ID code: 1K82, PD0264 *********************************** ************** ****** 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) GA 401 0.087 1 : 2) GA 402 0.088 1 : 3) CA 403 0.049 1 : 4) TA 404 0.071 1 : 5) TA 405 0.067 1 : 6) CA 406 0.048 2 : 1) CB 433 0.034 2 : 2) CB 432 0.046 2 : 3) GB 431 0.086 2 : 4) AB 430 0.046 2 : 5) AB 429 0.029 2 : 6) GB 428 0.093 Strand= 2 Nucleo= 12 Atoms = 243 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'): GGCTTC Strand 2 has 6 bases (3'-5'): CCGAAG FIRST SUM= 18.558 CPTS: 3.375 0.939 3.480 10.765 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 24 STEP 1 SUM= 18.558 DEL= 0.000E+00 STEP 2 SUM= 13.191 DEL= -0.537E+01 STEP 3 SUM= 21.276 DEL= 0.808E+01 STEP 4 SUM= 11.659 DEL= -0.962E+01 STEP 5 SUM= 10.389 DEL= -0.127E+01 STEP 6 SUM= 8.752 DEL= -0.164E+01 STEP 7 SUM= 13.192 DEL= 0.444E+01 STEP 8 SUM= 8.405 DEL= -0.479E+01 STEP 9 SUM= 7.783 DEL= -0.622E+00 STEP 10 SUM= 6.736 DEL= -0.105E+01 STEP 11 SUM= 61.042 DEL= 0.543E+02 STEP 12 SUM= 6.979 DEL= -0.541E+02 STEP 13 SUM= 6.687 DEL= -0.292E+00 STEP 14 SUM= 6.599 DEL= -0.880E-01 STEP 15 SUM= 6.413 DEL= -0.186E+00 STEP 16 SUM= 6.181 DEL= -0.232E+00 STEP 17 SUM= 8.645 DEL= 0.246E+01 STEP 18 SUM= 6.164 DEL= -0.248E+01 STEP 19 SUM= 6.134 DEL= -0.305E-01 STEP 20 SUM= 6.085 DEL= -0.489E-01 STEP 21 SUM= 5.950 DEL= -0.134E+00 STEP 22 SUM= 5.919 DEL= -0.314E-01 STEP 23 SUM= 5.861 DEL= -0.578E-01 STEP 24 SUM= 5.726 DEL= -0.136E+00 STEP 25 SUM= 5.596 DEL= -0.130E+00 STEP 26 SUM= 5.506 DEL= -0.894E-01 STEP 27 SUM= 5.457 DEL= -0.496E-01 STEP 28 SUM= 5.403 DEL= -0.533E-01 STEP 29 SUM= 5.370 DEL= -0.330E-01 STEP 30 SUM= 5.356 DEL= -0.147E-01 STEP 31 SUM= 5.371 DEL= 0.157E-01 STEP 32 SUM= 5.355 DEL= -0.169E-01 STEP 33 SUM= 5.354 DEL= -0.240E-03 STEP 34 SUM= 5.354 DEL= -0.311E-03 STEP 35 SUM= 5.354 DEL= -0.257E-03 STEP 36 SUM= 5.354 DEL= 0.237E-04 STEP 37 SUM= 5.354 DEL= -0.119E-03 STEP 38 SUM= 5.354 DEL= -0.129E-03 STEP 39 SUM= 5.353 DEL= -0.586E-04 STEP 40 SUM= 5.353 DEL= -0.313E-05 STEP 41 SUM= 5.353 DEL= -0.275E-07 STEP 42 SUM= 5.353 DEL= -0.140E-09 STEP 43 SUM= 5.353 DEL= -0.114E-11 STEP 44 SUM= 5.353 DEL= -0.195E-13 STEP 45 SUM= 5.353 DEL= 0.000E+00 STEP 46 SUM= 5.353 DEL= 0.000E+00 STEP 47 SUM= 5.353 DEL= 0.888E-15 STEP 48 SUM= 5.353 DEL= -0.888E-15 FINAL SUM= 5.353 CPTS: 2.005 2.133 0.283 0.933 GRA= 0.33E-11-0.32E-11-0.37E-12 0.56E-12 0.37E-11-0.72E-11 0.79E-12-0.15E-11 GRA= 0.68E-11 0.64E-11 0.63E-12 0.14E-11-0.41E-11 0.20E-11-0.11E-12-0.48E-12 GRA= 0.16E-11-0.14E-10 0.10E-11-0.41E-12 0.96E-11 0.14E-10 0.20E-12 0.33E-12 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.904 0.427 -0.014 P: 17.927 1.028 32.899 D: 0.874 2) U: -0.906 0.415 -0.086 P: 15.363 2.560 32.996 D: 0.667 3) U: -0.902 0.420 -0.095 P: 12.242 3.996 32.685 D: 0.564 4) U: -0.910 0.399 -0.114 P: 9.317 5.145 32.328 D: 1.338 5) U: -0.873 0.458 -0.169 P: 6.016 6.400 32.013 D: 1.910 6) U: -0.870 0.462 -0.175 P: 3.529 8.116 31.302 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 401 -1.79 0.71 7.33 -5.05 1 0 2) GA 402 -1.95 0.46 10.08 -2.07 1 5 3) CA 403 -1.85 0.25 4.92 -2.50 3 -7 4) TA 404 -1.47 0.18 6.99 -9.47 4 -19 5) TA 405 -1.16 0.24 4.93 -5.32 4 -18 6) CA 406 -1.08 0.44 18.25 -0.58 3 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CB 433 -1.68 -0.91 3.09 -12.90 3 0 2) CB 432 -1.88 -0.44 2.60 -13.21 3 -5 3) GB 431 -1.61 -0.34 11.87 -6.37 1 7 4) AB 430 -1.35 -0.15 12.71 -11.55 2 19 5) AB 429 -0.70 -0.27 19.05 -3.05 2 18 6) GB 428 -1.34 -0.62 10.17 -2.47 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) G401-C433 -1.74 0.81 5.21 3.92 1 0 2) G402-C432 -1.92 0.45 6.34 5.57 1 5 3) C403-G431 -1.73 0.30 8.39 1.93 3 -7 4) T404-A430 -1.41 0.17 9.85 1.04 4 -19 5) T405-A429 -0.93 0.26 11.99 -1.14 4 -18 6) C406-G428 -1.21 0.53 14.21 0.95 3 0 Average: -1.49 0.42 9.33 2.05 --------------------------------- |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) G401-C433 -0.11 -0.19 0.28 4.23 -17.95 -1.15 1 0 2) G402-C432 -0.07 0.02 0.05 7.48 -15.27 -0.95 1 5 3) C403-G431 -0.24 -0.09 0.34 -6.95 -8.87 -4.29 3 -7 4) T404-A430 -0.12 0.03 0.05 -5.72 -21.02 4.66 4 -19 5) T405-A429 -0.46 -0.03 0.04 -14.12 -8.37 1.44 4 -18 6) C406-G428 0.26 -0.19 -0.31 8.09 -3.05 -4.01 3 0 Average: -0.12 -0.07 0.07 -1.17 -12.42 -0.72 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G401/G402 -0.45 -0.52 2.85 2.65 7.13 39.72 1 3) G402/C403 0.11 -0.21 3.59 -4.50 -0.33 33.60 5 4) C403/T404 0.54 -0.06 3.02 2.89 -5.50 36.03 -3 5) T404/T405 0.66 0.10 3.52 -0.78 -0.78 37.53 -4 6) T405/C406 -0.27 0.40 2.91 13.32 4.29 26.69 -2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C433/C432 -0.49 0.74 3.08 -0.59 -4.45 39.53 -1 3) C432/G431 0.28 0.09 3.31 9.93 6.73 36.93 5 4) G431/A430 0.41 0.19 3.30 1.66 -6.65 27.08 3 5) A430/A429 1.00 -0.17 3.54 7.61 13.43 40.75 4 6) A429/G428 -0.98 -0.56 3.25 -8.89 1.03 32.15 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) G401/G402 -0.47 -0.63 2.96 1.03 5.79 39.62 1 3) G402/C403 0.19 -0.15 3.45 2.71 -3.53 35.27 5 4) C403/T404 0.47 -0.13 3.16 2.28 0.57 31.55 -3 5) T404/T405 0.83 0.14 3.53 3.41 -7.10 39.14 -4 6) T405/C406 -0.62 0.48 3.08 2.21 1.63 29.42 -2 Average: 0.08 -0.06 3.24 2.33 -0.53 35.00 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G401/G402 -0.67 -1.36 3.24 4.86 12.79 38.60 1 3) G402/C403 0.09 -0.84 3.74 -2.97 4.03 33.47 5 4) C403/T404 0.68 -0.72 3.12 6.44 -1.49 35.22 -3 5) T404/T405 0.95 -0.46 3.38 3.98 2.82 37.64 -4 6) T405/C406 -0.36 0.42 2.91 14.39 9.38 25.81 -2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C433/C432 -1.61 -1.77 3.02 -9.24 6.34 38.24 -1 3) C432/G431 -0.62 -0.72 3.39 3.18 -1.80 37.78 5 4) G431/A430 -0.25 -0.20 3.47 -2.44 12.19 26.22 3 5) A430/A429 0.33 0.46 3.55 2.23 -1.75 41.17 4 6) A429/G428 -1.28 0.77 3.14 -10.06 6.99 30.92 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) G401/G402 -1.13 -1.57 3.16 -2.22 9.54 38.88 1 3) G402/C403 -0.29 -0.79 3.58 0.17 1.18 35.82 5 4) C403/T404 0.23 -0.47 3.33 2.03 5.34 31.25 -3 5) T404/T405 0.65 0.00 3.50 3.07 0.53 39.33 -4 6) T405/C406 -0.81 0.59 3.02 2.17 8.13 28.20 -2 Average: -0.27 -0.45 3.32 1.04 4.94 34.70 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G401/G402 -0.29 -0.27 -0.10 4.14 0.39 4.14 2.99 1 3) G402/C403 0.00 0.00 0.66 0.11 0.01 0.67 3.45 5 4) C403/T404 0.16 0.00 0.83 1.47 0.16 1.68 3.16 -3 5) T404/T405 0.35 0.05 1.27 -4.92 0.35 5.08 3.55 -4 6) T405/C406 -0.34 0.20 -0.01 -0.46 0.40 0.46 3.10 -2 Overall axis bend ... UU= 9.66 PP= 15.56 Duplex Offset L.Dir ... wrt end-to-end vector 1) G401 0.00 0.00 2) G402 0.46 4.49 3) C403 0.45 -41.05 4) T404 0.39 -112.92 5) T405 0.60 178.87 6) C406 0.00 0.00 Path length= 16.25 End-to-end= 16.13 Shortening= 0.76 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 401 -28.16 21.27 321.61 28.09 C1'-endo 107.9 103.4 104.4 2)GA 402 24.35 -33.71 192.29 35.46 C3'-exo 108.1 103.1 101.4 3)CA 403 24.40 -22.95 156.54 25.10 C2'-endo 105.0 106.3 104.6 4)TA 404 34.93 -20.63 124.26 37.50 C1'-exo 104.8 102.9 105.1 5)TA 405 17.79 -0.40 91.18 30.10 O1'-endo 107.6 104.6 106.2 6)CA 406 -2.88 14.54 47.78 21.67 C4'-exo 107.1 106.7 105.1 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GA 401 177.70 178.15 108.90 -139.74 -69.70 -78.81 -148.36 2)GA 402 -106.60 47.82 155.16 -175.42 -102.18 -57.61 -179.54 3)CA 403 -117.02 47.33 124.92 -177.11 -86.44 -81.36 175.18 4)TA 404 -119.69 72.65 119.25 -153.67 -122.67 -35.60 147.59 5)TA 405 -115.53 33.15 104.58 -155.02 -112.89 -48.41 160.33 6)CA 406 -107.61 34.23 97.21 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CB 433 -29.92 43.71 13.96 45.48 C3'-endo 105.1 101.2 99.9 2)CB 432 -33.15 41.00 1.59 41.44 C3'-endo 105.1 101.5 101.4 3)GB 431 41.70 -39.29 159.67 43.07 C2'-endo 105.0 99.9 101.9 4)AB 430 35.08 -39.41 173.16 39.97 C2'-endo 103.3 102.9 101.4 5)AB 429 44.52 -44.29 162.19 47.14 C2'-endo 102.3 99.0 101.4 6)GB 428 28.97 -32.85 175.98 33.70 C2'-endo 106.7 103.0 102.5 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CB 433 -156.08 46.07 79.55 ...... ...... ...... ...... 2)CB 432 -167.24 -166.63 86.25 -130.67 -74.64 -56.58 164.34 3)GB 431 -77.25 24.67 153.37 -142.57 -174.16 79.70 -129.05 4)AB 430 -110.30 42.66 148.19 -152.63 -104.24 -60.95 176.87 5)AB 429 -75.89 40.71 152.48 -108.90 156.91 -66.14 145.23 6)GB 428 -92.12 40.96 147.21 -163.41 -103.03 -60.67 167.08