 104.4 6)GA 206 41.33 -38.70 159.31 42.58 C2'-endo 105.9 99.7 102.7 7)AA 207 26.68 -30.05 174.56 30.71 C2'-endo 106.4 103.8 103.4 8)AA 208 35.62 -30.67 151.31 35.86 C2'-endo 105.6 102.0 103.9 9)TA 209 41.06 -31.83 142.99 41.11 C1'-exo 104.4 100.8 103.6 10)TA 210 42.73 -37.05 152.92 42.95 C2'-endo 105.3 100.0 102.7 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)TA 201 -78.37 38.60 140.54 -111.02 160.19 -58.71 142.05 2)AA 202 -106.43 38.41 144.50 -179.35 -99.69 -57.06 174.16 3)AA 203 -112.18 48.17 136.96 -160.19 -128.89 -42.86 156.99 4)TA 204 -117.63 43.60 132.74 -154.95 -126.07 -51.40 158.96 5)TA 205 -112.09 45.75 129.31 -154.30 -112.50 -47.67 159.35 6)GA 206 -84.69 41.04 148.92 -105.02 160.91 -63.66 144.58 7)AA 207 -96.41 38.34 141.11 178.54 -96.56 -75.24 166.67 8)AA 208 -117.18 71.05 131.32 -157.47 -117.89 -56.43 162.37 9)TA 209 -122.87 46.73 137.59 -131.07 -130.53 -46.25 153.98 10)TA 210 -81.42 14.09 155.02 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)AB 220 40.21 -36.75 156.29 41.10 C2'-endo 105.0 100.6 103.0 2)TB 219 45.98 -39.70 152.53 46.22 C2'-endo 104.6 98.8 102.1 3)TB 218 38.58 -34.78 155.21 39.28 C2'-endo 105.7 100.8 103.8 4)AB 217 41.83 -37.35 154.23 42.30 C2'-endo 104.9 101.1 103.4 5)AB 216 38.39 -36.70 160.36 39.86 C2'-endo 105.5 100.9 103.1 6)CB 215 42.69 -33.23 142.86 42.83 C1'-exo 104.2 100.5 103.4 7)TB 214 40.68 -34.94 151.48 40.92 C2'-endo 105.6 100.3 103.5 8)TB 213 38.36 -31.89 148.72 38.35 C2'-endo 105.1 101.9 103.2 9)AB 212 41.56 -34.29 148.54 41.40 C2'-endo 104.8 101.2 102.9 10)AB 211 48.03 -40.37 150.11 48.01 C2'-endo 104.1 98.5 102.5 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)AB 220 -66.19 14.68 146.75 ...... ...... ...... ...... 2)TB 219 -81.63 36.33 151.33 -70.61 167.73 -53.98 131.83 3)TB 218 -146.20 -143.31 142.36 -122.79 -112.35 -64.78 150.48 4)AB 217 -127.44 -163.87 146.11 -109.21 -148.25 66.51 -121.67 5)AB 216 -99.31 57.43 143.05 -163.05 -129.11 113.06 -152.12 6)CB 215 -93.76 26.21 137.33 -99.75 171.73 -83.73 138.72 7)TB 214 -107.04 39.23 140.10 -144.30 -150.63 -11.96 124.14 8)TB 213 -115.18 47.49 137.24 -162.51 -120.06 -42.78 166.67 9)AB 212 -96.89 8.79 134.44 177.59 -133.60 -23.35 151.25 10)AB 211 -80.37 30.85 150.10 -76.42 157.73 -60.49 141.36