TITL (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY CELL 1., 1., 1., 90., 90., 90. Comments: In this test example, the DNA hexadecamer of sequence C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G has been treated as a non-self- complementary octamer with strand sequences C-G-C-G-C-G-T-T and T-T-C-G-C-G-C-G, by deleting the P and two O's of P9. This allows one to examine twist, roll, torsion angles and other parameters of the T's well as of the Z-DNA C-G-C-G-C-G stem. The "helix" parameters for the are wild, but are interesting. (Deleting the two phosphates is accomplished, in BRKH input format, by changing the ATOM at the beginning of each of the three coordinate lines to anything else, in this case PHOS. The BRKH input therefore ignores the three lines.) Only the first six base pairs of the octamer should be used to define the overall helix axis; the T's are not really part of the helix. Henc the two HELX cards below are inactivated in favor of a HLX2 and continu ation that list explicitly the numbers of C1', N1 and N9 atoms of C and For Z-DNA, the true helix repeats are between alternating C1' atoms: C to C and G to G, not C to following G or G to C. (These comments are ignored by NEWHELIX because they are indented four or more spaces.) BRKH FLGP 0 FPUN 0 PMIN 0 PMAX 0 NATM 320 BASE 8 HELX RC1' YC1' HELX RN9 YN1 HLX2 8,49,49,90,27,68,68,109,309,268,268,227,290,249,249,208,= 9,50,50,91,28,69,69,110,310,269,269,228,291,250,250,209 BROL CYLN TRNG END 1 (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY INPUT FRAC.COORDS. X,Y,Z AND ATOM NAME IN FORMAT: 1 (A4,T31,3F8.3,T20,A1,T25,2A1,T14,3A1) WILL READ 320 ATOMS: PRINT FLAG= 0 CELL CONSTANTS A,B,C,ALPHA,BETA,GAMMA ARE: 1.000 1.000 1.000 90.000 90.000 90.000 COORDINATES IN ORTHONORMAL SYSTEM: PRINT FLAG= 0 ************************************** ATOM PAIRS USED TO DETERMINE THE HELIX AXIS ARE: 8 C01C1' 49 C03C1' 49 C03C1' 90 C05C1' 27 G02C1' 68 G04C1' 68 G04C1' 109 G06C1' 309 G16C1' 268 G14C1' 268 G14C1' 227 G12C1' 290 C15C1' 249 C13C1' 249 C13C1' 208 C11C1' 9 C01N1 50 C03N1 50 C03N1 91 C05N1 28 G02N9 69 G04N9 69 G04N9 110 G06N9 310 G16N9 269 G14N9 269 G14N9 228 G12N9 291 C15N1 250 C13N1 250 C13N1 209 C11N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.89861*S + 0.23021 Y = -0.20848*S + 3.23725 Z = 0.38605*S + 1.21237 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.89861*S + 0.23021 Y = -0.20848*S + 3.23725 Z = 0.38605*S + 1.21237 >>>>>> HELIX ROTATION: -59.146 DISPLACEMENT: 7.7174 STATISTICS: OVERALL STANDARD DEV.: 0.7580 SIGMA(X): 0.2884, SIGMA(Y): 0.4547, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.4678, SIGMA(ROTATION): 6.728 THERE ARE 6.09 RESIDUES PER TURN ***************************************************** THE FOLLOWING DIAMOND LIST HAS BEEN OUTPUT ON UNIT: 12 (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY NORMAL END OF JOB: YOU HAVE GIVEN BIRTH TO A HELIX 1 BASE ROLL AND TILT OUTPUT, CAMBRIDGE CONVENTION (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY 320 ATOMS AND 8 BASE PAIRS BASE PAIR 1 16 311 9 16 310 320 9 10 11 12 13 14 15 16 310 311 312 313 314 315 316 317 318 319 320 BASE PAIR 2 29 298 28 38 291 298 28 29 30 31 32 33 34 35 36 37 38 291 292 293 294 295 296 297 298 BASE PAIR 3 57 270 50 57 269 279 50 51 52 53 54 55 56 57 269 270 271 272 273 274 275 276 277 278 279 BASE PAIR 4 70 257 69 79 250 257 69 70 71 72 73 74 75 76 77 78 79 250 251 252 253 254 255 256 257 BASE PAIR 5 98 229 91 98 228 238 91 92 93 94 95 96 97 98 228 229 230 231 232 233 234 235 236 237 238 BASE PAIR 6 111 216 110 120 209 216 110 111 112 113 114 115 116 117 118 119 120 209 210 211 212 213 214 215 216 BASE PAIR 7 140 197 132 140 189 197 132 133 134 135 136 137 138 139 140 189 190 191 192 193 194 195 196 197 BASE PAIR 8 160 177 152 160 169 177 152 153 154 155 156 157 158 159 160 169 170 171 172 173 174 175 176 177 1 BASE ROLL AND TILT OUTPUT, CAMBRIDGE CONVENTION (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY STRAND 1 BASE NORMAL COSINES AND ANGLES -0.05568 0.19666 0.97889 93.19 78.66 11.79 -0.08528 0.08938 0.99234 94.89 84.87 7.10 -0.09861 0.08810 0.99122 95.66 84.95 7.60 -0.04982 0.02252 0.99850 92.86 88.71 3.13 0.19338 0.18930 0.96269 78.85 79.09 15.70 0.21447 0.05965 0.97491 77.62 86.58 12.86 -0.07423 -0.57733 0.81313 94.26 125.26 35.60 -0.91141 -0.31110 0.26936 155.70 108.13 74.37 STRAND 2 BASE NORMAL COSINES AND ANGLES -0.01940 0.07114 0.99728 91.11 85.92 4.23 -0.26183 0.08836 0.96106 105.18 84.93 16.04 -0.21513 0.08524 0.97286 102.42 85.11 13.38 -0.01139 0.22029 0.97537 90.65 77.27 12.74 -0.03117 0.05452 0.99803 91.79 86.87 3.60 0.19445 0.12546 0.97286 78.79 82.79 13.38 -0.01277 0.40385 0.91474 90.73 66.18 23.83 -0.91480 -0.33836 0.22056 156.18 109.78 77.26 BASE PAIR NORMAL COSINES AND ANGLES -0.10671 0.12344 0.98660 96.13 82.91 9.39 -0.15902 0.11046 0.98108 99.15 83.66 11.16 -0.17986 0.11591 0.97684 100.36 83.34 12.36 -0.00847 0.14251 0.98976 90.49 81.81 8.21 0.04299 0.11242 0.99273 87.54 83.54 6.91 0.15840 0.07490 0.98453 80.89 85.70 10.09 0.18720 0.11497 0.97557 79.21 83.40 12.69 0.00639 -0.38175 0.92424 89.63 112.44 22.45 1 BASE ROLL AND TILT OUTPUT, CAMBRIDGE CONVENTION (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY STRAND 1 ROLL AND TILT ANGLES STRAND 2 ROLL AND TILT ANGLES TIP INCL ROLL TILT TIP INCL ROLL TILT -9.51 6.91 -6.27 1.24 -3.44 2.45 -5.35 -12.97 -1.78 6.87 -0.67 -0.37 3.61 15.61 2.11 1.65 4.60 6.04 2.40 4.02 11.25 7.15 12.50 -6.53 2.86 1.27 9.13 -14.40 0.74 12.72 2.67 9.22 0.69 15.68 6.96 2.89 3.52 0.75 3.37 -13.24 -3.14 12.46 11.22 42.20 0.71 13.36 -19.78 -4.41 -35.54 1.83 61.44 -0.93 23.25 -4.93 38.06 -82.85 7.30 -72.67 0.00 0.00 5.98 -75.88 0.00 0.00 BEST PLANE THROUGH BOTH BASES TIP INCL ROLL TILT INCL* PR TW BUCKLE SLIDE X DSP Y DSP C6/C8 -4.52 8.21 -2.01 -2.35 7.07 -6.06 -4.54 4.78 -2.37 -1.35 9.74 -0.58 11.15 -0.81 -0.93 10.95 -5.40 8.76 -0.41 -3.07 2.33 9.72 8.90 8.50 9.97 -0.52 7.85 -6.65 1.24 5.40 -3.20 -1.61 9.67 0.54 8.19 3.39 0.43 7.82 -2.14 11.44 -0.45 -3.42 2.65 9.69 3.16 6.14 5.32 -4.49 6.54 -2.84 -14.92 5.53 -3.54 -1.51 9.88 -0.78 10.06 -0.24 -2.82 10.66 -3.85 0.88 0.52 -3.59 2.78 9.73 8.46 9.39 0.69 -31.90 7.28 -59.41 -7.51 1.43 -2.68 -0.24 18.29 -20.16 -9.45 - - 35.33 -5.63 2.42 - 0.47 1.99 3.70 _____ _____ _____ _____ _____ _____ _____ _____ _____ _____ _____ -0.62 6.52 2.33 -6.08 11.69 -11.50 -0.28 2.40 -2.67 0.63 10.05 AV. 9.15 6.62 4.21 11.50 9.69 19.42 8.58 2.74 1.34 1.99 3.94 S.D. NOTE: ANGLES ARE CALCULATED FROM 5" END TO 3" END OF STRAND 1, AND SIGNS OF ANGLES ALSO ARE CALCULATED WITH RESPECT TO STRAND 1. TO EXAMINE INDIVIDUAL STRAND 2 BASES W.R.T. STRAND 2, REVERSE SIGNS OF TIP AND TILT. FOR Z-DNA, REVERSE SIGNS OF INCL AND X DSP. Y DSP IS CORRECT AS PRINTED. 1 CYLINDRICAL PARAMETERS, CAMBRIDGE CONVENTION (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY 320 ATOMS AND 8 BASE PAIRS PHOSPHATE BACKBONE TABLE, 5" TO 3" DIRECTION IN EACH STRAND R PHI Z D Q H PI STRAND 1 6.90 305.64 4.05 6.37 1.45 6.20 76.83 8.15 300.06 10.26 6.21 6.20 0.21 1.93 6.69 251.91 10.46 7.00 1.72 6.78 75.75 8.33 247.75 17.25 6.53 6.36 1.46 12.93 6.77 199.26 18.71 5.87 2.08 5.49 69.26 8.03 186.40 24.20 7.22 5.36 4.84 42.08 9.75 219.74 29.04 - - - - STRAND 2 6.74 307.01 25.96 7.32 6.98 -2.20 -17.48 6.97 8.25 23.76 6.18 5.85 -1.99 -18.80 5.49 62.70 21.77 6.56 1.54 -6.37 -76.45 6.86 69.23 15.40 5.61 5.41 -1.47 -15.23 5.73 119.16 13.92 6.45 1.91 -6.16 -72.76 6.92 132.81 7.76 5.52 5.44 -0.97 -10.06 5.96 182.06 6.80 - - - - ______ ______ ______ ______ ______ ______ ______ 7.09 185.14 16.38 6.40 4.19 0.48 5.67 AV. 1.14 95.75 7.85 0.58 2.22 4.55 52.33 S.D. 1 CYLINDRICAL PARAMETERS, CAMBRIDGE CONVENTION (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY ROTATION AND RISE TABLE, 5" TO 3" DIRECTION S5" S3" Q(C1") T(C1") TWIST H(C1") RISE SLIDE X DSP Y DSP C1/C1 STRAND 1 - -32.73 4.49 -5.57 11.78 4.070 3.720 4.92 0.10 -1.61 10.26 27.16 -32.74 5.86 -40.42 47.98 3.116 3.381 -2.89 -0.63 2.69 10.53 -7.68 -40.47 4.99 -16.03 10.93 4.106 4.281 5.31 -0.69 -1.88 10.26 24.45 -28.60 5.58 -38.05 47.85 3.940 3.939 -2.63 -0.98 2.73 10.63 -9.44 -39.05 4.77 -20.59 11.51 4.372 3.944 5.37 -1.12 -1.71 10.86 18.45 -31.31 3.22 -22.87 31.12 6.075 5.709 -1.41 -1.10 2.88 10.51 8.45 24.89 3.88 29.97 20.55 -2.792 2.013 1.61 -1.97 -0.69 15.16 5.09 - - - - - - - -2.02 2.23 4.07 _____ _____ _____ _____ _____ _____ _____ _____ _____ _____ _____ 9.50 -25.72 4.72 -16.22 25.96 3.27 3.86 1.47 -1.05 0.58 10.28 AV. 14.66 22.71 1.01 23.71 16.61 2.82 1.10 3.79 0.70 2.23 3.00 S.D. STRAND 2 0.00 23.01 7.74 61.49 20.55 1.234 2.013 0.00 0.00 0.00 0.00 38.48 22.76 6.10 19.64 31.12 -5.344 5.709 0.00 0.00 0.00 0.00 -3.12 57.57 5.05 27.46 11.51 -3.516 3.944 0.00 0.00 0.00 0.00 -30.12 36.65 5.24 36.00 47.85 -3.938 3.939 0.00 0.00 0.00 0.00 -0.65 50.58 4.71 26.06 10.93 -4.456 4.281 0.00 0.00 0.00 0.00 -24.51 38.17 5.29 39.91 47.98 -3.646 3.381 0.00 0.00 0.00 0.00 1.75 47.51 4.52 26.40 11.78 -3.369 3.720 0.00 0.00 0.00 0.00 -21.11 0.00 0.00 0.00 0.00 0.000 0.000 0.00 0.00 0.00 0.00 D,Q,TG AND HG ARE MAGNITUDES. ALL OTHER DERIVED QUANTITIES HAVE PROPER SIGNS--OPPOSITE FOR DESCENDING AND ASCENDING STRANDS. 1 CYLINDRICAL PARAMETERS, CAMBRIDGE CONVENTION (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY ANGLES BETWEEN GLYCOSIDIC BONDS AND C1' - C1' BASE - PAIR VECTORS RESIDUE LAMBDA(1) LAMBDA(2) C01.G16 61.76 54.43 G02.C15 46.30 58.31 C03.G14 65.78 51.62 G04.C13 52.89 53.25 C05.G12 55.74 45.23 G06.C11 50.89 56.61 T07.T10 137.15 126.71 T08.T09 90.59 86.17 1 CYLINDRICAL PARAMETERS, CAMBRIDGE CONVENTION (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY PHOSPHORUS-PHOSPHORUS DISTANCES LESS 5.8 A STRAND 1 DOWN, STRAND 2 ACROSS, 5" TO 3" DIRECTION 16.11 15.19 14.85 10.81 10.22 8.48 5.87 10.00 10.18 10.86 8.72 8.56 9.39 6.84 10.90 11.85 10.80 8.62 6.11 6.25 2.34 5.75 9.01 8.73 9.50 7.35 10.20 7.36 7.30 8.77 6.00 6.99 3.59 7.47 6.29 7.16 9.20 6.42 9.67 7.13 11.99 11.73 6.19 11.15 10.83 15.29 13.61 18.46 17.29 1 MAIN CHAIN AND GLYCOSYL TORSION ANGLE CALCULATION (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY 320 ATOMS AND 8 BASE PAIRS STRAND 1 ALPHA BETA GAMMA DELTA EPSILON ZETA CHI DEL EP-ZE - - 27.6 172.6 262.9 86.7 218.6 10.0 176.2 67.2 202.2 160.1 84.2 314.0 268.4 47.5 -42.8 45.5 316.2 156.4 330.5 163.2 262.0 54.8 239.2 57.2 207.2 64.2 173.4 187.5 80.3 153.7 88.2 60.6 -54.5 65.5 196.4 171.6 16.5 146.0 316.1 47.9 205.9 25.7 268.2 270.9 226.9 331.3 138.3 178.0 277.4 106.2 2.1 -99.3 277.5 178.4 183.9 96.5 95.7 307.5 242.9 -26.4 -211.8 337.9 200.0 317.8 166.3 - - 318.1 92.8 0.0 STRAND 2 ALPHA BETA GAMMA DELTA EPSILON ZETA CHI MEAN EP-ZE - - 23.2 73.5 240.6 236.1 59.3 119.9 4.5 348.8 113.5 152.8 122.9 175.4 145.3 166.6 109.7 30.1 246.0 155.9 13.6 136.2 270.4 80.5 192.8 137.3 189.8 44.6 177.2 192.0 120.3 259.9 267.9 62.1 133.1 -8.0 191.5 235.1 69.6 134.8 281.9 58.9 214.9 107.6 223.0 108.4 158.6 147.7 106.0 242.5 282.7 74.2 134.6 -40.2 205.5 235.1 63.4 127.0 255.4 70.6 198.5 105.6 184.8 87.8 196.9 169.1 162.7 - - 92.6 167.6 0.0 ______ ______ ______ ______ ______ ______ ______ ______ 197.35 184.36 149.17 126.93 236.32 162.36 156.25 AV. 107.07 34.34 109.50 31.77 63.05 103.26 84.12 S.D. 1 PSEUDOROTATION PARAMETERS FOR SUGAR RINGS (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY STRAND 1 V0 V1 V2 V3 V4 Pseud. Delta -2.7 28.5 -45.8 45.1 -25.5 195.6 172.6 -1.5 -23.1 37.4 -38.0 26.0 20.2 84.2 6.5 24.2 -43.3 48.2 -35.7 206.4 163.2 -11.6 -9.0 25.2 -34.0 28.1 39.9 80.3 -16.9 27.8 -26.4 18.4 -1.5 163.0 146.0 18.9 -5.1 -9.0 21.0 -25.9 248.6 138.3 18.9 -32.5 33.3 -23.0 3.3 -13.8 96.5 -4.0 32.0 -45.5 45.6 -26.4 194.4 166.3 STRAND 2 V0 V1 V2 V3 V4 Pseud. Delta -45.4 13.5 22.1 -51.9 59.6 68.2 73.5 -12.7 14.6 -12.6 4.9 4.9 144.9 122.9 -24.8 34.5 -30.7 17.2 4.6 153.7 136.2 12.6 -16.5 13.5 -6.4 -3.7 -32.4 120.3 -35.5 46.8 -42.1 22.0 8.2 152.1 134.8 -9.1 3.9 2.1 -7.3 10.0 78.0 106.0 -26.8 30.4 -23.2 7.9 11.5 139.6 127.0 -33.5 55.8 -55.1 39.1 -3.9 164.8 162.7 ______ ______ ______ ______ ______ ______ -10.47 14.11 -12.52 6.80 2.10 120.20 AV. 19.38 25.57 31.18 31.40 23.96 83.36 S.D. 1 (C-G)3-T4-(C-G)3 UCLA 1D16 OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY STRAND 1 SUGAR ANGLES C4-O4-C1 O4-C1-C2 C1-C2-C3 C2-C3-C4 C3-C4-O4 AVERAGE THAU(M) 109.9 107.3 96.1 105.6 98.6 103.5 49.2609 111.7 103.2 105.0 99.5 104.6 104.8 41.5698 109.1 104.0 102.1 96.9 103.1 103.0 51.6605 105.9 110.7 101.6 104.6 106.4 105.8 34.0292 106.3 110.0 102.0 102.9 110.7 106.4 29.5702 109.2 106.1 107.8 101.8 109.3 106.8 25.0330 110.5 106.3 102.5 102.3 106.4 105.6 36.0360 108.7 105.5 99.2 98.3 104.2 103.2 50.9154 STRAND 2 SUGAR ANGLES C4-O4-C1 O4-C1-C2 C1-C2-C3 C2-C3-C4 C3-C4-O4 AVERAGE THAU(M) 95.8 107.1 101.3 98.9 99.9 100.6 63.1572 116.9 103.0 107.6 106.7 103.7 107.6 15.3000 109.6 105.4 102.1 103.2 107.6 105.6 35.9856 108.4 108.3 106.0 103.1 111.7 107.5 16.5143 109.4 100.5 99.0 101.4 106.3 103.3 50.3279 111.6 109.9 103.6 108.3 105.6 107.8 10.0200 110.6 105.4 103.9 104.3 106.8 106.2 31.2776 105.4 101.3 92.6 96.3 106.6 100.4 63.7800