ID code: 1ZQB, PDE028 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 18 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) CA 1 0.059 1 : 2) AA 2 0.059 1 : 3) TA 3 0.056 1 : 4) TA 4 0.219 1 : 5) AA 5 0.053 1 : 6) GA 6 0.245 1 : 7) AA 7 0.244 2 : 1) GB 7 0.142 2 : 2) TB 6 0.163 2 : 3) AB 5 0.119 2 : 4) AB 4 0.035 2 : 5) TB 3 0.114 2 : 6) CB 2 0.096 2 : 7) TB 1 0.190 Strand= 2 Nucleo= 14 Atoms = 281 Units = 14 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 7 levels ... Strand 1 has 7 bases (5'-3'): CATTAGA Strand 2 has 7 bases (3'-5'): GTAATCT FIRST SUM= 18.988 CPTS: 2.804 6.444 1.616 8.123 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 18.988 DEL= 0.000E+00 STEP 2 SUM= 14.511 DEL= -0.448E+01 STEP 3 SUM= 20.612 DEL= 0.610E+01 STEP 4 SUM= 13.179 DEL= -0.743E+01 STEP 5 SUM= 11.688 DEL= -0.149E+01 STEP 6 SUM= 10.720 DEL= -0.967E+00 STEP 7 SUM= 11.717 DEL= 0.996E+00 STEP 8 SUM= 10.401 DEL= -0.132E+01 STEP 9 SUM= 9.921 DEL= -0.480E+00 STEP 10 SUM= 9.390 DEL= -0.531E+00 STEP 11 SUM= 9.261 DEL= -0.129E+00 STEP 12 SUM= 9.024 DEL= -0.237E+00 STEP 13 SUM= 8.483 DEL= -0.542E+00 STEP 14 SUM= 11.793 DEL= 0.331E+01 STEP 15 SUM= 8.358 DEL= -0.343E+01 STEP 16 SUM= 8.928 DEL= 0.570E+00 STEP 17 SUM= 8.339 DEL= -0.589E+00 STEP 18 SUM= 8.311 DEL= -0.283E-01 STEP 19 SUM= 8.264 DEL= -0.466E-01 STEP 20 SUM= 8.240 DEL= -0.246E-01 STEP 21 SUM= 8.196 DEL= -0.440E-01 STEP 22 SUM= 8.123 DEL= -0.725E-01 STEP 23 SUM= 8.394 DEL= 0.271E+00 STEP 24 SUM= 8.096 DEL= -0.298E+00 STEP 25 SUM= 8.067 DEL= -0.290E-01 STEP 26 SUM= 8.048 DEL= -0.197E-01 STEP 27 SUM= 8.024 DEL= -0.236E-01 STEP 28 SUM= 8.012 DEL= -0.122E-01 STEP 29 SUM= 7.998 DEL= -0.142E-01 STEP 30 SUM= 7.997 DEL= -0.719E-03 STEP 31 SUM= 7.996 DEL= -0.680E-03 STEP 32 SUM= 7.996 DEL= -0.804E-04 STEP 33 SUM= 7.996 DEL= 0.488E-05 STEP 34 SUM= 7.996 DEL= -0.289E-04 STEP 35 SUM= 7.996 DEL= -0.380E-05 STEP 36 SUM= 7.996 DEL= -0.131E-05 STEP 37 SUM= 7.996 DEL= -0.142E-05 STEP 38 SUM= 7.996 DEL= -0.870E-07 STEP 39 SUM= 7.996 DEL= -0.129E-06 STEP 40 SUM= 7.996 DEL= -0.150E-06 STEP 41 SUM= 7.996 DEL= -0.104E-06 STEP 42 SUM= 7.996 DEL= -0.529E-07 STEP 43 SUM= 7.996 DEL= -0.603E-08 STEP 44 SUM= 7.996 DEL= -0.118E-08 STEP 45 SUM= 7.996 DEL= -0.112E-09 STEP 46 SUM= 7.996 DEL= -0.303E-10 STEP 47 SUM= 7.996 DEL= -0.388E-12 STEP 48 SUM= 7.996 DEL= -0.444E-14 STEP 49 SUM= 7.996 DEL= 0.000E+00 STEP 50 SUM= 7.996 DEL= -0.178E-14 STEP 51 SUM= 7.996 DEL= 0.000E+00 FINAL SUM= 7.996 CPTS: 1.814 4.638 0.471 1.073 GRA=-0.62E-11-0.55E-12 0.39E-11-0.50E-12 0.12E-10-0.25E-11-0.21E-11 0.48E-11 GRA= 0.62E-11-0.12E-11-0.33E-11-0.32E-11 0.14E-10-0.17E-10 0.37E-11-0.54E-11 GRA=-0.12E-10-0.29E-10 0.33E-11 0.25E-11 0.11E-10-0.70E-11-0.28E-11-0.11E-11 GRA= 0.50E-11 0.86E-11 0.89E-12-0.18E-11 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.496 -0.864 -0.083 P: 60.081 35.131 46.939 D: 1.335 2) U: -0.559 -0.825 -0.089 P: 58.381 32.040 46.388 D: 1.268 3) U: -0.604 -0.795 -0.060 P: 56.023 29.541 46.307 D: 1.085 4) U: -0.630 -0.770 -0.102 P: 54.096 26.988 46.364 D: 0.611 5) U: -0.660 -0.737 -0.147 P: 51.760 24.256 45.900 D: 3.109 6) U: -0.639 -0.742 -0.203 P: 49.667 22.202 45.225 D: 0.588 7) U: -0.664 -0.732 -0.151 P: 47.497 19.619 44.743 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -0.52 0.78 8.79 -3.33 3 0 2) AA 2 -0.76 0.65 4.69 -9.74 2 30 3) TA 3 -0.59 0.58 -0.76 -12.29 4 -24 4) TA 4 -0.80 0.08 -0.08 -2.10 4 -28 5) AA 5 -0.27 0.10 -1.69 0.12 2 27 6) GA 6 -1.17 -0.23 2.08 -1.98 1 4 7) AA 7 -1.09 -0.00 5.66 1.49 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 7 -0.61 -0.49 11.12 3.34 1 0 2) TB 6 -1.04 -0.70 6.64 -2.91 4 -30 3) AB 5 -0.48 -0.45 4.97 -8.47 2 24 4) AB 4 -0.78 -0.63 3.10 -5.25 2 28 5) TB 3 -1.23 -0.57 6.13 -5.33 4 -27 6) CB 2 -0.05 -0.25 1.26 -15.64 3 -4 7) TB 1 -0.13 -0.30 -3.23 -6.48 4 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 7 -0.56 0.63 9.96 -3.33 3 0 2) A 2-T 6 -0.90 0.68 5.67 -3.42 2 30 3) T 3-A 5 -0.54 0.51 2.11 -1.91 4 -24 4) T 4-A 4 -0.79 0.35 1.51 1.57 4 -28 5) A 5-T 3 -0.75 0.33 2.22 2.73 2 27 6) G 6-C 2 -0.61 0.01 1.67 6.83 1 4 7) A 7-T 1 -0.61 0.15 1.22 3.99 2 0 Average: -0.68 0.38 3.48 0.92 --------------------------------- |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 7 0.09 0.29 -0.67 -2.33 0.01 12.22 3 0 2) A 2-T 6 0.28 -0.05 -0.01 -1.95 -12.65 5.89 2 30 3) T 3-A 5 -0.11 0.13 0.25 -5.73 -20.77 17.50 4 -24 4) T 4-A 4 -0.02 -0.54 0.17 -3.19 -7.35 -0.70 4 -28 5) A 5-T 3 0.95 -0.47 0.09 -7.82 -5.21 -4.04 2 27 6) G 6-C 2 -1.12 -0.48 0.20 0.82 -17.62 -9.01 1 4 7) A 7-T 1 -0.96 -0.31 0.38 8.89 -4.99 -4.94 2 0 Average: -0.13 -0.20 0.06 -1.61 -9.80 2.42 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/A 2 -0.53 0.00 3.89 -6.42 -2.81 23.09 9 3) A 2/T 3 0.62 -0.27 3.53 -3.71 0.47 40.65 7 4) T 3/T 4 -0.45 -0.70 3.14 0.04 13.34 28.09 -4 5) T 4/A 5 0.53 0.02 3.59 0.25 5.30 38.78 10 6) A 5/G 6 -0.80 -0.58 3.05 3.48 1.37 12.75 3 7) G 6/A 7 0.04 0.37 3.50 2.86 0.17 33.88 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.72 -0.34 3.23 -6.80 -9.85 29.42 -9 3) T 6/A 5 1.01 0.44 3.27 0.07 -8.59 29.04 7 4) A 5/A 4 -0.54 0.03 3.23 -2.50 0.07 46.29 4 5) A 4/T 3 -0.44 0.05 3.67 4.88 -3.16 42.12 10 6) T 3/C 2 1.27 0.56 2.94 -5.16 -13.78 17.71 -3 7) C 2/T 1 -0.12 -0.19 3.32 -5.21 12.46 29.81 -2 --------------------------------------- |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/A 2 -0.63 0.17 3.56 -6.61 3.52 26.26 9 3) A 2/T 3 0.81 -0.35 3.40 -1.82 4.53 34.84 7 4) T 3/T 4 -0.50 -0.37 3.18 -1.23 6.63 37.19 -4 5) T 4/A 5 0.05 -0.02 3.63 2.57 4.23 40.45 10 6) A 5/G 6 0.24 -0.57 3.00 -0.84 7.57 15.23 3 7) G 6/A 7 -0.04 0.28 3.41 -1.18 -6.15 31.85 2 Average: -0.01 -0.14 3.36 -1.52 3.39 30.97 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/A 2 -0.34 0.26 3.97 -3.46 0.16 23.02 9 3) A 2/T 3 0.86 -0.64 3.51 4.56 1.80 40.38 7 4) T 3/T 4 -0.23 -1.10 3.21 3.78 12.86 28.04 -4 5) T 4/A 5 0.52 -0.41 3.60 0.94 4.62 38.83 10 6) A 5/G 6 -0.72 -0.71 3.11 3.46 1.40 12.68 3 7) G 6/A 7 0.07 -0.11 3.44 3.05 2.24 34.03 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.97 0.34 3.28 -6.92 13.88 28.79 -9 3) T 6/A 5 0.40 -0.48 3.45 -3.03 11.46 28.54 7 4) A 5/A 4 -1.27 -0.31 3.18 -7.92 3.28 45.36 4 5) A 4/T 3 -1.20 -0.49 3.69 0.96 6.42 42.05 10 6) T 3/C 2 0.58 -0.61 3.20 -8.12 14.75 16.42 -3 7) C 2/T 1 -0.82 0.16 3.24 -10.95 -12.54 28.44 -2 -------------------------------------- |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/A 2 -0.66 0.32 3.63 -4.60 7.14 25.98 9 3) A 2/T 3 0.62 -0.53 3.48 1.30 6.99 34.90 7 4) T 3/T 4 -0.72 -0.66 3.25 -2.46 8.51 36.70 -4 5) T 4/A 5 -0.33 -0.47 3.68 0.93 5.52 40.50 10 6) A 5/G 6 -0.07 -0.62 3.06 -2.69 7.75 14.75 3 7) G 6/A 7 -0.39 -0.00 3.35 -3.48 -5.59 31.62 2 Average: -0.26 -0.33 3.41 -1.83 5.05 30.74 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/A 2 -0.29 0.12 -2.32 3.60 0.31 4.29 3.57 9 3) A 2/T 3 0.45 -0.19 1.74 3.02 0.49 3.48 3.44 7 4) T 3/T 4 -0.25 -0.21 -0.64 3.15 0.32 3.21 3.20 -4 5) T 4/A 5 0.01 0.01 1.86 3.08 0.01 3.59 3.62 10 6) A 5/G 6 0.10 -0.25 -0.30 3.47 0.27 3.48 3.01 3 7) G 6/A 7 -0.05 0.14 -0.72 -3.30 0.15 3.38 3.41 2 Overall axis bend ... UU= 12.87 PP= 11.11 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) A 2 0.65 -2.01 3) T 3 0.39 -8.96 4) T 4 0.72 -8.13 5) A 5 0.61 -44.73 6) G 6 0.12 -44.89 7) A 7 0.00 0.00 Path length= 20.25 End-to-end= 20.09 Shortening= 0.76 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 15.61 -27.73 205.38 31.41 C3'-exo 108.1 103.8 102.8 2)AA 2 34.43 -24.71 138.55 34.31 C1'-exo 106.8 103.3 103.8 3)TA 3 29.86 -14.54 116.10 34.46 C1'-exo 105.9 102.9 105.5 4)TA 4 50.01 -20.81 112.06 59.27 C1'-exo 101.2 97.6 104.3 5)AA 5 18.02 -27.94 199.51 30.67 C3'-exo 109.1 102.7 102.6 6)GA 6 43.28 -31.71 139.04 43.25 C1'-exo 103.7 101.5 103.6 7)AA 7 21.98 -7.51 106.64 27.98 O1'-endo 108.4 103.6 105.7 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CA 1 -51.74 163.80 145.38 125.68 -82.12 -85.07 -165.26 2)AA 2 -107.87 74.58 128.19 176.21 -118.68 -26.81 160.81 3)TA 3 -124.95 40.51 122.46 -163.14 -98.28 -54.05 147.57 4)TA 4 -142.10 66.69 106.67 -174.01 -85.62 -62.18 -153.09 5)AA 5 -108.12 38.01 150.20 -177.45 -83.19 -91.27 170.19 6)GA 6 -115.88 64.92 131.96 -96.41 172.07 -28.72 102.68 7)AA 7 -107.03 26.72 106.72 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 7 12.80 -30.40 215.88 38.53 C3'-exo 107.6 103.1 101.2 2)TB 6 17.68 -23.09 188.60 24.12 C3'-exo 107.3 105.1 102.5 3)AB 5 26.86 -10.32 108.12 34.01 C1'-exo 104.5 105.1 103.5 4)AB 4 30.03 -13.28 113.30 35.38 C1'-exo 106.6 102.1 106.1 5)TB 3 49.80 -33.53 134.02 50.81 C1'-exo 104.7 95.9 104.7 6)CB 2 35.28 -29.41 147.32 35.48 C2'-endo 103.9 103.6 103.7 7)TB 1 17.50 5.91 81.51 39.45 O1'-endo 107.1 102.8 104.7 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 7 -113.43 -109.43 161.13 ...... ...... ...... ...... 2)TB 6 -125.62 -88.87 145.14 -159.09 -95.88 71.99 -161.27 3)AB 5 -122.09 52.54 104.32 -165.79 -105.46 52.53 -171.10 4)AB 4 -130.36 62.34 107.87 -153.46 -87.13 -68.80 167.93 5)TB 3 -95.18 40.63 126.20 -150.26 -155.08 -35.98 126.77 6)CB 2 -114.58 53.93 130.83 -160.11 -119.63 -27.26 132.73 7)TB 1 -141.94 40.93 90.27 -168.04 -89.25 -40.12 158.55