ID code: 9ICJ, PDE099 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 19 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 0.035 1 : 2) AA 2 0.094 1 : 3) TA 3 0.055 1 : 4) TA 4 0.199 1 : 5) AA 5 0.104 1 : 6) GA 6 0.053 1 : 7) AA 7 0.167 2 : 1) GB 7 0.105 2 : 2) TB 6 0.225 2 : 3) AB 5 0.135 2 : 4) AB 4 0.052 2 : 5) TB 3 0.176 2 : 6) CB 2 0.158 2 : 7) TB 1 0.216 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= 14.514 CPTS: 1.380 2.835 1.901 8.398 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 14.514 DEL= 0.000E+00 STEP 2 SUM= 10.818 DEL= -0.370E+01 STEP 3 SUM= 13.362 DEL= 0.254E+01 STEP 4 SUM= 9.443 DEL= -0.392E+01 STEP 5 SUM= 9.477 DEL= 0.335E-01 STEP 6 SUM= 8.764 DEL= -0.713E+00 STEP 7 SUM= 8.072 DEL= -0.692E+00 STEP 8 SUM= 7.520 DEL= -0.552E+00 STEP 9 SUM= 7.008 DEL= -0.512E+00 STEP 10 SUM= 6.259 DEL= -0.749E+00 STEP 11 SUM= 11.894 DEL= 0.563E+01 STEP 12 SUM= 6.180 DEL= -0.571E+01 STEP 13 SUM= 6.047 DEL= -0.134E+00 STEP 14 SUM= 5.806 DEL= -0.241E+00 STEP 15 SUM= 5.367 DEL= -0.439E+00 STEP 16 SUM= 6.541 DEL= 0.117E+01 STEP 17 SUM= 5.184 DEL= -0.136E+01 STEP 18 SUM= 6.117 DEL= 0.933E+00 STEP 19 SUM= 5.159 DEL= -0.959E+00 STEP 20 SUM= 5.112 DEL= -0.461E-01 STEP 21 SUM= 5.033 DEL= -0.797E-01 STEP 22 SUM= 4.946 DEL= -0.871E-01 STEP 23 SUM= 4.848 DEL= -0.980E-01 STEP 24 SUM= 4.718 DEL= -0.130E+00 STEP 25 SUM= 4.647 DEL= -0.708E-01 STEP 26 SUM= 4.542 DEL= -0.105E+00 STEP 27 SUM= 4.429 DEL= -0.113E+00 STEP 28 SUM= 4.408 DEL= -0.211E-01 STEP 29 SUM= 4.377 DEL= -0.315E-01 STEP 30 SUM= 4.366 DEL= -0.108E-01 STEP 31 SUM= 4.352 DEL= -0.141E-01 STEP 32 SUM= 4.349 DEL= -0.278E-02 STEP 33 SUM= 4.351 DEL= 0.182E-02 STEP 34 SUM= 4.348 DEL= -0.253E-02 STEP 35 SUM= 4.348 DEL= -0.763E-04 STEP 36 SUM= 4.348 DEL= -0.164E-03 STEP 37 SUM= 4.348 DEL= 0.219E-03 STEP 38 SUM= 4.348 DEL= -0.277E-03 STEP 39 SUM= 4.348 DEL= 0.145E-05 STEP 40 SUM= 4.348 DEL= -0.307E-05 STEP 41 SUM= 4.348 DEL= -0.423E-06 STEP 42 SUM= 4.348 DEL= -0.441E-06 STEP 43 SUM= 4.348 DEL= -0.351E-06 STEP 44 SUM= 4.348 DEL= -0.288E-06 STEP 45 SUM= 4.348 DEL= -0.102E-07 STEP 46 SUM= 4.348 DEL= -0.851E-09 STEP 47 SUM= 4.348 DEL= -0.466E-10 STEP 48 SUM= 4.348 DEL= -0.299E-11 STEP 49 SUM= 4.348 DEL= -0.497E-13 STEP 50 SUM= 4.348 DEL= -0.355E-14 STEP 51 SUM= 4.348 DEL= 0.000E+00 FINAL SUM= 4.348 CPTS: 0.953 2.507 0.358 0.530 GRA=-0.23E-09 0.45E-10 0.18E-09 0.62E-10 0.53E-10 0.15E-08 0.10E-09 0.28E-09 GRA= 0.49E-09-0.48E-09-0.14E-09-0.20E-09-0.13E-08-0.12E-08-0.32E-10 0.16E-10 GRA= 0.18E-08 0.16E-08-0.17E-09-0.84E-10-0.13E-08-0.21E-08 0.59E-10-0.76E-10 GRA= 0.14E-08 0.34E-09 0.15E-09-0.26E-10 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.431 -0.885 -0.175 P: 59.726 35.735 47.163 D: 0.902 2) U: -0.490 -0.857 -0.159 P: 58.096 32.317 46.376 D: 0.564 3) U: -0.492 -0.856 -0.156 P: 56.378 29.743 45.919 D: 0.629 4) U: -0.547 -0.821 -0.162 P: 54.640 27.182 45.588 D: 0.706 5) U: -0.566 -0.814 -0.129 P: 52.824 24.340 45.164 D: 0.358 6) U: -0.568 -0.811 -0.139 P: 50.883 21.908 44.656 D: 1.188 7) U: -0.582 -0.811 -0.054 P: 49.083 19.010 44.486 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -1.28 0.29 12.85 -1.78 3 0 2) AA 2 -1.73 0.23 7.38 -1.13 2 30 3) TA 3 -1.69 0.12 5.73 -4.66 4 -24 4) TA 4 -1.97 -0.25 8.06 -3.15 4 -28 5) AA 5 -1.54 -0.09 8.09 -1.25 2 27 6) GA 6 -1.64 -0.34 9.85 -0.72 1 4 7) AA 7 -1.45 0.10 17.37 -3.53 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 7 -1.92 0.07 13.28 -10.70 1 0 2) TB 6 -1.90 -0.02 15.02 -12.47 4 -30 3) AB 5 -1.60 -0.11 11.01 -11.75 2 24 4) AB 4 -1.25 -0.25 9.55 -15.45 2 28 5) TB 3 -1.72 -0.30 12.48 -11.08 4 -27 6) CB 2 -1.35 -0.13 13.49 -12.85 3 -4 7) TB 1 -1.34 -0.26 3.23 -8.91 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 -1.60 0.11 13.07 4.46 3 0 2) A 2-T 6 -1.82 0.13 11.20 5.67 2 30 3) T 3-A 5 -1.65 0.12 8.37 3.54 4 -24 4) T 4-A 4 -1.61 0.00 8.80 6.15 4 -28 5) A 5-T 3 -1.63 0.10 10.29 4.91 2 27 6) G 6-C 2 -1.50 -0.11 11.67 6.07 1 4 7) A 7-T 1 -1.40 0.18 10.30 2.69 2 0 Average: -1.60 0.08 10.53 4.79 --------------------------------- |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 0.65 0.36 -1.10 -0.43 -12.48 9.54 3 0 2) A 2-T 6 0.16 0.21 -0.28 -7.64 -13.61 5.51 2 30 3) T 3-A 5 -0.09 0.01 0.35 -5.28 -16.41 6.15 4 -24 4) T 4-A 4 -0.72 -0.49 0.11 -1.49 -18.59 5.63 4 -28 5) A 5-T 3 0.17 -0.39 -0.25 -4.38 -12.33 -0.70 2 27 6) G 6-C 2 -0.29 -0.47 -0.41 -3.65 -13.58 -0.64 1 4 7) A 7-T 1 -0.11 -0.16 0.08 14.14 -12.44 2.20 2 0 Average: -0.03 -0.13 -0.21 -1.25 -14.21 3.96 ---------------------------------- |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 -0.66 -0.00 4.27 -6.40 4.42 20.83 9 3) A 2/T 3 0.25 -0.15 3.44 -1.48 -3.41 35.79 7 4) T 3/T 4 -0.27 -0.58 2.99 4.19 4.75 32.77 -4 5) T 4/A 5 0.32 0.22 3.22 1.73 0.45 35.86 10 6) A 5/G 6 -0.06 -0.46 3.07 2.06 1.05 27.86 3 7) G 6/A 7 0.22 0.70 3.65 4.65 -6.83 33.24 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.18 -0.14 3.45 0.81 -5.55 24.86 -9 3) T 6/A 5 0.51 -0.06 2.81 -3.84 0.61 35.15 7 4) A 5/A 4 0.36 0.08 3.23 0.40 -6.94 33.30 4 5) A 4/T 3 -0.56 -0.12 3.58 4.63 5.81 42.19 10 6) T 3/C 2 0.40 0.39 3.22 1.33 -2.29 27.79 -3 7) C 2/T 1 0.04 -0.39 3.16 -13.13 7.97 30.40 -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 -0.42 0.07 3.86 -2.80 4.98 22.85 9 3) A 2/T 3 0.38 -0.05 3.12 -2.66 -2.01 35.47 7 4) T 3/T 4 0.05 -0.33 3.11 2.30 5.85 33.03 -4 5) T 4/A 5 -0.12 0.17 3.40 3.18 -2.68 39.02 10 6) A 5/G 6 0.17 -0.43 3.15 1.70 1.67 27.82 3 7) G 6/A 7 0.13 0.55 3.41 -4.24 -7.40 31.82 2 Average: 0.03 -0.00 3.34 -0.42 0.07 31.67 --------------------------------- |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 -0.62 0.22 4.43 -5.58 8.03 20.03 9 3) A 2/T 3 0.33 -0.79 3.55 0.38 0.77 35.56 7 4) T 3/T 4 -0.03 -1.24 3.25 6.45 8.44 31.88 -4 5) T 4/A 5 0.53 -0.45 3.24 3.05 5.29 35.66 10 6) A 5/G 6 0.09 -0.75 3.23 2.48 5.33 27.42 3 7) G 6/A 7 0.34 0.63 3.49 5.52 1.12 33.08 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.88 0.17 3.55 -4.15 11.36 22.92 -9 3) T 6/A 5 -0.12 -0.36 3.01 -10.70 7.20 32.82 7 4) A 5/A 4 -0.52 -0.35 3.41 -7.26 12.67 31.52 4 5) A 4/T 3 -1.53 -0.26 3.41 -5.01 2.42 41.64 10 6) T 3/C 2 -0.41 -0.40 3.40 -4.29 8.41 26.72 -3 7) C 2/T 1 -0.56 0.15 3.06 -18.29 -3.37 27.98 -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 -0.79 0.22 3.98 -4.78 9.66 21.64 9 3) A 2/T 3 0.08 -0.55 3.29 -5.03 4.28 34.56 7 4) T 3/T 4 -0.25 -0.78 3.35 -0.28 10.90 32.05 -4 5) T 4/A 5 -0.49 -0.34 3.43 -1.02 3.94 38.91 10 6) A 5/G 6 -0.15 -0.58 3.33 -0.92 6.85 27.27 3 7) G 6/A 7 -0.13 0.38 3.30 -6.42 -1.08 30.63 2 Average: -0.29 -0.27 3.45 -3.07 5.76 30.84 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/A 2 -0.20 0.05 -0.93 3.77 0.21 3.89 3.87 9 3) A 2/T 3 0.21 -0.04 0.17 0.12 0.21 0.21 3.13 7 4) T 3/T 4 0.01 -0.21 1.87 3.24 0.21 3.74 3.11 -4 5) T 4/A 5 -0.10 0.07 1.70 -1.44 0.12 2.23 3.40 10 6) A 5/G 6 0.04 -0.22 0.31 0.52 0.22 0.60 3.15 3 7) G 6/A 7 0.03 0.26 -2.87 -4.02 0.26 4.95 3.42 2 Overall axis bend ... UU= 11.95 PP= 10.90 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) A 2 0.54 -16.70 3) T 3 0.50 -60.25 4) T 4 0.38 -91.52 5) A 5 0.36 -124.00 6) G 6 0.29 144.83 7) A 7 0.00 0.00 Path length= 20.08 End-to-end= 20.00 Shortening= 0.36 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 19.66 -30.08 199.41 33.22 C3'-exo 110.5 101.8 102.2 2)AA 2 23.30 -26.21 175.11 26.97 C2'-endo 108.0 103.2 104.5 3)TA 3 39.01 -24.71 128.58 41.16 C1'-exo 104.8 100.2 105.8 4)TA 4 46.33 -24.12 119.85 50.93 C1'-exo 102.5 99.9 103.3 5)AA 5 2.93 -10.67 224.00 15.22 C4'-endo 107.8 104.9 106.1 6)GA 6 42.46 -28.14 133.05 43.09 C1'-exo 105.3 100.6 104.0 7)AA 7 19.61 -11.06 123.28 20.99 C1'-exo 108.7 104.9 105.8 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 -47.07 137.27 150.85 137.92 -94.68 -43.40 -163.10 2)AA 2 -87.53 40.71 140.93 166.38 -121.16 -28.76 152.40 3)TA 3 -117.58 49.08 120.17 -167.35 -112.25 -37.16 147.88 4)TA 4 -123.85 52.33 113.01 -175.46 -103.92 -57.84 -177.38 5)AA 5 -113.50 51.45 128.27 -176.43 -73.12 -92.23 -176.34 6)GA 6 -109.42 55.10 131.09 -87.89 153.51 -22.57 116.14 7)AA 7 -92.31 3.82 119.01 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 7 0.58 -14.16 233.88 24.39 C4'-endo 108.2 105.7 104.0 2)TB 6 39.07 -48.25 182.68 49.49 C3'-exo 105.3 98.2 99.3 3)AB 5 30.06 -11.97 108.66 37.96 C1'-exo 102.7 104.3 104.3 4)AB 4 30.55 -16.12 119.84 33.87 C1'-exo 106.2 103.1 104.4 5)TB 3 41.87 -32.88 145.01 41.74 C2'-endo 105.3 100.1 103.1 6)CB 2 38.54 -48.47 182.54 49.27 C3'-exo 104.8 98.1 100.8 7)TB 1 10.38 12.42 70.84 38.29 C4'-exo 107.1 104.6 103.5 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 7 -116.56 -105.83 138.24 ...... ...... ...... ...... 2)TB 6 -88.32 -57.70 163.50 -143.77 -127.58 53.04 -146.32 3)AB 5 -116.04 51.06 107.13 170.88 -104.42 48.72 173.26 4)AB 4 -121.61 53.94 114.89 -160.87 -88.16 -69.81 169.36 5)TB 3 -87.90 25.34 133.48 -169.96 -117.79 -62.17 168.42 6)CB 2 -83.15 19.54 162.22 -158.60 -136.14 -36.81 154.85 7)TB 1 -153.09 68.61 83.27 -153.56 -87.32 -26.84 174.96