ID code: 1A02, PDT050 C ********************************************************************* C FREEHEL98.FOR 1 June 1998 C This is the Fortran program code for helix analysis program FREEHELIX. C For operating instructions, see the separate file FREEHEL98.TEX. This C program is radically changed from the earlier NEWHELIX, deleting the C old RADJ and TADJ, and adding the helix-independent parameters VALL C (total bending), VROL (roll), VTIL (tilt), VTWI (twist), VSLI (slide), C VRIS (rise) and VSHF (shift). This program can be used with DNA C helices of any degree of bending. C Richard E. Dickerson, Oxford C ********************************************************************* TITL CELL 1., 1., 1., 90., 90., 90. BRKH FPUN 0 PMIN 0 PMAX 0 BASE 18 HELX RC1' YC1' HELX RN9 YN1 BROL CYLN TRNG END 1 INPUT FRAC.COORDS. X,Y,Z AND ATOM NAME IN FORMAT: (T31,3F8.3,T20,A1,T25,2A1,T14,3A1) WILL READ 732 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 G03C1' 30 G04C1' 30 G04C1' 52 A05C1' 52 A05C1' 73 A06C1' 73 A06C1' 94 A07C1' 94 A07C1' 115 A08C1' 115 A08C1' 136 T09C1' 136 T09C1' 156 T10C1' 156 T10C1' 176 T11C1' 176 T11C1' 196 G12C1' 196 G12C1' 218 T13C1' 218 T13C1' 238 T14C1' 238 T14C1' 258 T15C1' 258 T15C1' 278 C16C1' 278 C16C1' 297 A17C1' 297 A17C1' 318 T18C1' 318 T18C1' 338 A19C1' 338 A19C1' 359 G20C1' 397 T04C1' 378 C03C1' 417 A05C1' 397 T04C1' 438 T06C1' 417 A05C1' 458 G07C1' 438 T06C1' 480 A08C1' 458 G07C1' 501 A09C1' 480 A08C1' 522 A10C1' 501 A09C1' 543 C11C1' 522 A10C1' 562 A12C1' 543 C11C1' 583 A13C1' 562 A12C1' 604 A14C1' 583 A13C1' 625 T15C1' 604 A14C1' 645 T16C1' 625 T15C1' 665 T17C1' 645 T16C1' 685 T18C1' 665 T17C1' 705 C19C1' 685 T18C1' 724 C20C1' 705 C19C1' 9 G03N9 31 G04N9 31 G04N9 53 A05N9 53 A05N9 74 A06N9 74 A06N9 95 A07N9 95 A07N9 116 A08N9 116 A08N9 137 T09N1 137 T09N1 157 T10N1 157 T10N1 177 T11N1 177 T11N1 197 G12N9 197 G12N9 219 T13N1 219 T13N1 239 T14N1 239 T14N1 259 T15N1 259 T15N1 279 C16N1 279 C16N1 298 A17N9 298 A17N9 319 T18N1 319 T18N1 339 A19N9 339 A19N9 360 G20N9 398 T04N1 379 C03N1 418 A05N9 398 T04N1 439 T06N1 418 A05N9 459 G07N9 439 T06N1 481 A08N9 459 G07N9 502 A09N9 481 A08N9 523 A10N9 502 A09N9 544 C11N1 523 A10N9 563 A12N9 544 C11N1 584 A13N9 563 A12N9 605 A14N9 584 A13N9 626 T15N1 605 A14N9 646 T16N1 626 T15N1 666 T17N1 646 T16N1 686 T18N1 666 T17N1 706 C19N1 686 T18N1 725 C20N1 706 C19N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.99882*S + -2.50338 Y = 0.04022*S + 34.93478 Z = 0.02708*S + 40.45698 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.99882*S + -2.50338 Y = 0.04022*S + 34.93478 Z = 0.02708*S + 40.45698 >>>>>> HELIX ROTATION: 35.468 DISPLACEMENT: 3.2359 STATISTICS: OVERALL STANDARD DEV.: 1.1514 SIGMA(X): 1.5642, SIGMA(Y): 1.6857, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.3778, SIGMA(ROTATION): 9.305 THERE ARE 10.15 RESIDUES PER TURN ***************************************************** THE FOLLOWING DIAMOND LIST HAS BEEN OUTPUT ON UNIT: 12 NORMAL END OF JOB: YOU HAVE GIVEN BIRTH TO A HELIX NUMBER BASE PAIRS = 18 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.01680 -0.13162 0.99116 89.04 97.56 7.62 0.00806 -0.09518 0.99543 89.54 95.46 5.48 -0.03132 0.00623 0.99949 91.79 89.64 1.83 0.08264 0.13688 0.98713 85.26 82.13 9.20 0.06089 0.13386 0.98913 86.51 82.31 8.46 -0.01628 0.10166 0.99469 90.93 84.17 5.91 -0.01722 -0.02220 0.99961 90.99 91.27 1.61 0.02266 -0.02168 0.99951 88.70 91.24 1.80 0.02296 -0.09245 0.99545 88.68 95.30 5.47 -0.02467 -0.01689 0.99955 91.41 90.97 1.71 0.09729 -0.02248 0.99500 84.42 91.29 5.73 0.01867 0.07447 0.99705 88.93 85.73 4.40 -0.05127 0.12914 0.99030 92.94 82.58 7.99 -0.21140 0.10439 0.97181 102.20 84.01 13.64 -0.31581 0.01409 0.94872 108.41 89.19 18.43 -0.21166 -0.12356 0.96950 102.22 97.10 14.19 -0.24263 -0.18887 0.95156 104.04 100.89 17.91 -0.08812 -0.23557 0.96785 95.06 103.63 14.57 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.06284 -0.05751 0.99637 86.40 93.30 4.89 -0.03765 -0.12051 0.99200 92.16 96.92 7.25 -0.04448 -0.18397 0.98192 92.55 100.60 10.91 0.12818 -0.14415 0.98122 82.64 98.29 11.12 0.17750 -0.12396 0.97628 79.78 97.12 12.50 0.17104 -0.02684 0.98490 80.15 91.54 9.97 0.24758 0.08967 0.96471 75.67 84.86 15.27 0.17825 0.16022 0.97085 79.73 80.78 13.87 0.13180 0.14205 0.98105 82.43 81.83 11.17 0.12162 0.12275 0.98496 83.01 82.95 9.95 0.00143 0.08321 0.99653 89.92 85.23 4.77 -0.19573 0.10447 0.97508 101.29 84.00 12.82 -0.21841 0.01693 0.97571 102.62 89.03 12.65 -0.28169 -0.07151 0.95684 106.36 94.10 16.90 -0.26400 -0.12668 0.95617 105.31 97.28 17.03 -0.09539 -0.16183 0.98220 95.47 99.31 10.83 -0.08002 -0.16468 0.98310 94.59 99.48 10.55 0.04942 -0.12296 0.99118 87.17 97.06 7.62 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.02292 -0.13394 0.99072 88.69 97.70 7.81 0.00086 -0.14058 0.99007 89.95 98.08 8.08 -0.00874 -0.15585 0.98774 90.50 98.97 8.98 0.15163 -0.03691 0.98775 81.28 92.12 8.98 0.17669 -0.00575 0.98425 79.82 90.33 10.18 0.13028 0.07595 0.98856 82.51 85.64 8.67 0.07990 0.06940 0.99438 85.42 86.02 6.08 0.07155 0.05912 0.99568 85.90 86.61 5.33 0.10931 -0.00773 0.99398 83.72 90.44 6.29 0.04267 0.06361 0.99706 87.55 86.35 4.39 0.08392 0.05834 0.99476 85.19 86.66 5.87 -0.06681 0.10954 0.99174 93.83 83.71 7.37 -0.13700 0.11070 0.98437 97.87 83.64 10.14 -0.23533 -0.00871 0.97188 103.61 90.50 13.62 -0.27331 -0.06776 0.95954 105.86 93.89 16.35 -0.21047 -0.17507 0.96180 102.15 100.08 15.89 -0.14607 -0.18331 0.97214 98.40 100.56 13.56 -0.03241 -0.18589 0.98204 91.86 100.71 10.88 1 I= 1 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 2 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 3 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 4 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 5 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 6 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 7 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 8 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 9 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 10 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 11 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 12 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 13 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 14 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 15 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 16 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 17 PS= 90.0000 LS= 90.0000 PL= 90.0000 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 I= 1 0 1 2 9 11 13 12 11 8 11 11 14 16 16 17 13 10 4 I= 2 1 0 1 10 12 14 12 12 9 11 12 14 16 15 16 12 8 3 I= 3 2 1 0 11 13 15 13 13 10 12 13 15 17 15 16 11 8 2 I= 4 9 10 11 0 2 6 7 7 2 8 6 15 18 22 24 22 19 13 I= 5 11 12 13 2 0 5 7 7 3 8 6 15 19 23 26 24 21 15 I= 6 13 14 15 6 5 0 2 3 4 5 2 11 15 21 24 24 21 17 I= 7 12 12 13 7 7 2 0 0 4 2 0 8 12 18 21 21 19 16 I= 8 11 12 13 7 7 3 0 0 4 1 0 8 12 18 21 21 18 15 I= 9 8 9 10 2 3 4 4 4 0 5 4 12 15 19 22 20 17 13 I= 10 11 11 12 8 8 5 2 1 5 0 2 6 10 16 19 20 17 14 I= 11 11 12 13 6 6 2 0 0 4 2 0 9 13 18 21 21 19 15 I= 12 14 14 15 15 15 11 8 8 12 6 9 0 4 11 15 18 17 17 I= 13 16 16 17 18 19 15 12 12 15 10 13 4 0 8 12 17 16 18 I= 14 16 15 15 22 23 21 18 18 19 16 18 11 8 0 4 9 11 15 I= 15 17 16 16 24 26 24 21 21 22 19 21 15 12 4 0 7 9 15 I= 16 13 12 11 22 24 24 21 21 20 20 21 18 17 9 7 0 3 10 I= 17 10 8 8 19 21 21 19 18 17 17 19 17 16 11 9 3 0 6 I= 18 4 3 2 13 15 17 16 15 13 14 15 17 18 15 15 10 6 0 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 ROLL AND TILT ANGLES STRAND 2 ROLL AND TILT ANGLES TIP INCL ROLL TILT RADJ TADJ TIP INCL ROLL TILT RADJ TADJ -4.50 -6.14 0.99 1.91 0.00 0.00 -4.75 -1.14 4.72 -4.90 -0.00 0.00 -0.41 -5.47 0.67 6.21 0.00 0.00 2.23 -6.90 1.32 -3.41 0.00 0.00 1.39 1.19 -9.97 -0.47****** 0.00 7.38 -7.99 -7.95 -6.35 0.00 0.00 -8.82 -2.60 0.07 1.26 0.00 0.00 6.15 -9.23 -0.93 -2.91 0.00 0.00 -5.70 -6.23 -1.57 4.53 -0.01 0.00 10.58 -6.59 -4.40 -3.43 0.00 0.50 -3.70 -4.60 1.51 6.95 0.00 0.00 9.31 -3.52 2.81 -7.50 0.00 0.00 -1.05 1.22 2.13 0.83 -0.00 0.00 14.59 -4.41 -2.16 -5.25 0.00 0.00 0.19 1.79 -3.41 2.20 0.00 0.00 13.86 -0.40 -2.31 -1.68 0.00 0.00 -4.87 2.48 4.62 -2.22 -0.00 0.00 9.69 5.52 -1.03 -0.70 -0.00 0.00 -0.20 -1.70 -5.09 4.81 0.00 0.00 3.01 9.48 3.15 -6.54 0.00 0.00 -5.37 1.99 6.02 3.88 -0.00 0.00 2.55 4.03 11.18 -2.36 0.00 0.00 -1.07 4.27 2.60 4.38 0.00 0.00 11.29 6.00 3.03 -4.20 0.00 0.00 -2.29 7.65 6.36 6.80 -0.00 0.00 9.24 8.57 6.24 0.14 -0.00 -0.01 -1.98 13.49 4.93 6.20 0.00 0.00 8.89 14.25 3.20 -0.88 0.00 0.00 -6.41 17.20 9.89 -1.02 -0.00 0.00 2.19 16.88 6.74 -7.24 -0.00 -0.00 -3.41 13.75 0.07 4.14 0.00 0.00 2.81 10.45 0.86 -0.24 0.00 0.00 -13.42 11.64 8.03 4.64 0.00 0.00 -4.07 9.72 7.79 -0.62 -0.00 0.00 -11.75 8.49 0.00 0.00 0.00 0.00 -1.53 7.46 0.00 0.00 0.00 0.00 BEST PLANE THROUGH BOTH BASES VALL VTIL VROL VSLI VTWI VRIS VSHF INCL TIP TILT ROLL SLIDE CUP PROP BUCK X DSP Y DSP 1.32 -0.68 1.13 -0.74 29.39 3.51 0.02 -6.09 -4.87 -0.67 1.14 -0.69 -6.44 0.27 5.00 2.01 0.53 1.04 0.72 0.76 -0.61 28.44 3.56 0.23 -8.08 0.03 -0.70 0.76 -0.54 -7.78 -2.63 -1.44 1.81 -0.76 11.46 -3.08 -11.04 0.63 45.80 3.16 -0.56 -7.57 4.80 -2.98 -11.12 0.59 2.64 -5.98 -9.22 1.56 -1.73 2.30 -1.58 -1.68 -0.24 37.26 2.97 -0.00 -8.98 -0.14 -1.57 -1.67 -0.19 6.11 -15.01 -6.58 -0.19 -1.23 5.39 -1.09 -5.28 -0.51 36.97 3.26 0.23 -9.23 4.27 -1.13 -5.27 -0.49 1.47 -16.28 -0.47 -0.73 -0.66 2.93 1.06 -2.73 -0.55 32.69 3.26 0.02 -7.50 4.33 1.00 -2.73 -0.52 -6.74 -13.03 1.01 -0.55 -0.29 0.76 0.37 -0.66 -0.62 37.51 3.16 0.11 -3.74 4.78 0.37 -0.66 -0.59 3.56 -15.64 -5.73 -0.40 -0.26 4.40 3.84 -2.14 -0.04 36.83 3.14 0.32 0.07 5.33 3.89 -2.06 -0.06 5.27 -13.68 -2.17 -0.25 -0.58 5.60 -3.28 4.54 -0.37 40.49 3.05 -0.24 6.21 0.99 -3.33 4.50 -0.33 8.08 -14.56 3.10 -0.11 -0.72 2.39 1.56 -1.81 -0.15 29.02 3.49 -0.46 3.86 2.10 1.49 -1.86 -0.18 -9.15 -3.23 11.18 -0.93 -0.97 9.13 0.35 9.12 0.24 33.19 3.12 -0.16 5.44 -2.18 0.10 9.16 0.30 -0.18 -7.93 2.03 -1.84 -0.72 4.05 1.43 3.79 -0.33 38.15 3.21 0.64 6.29 3.83 1.52 3.73 -0.30 -0.81 -12.36 1.85 -2.05 0.42 8.90 0.85 8.86 -0.21 33.20 3.21 -0.19 9.90 2.21 0.80 8.86 -0.12 -0.12 -11.54 1.04 -0.81 0.61 4.09 2.29 3.39 0.58 34.79 3.32 0.40 12.79 4.62 2.31 3.29 0.65 -1.34 -10.86 0.92 -0.55 0.19 7.13 -0.08 7.13 -0.37 25.22 3.33 0.52 16.31 -1.18 0.11 7.14 -0.34 -2.90 -8.60 -0.42 0.07 0.05 3.77 1.20 3.57 0.60 41.54 3.21 -0.35 15.84 -1.25 -1.21 3.52 0.61 1.11 -6.24 -3.32 0.24 -1.32 6.54 1.73 6.31 0.54 36.17 3.40 1.03 11.01 -7.81 1.64 6.32 0.62 1.00 -9.35 -2.21 -1.37 -1.06 - - - - - - - 7.88 -7.45 - - - - -10.21 -1.21 -1.21 -0.22 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. ROLL and TILT are the simple components of base pair normals along minor and major axes of base pairs. They are the values that were calculated in NEWHEL90 and earlier. VALL, VTIL, VROL, VSLI and VTWI are the total angle betw een base pair normal vectors, and the Tilt, Roll, Slide and Twist calculated relative to a set of local axes halfway between each of the long axes, the short axes, and normal vectors for the two base pairs. They are completely independent of the choice of overall helix axis.