ID code: 1FOS, PDT014 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 19 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 773 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 A02C1' 29 T03C1' 29 T03C1' 49 G04C1' 49 G04C1' 71 G05C1' 71 G05C1' 93 A06C1' 93 A06C1' 114 T07C1' 114 T07C1' 134 G08C1' 134 G08C1' 156 A09C1' 156 A09C1' 177 G10C1' 177 G10C1' 199 T11C1' 199 T11C1' 219 C12C1' 219 C12C1' 238 A13C1' 238 A13C1' 259 T14C1' 259 T14C1' 279 A15C1' 279 A15C1' 300 G16C1' 300 G16C1' 322 G17C1' 322 G17C1' 344 A18C1' 344 A18C1' 365 G19C1' 365 G19C1' 387 A20C1' 425 C23C1' 405 T22C1' 444 T24C1' 425 C23C1' 464 C25C1' 444 T24C1' 483 C26C1' 464 C25C1' 502 T27C1' 483 C26C1' 522 A28C1' 502 T27C1' 543 T29C1' 522 A28C1' 563 G30C1' 543 T29C1' 585 A31C1' 563 G30C1' 606 C32C1' 585 A31C1' 625 T33C1' 606 C32C1' 645 C34C1' 625 T33C1' 664 A35C1' 645 C34C1' 685 T36C1' 664 A35C1' 705 C37C1' 685 T36C1' 724 C38C1' 705 C37C1' 743 A39C1' 724 C38C1' 764 T40C1' 743 A39C1' 9 A02N9 30 T03N1 30 T03N1 50 G04N9 50 G04N9 72 G05N9 72 G05N9 94 A06N9 94 A06N9 115 T07N1 115 T07N1 135 G08N9 135 G08N9 157 A09N9 157 A09N9 178 G10N9 178 G10N9 200 T11N1 200 T11N1 220 C12N1 220 C12N1 239 A13N9 239 A13N9 260 T14N1 260 T14N1 280 A15N9 280 A15N9 301 G16N9 301 G16N9 323 G17N9 323 G17N9 345 A18N9 345 A18N9 366 G19N9 366 G19N9 388 A20N9 426 C23N1 406 T22N1 445 T24N1 426 C23N1 465 C25N1 445 T24N1 484 C26N1 465 C25N1 503 T27N1 484 C26N1 523 A28N9 503 T27N1 544 T29N1 523 A28N9 564 G30N9 544 T29N1 586 A31N9 564 G30N9 607 C32N1 586 A31N9 626 T33N1 607 C32N1 646 C34N1 626 T33N1 665 A35N9 646 C34N1 686 T36N1 665 A35N9 706 C37N1 686 T36N1 725 C38N1 706 C37N1 744 A39N9 725 C38N1 765 T40N1 744 A39N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.03708*S + 53.68221 Y = -0.00944*S + 2.41123 Z = 0.99927*S + 2.01444 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.03708*S + 53.68221 Y = -0.00944*S + 2.41123 Z = 0.99927*S + 2.01444 >>>>>> HELIX ROTATION: 35.662 DISPLACEMENT: 3.2937 STATISTICS: OVERALL STANDARD DEV.: 0.7886 SIGMA(X): 1.1308, SIGMA(Y): 1.1567, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.2609, SIGMA(ROTATION): 5.749 THERE ARE 10.09 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 = 19 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.08075 0.09483 0.99221 85.37 84.56 7.16 0.21764 0.06982 0.97353 77.43 86.00 13.21 -0.02341 0.10172 0.99454 91.34 84.16 5.99 -0.10348 0.04447 0.99364 95.94 87.45 6.47 -0.11011 0.00166 0.99392 96.32 89.90 6.32 -0.17030 -0.06662 0.98314 99.81 93.82 10.54 -0.10342 -0.09018 0.99054 95.94 95.17 7.89 -0.14939 -0.17485 0.97320 98.59 100.07 13.30 -0.04209 -0.08580 0.99542 92.41 94.92 5.48 -0.02212 -0.06348 0.99774 91.27 93.64 3.85 -0.03888 0.04961 0.99801 92.23 87.16 3.61 0.00629 0.05101 0.99868 89.64 87.08 2.95 0.00818 0.06243 0.99802 89.53 86.42 3.61 0.08746 0.01935 0.99598 84.98 88.89 5.14 0.07011 0.01132 0.99748 85.98 89.35 4.07 -0.01542 0.01370 0.99979 90.88 89.21 1.18 -0.10626 -0.02278 0.99408 96.10 91.31 6.24 -0.02074 -0.02849 0.99938 91.19 91.63 2.02 0.03046 -0.13853 0.98989 88.25 97.96 8.15 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.01944 0.10568 0.99421 91.11 83.93 6.17 0.02509 0.02734 0.99931 88.56 88.43 2.13 -0.01309 0.05693 0.99829 90.75 86.74 3.35 -0.13108 -0.02201 0.99113 97.53 91.26 7.64 -0.29333 -0.04826 0.95479 107.06 92.77 17.29 -0.15311 -0.06807 0.98586 98.81 93.90 9.65 -0.02107 -0.03765 0.99907 91.21 92.16 2.47 0.02126 -0.06882 0.99740 88.78 93.95 4.13 0.05948 -0.06689 0.99599 86.59 93.84 5.14 0.03624 -0.07022 0.99687 87.92 94.03 4.53 0.05409 0.02158 0.99830 86.90 88.76 3.34 0.09014 0.16580 0.98203 84.83 80.46 10.88 -0.00541 0.12499 0.99214 90.31 82.82 7.19 0.00252 0.13854 0.99035 89.86 82.04 7.96 0.01831 0.07973 0.99665 88.95 85.43 4.69 0.01326 -0.02624 0.99957 89.24 91.50 1.68 0.12884 0.03649 0.99099 82.60 87.91 7.70 0.17872 0.00788 0.98387 79.71 89.55 10.31 0.05734 0.07252 0.99572 86.71 85.84 5.30 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.04072 0.10153 0.99400 87.67 84.17 6.28 0.10263 0.00330 0.99471 84.11 89.81 5.89 -0.01315 0.06222 0.99798 90.75 86.43 3.65 -0.11608 0.02060 0.99303 96.67 88.82 6.77 -0.21466 -0.04177 0.97580 102.40 92.39 12.63 -0.20073 -0.06883 0.97723 101.58 93.95 12.25 -0.11105 -0.13639 0.98441 96.38 97.84 10.13 -0.05748 -0.14096 0.98835 93.29 98.10 8.76 0.03011 -0.11067 0.99340 88.27 96.35 6.59 0.04136 -0.08739 0.99532 87.63 95.01 5.55 0.09049 0.02147 0.99567 84.81 88.77 5.34 0.05071 0.12110 0.99134 87.09 83.04 7.54 0.01207 0.12009 0.99269 89.31 83.10 6.93 0.02699 0.09453 0.99516 88.45 84.58 5.64 0.04274 0.03890 0.99833 87.55 87.77 3.31 0.02281 0.00463 0.99973 88.69 89.73 1.33 0.02476 0.00916 0.99965 88.58 89.48 1.51 0.06136 0.02004 0.99791 86.48 88.85 3.70 0.03769 0.00542 0.99927 87.84 89.69 2.18 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 I= 18 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 19 I= 1 0 6 3 10 16 17 16 15 12 10 5 1 1 0 3 5 5 4 5 I= 2 6 0 7 12 18 17 14 12 7 6 1 7 8 6 3 4 4 2 3 I= 3 3 7 0 6 13 13 12 11 10 9 6 4 3 2 3 3 3 4 4 I= 4 10 12 6 0 6 7 9 9 11 10 11 11 9 9 9 8 8 10 8 I= 5 16 18 13 6 0 1 8 10 14 14 17 17 16 15 15 13 14 16 14 I= 6 17 17 13 7 1 0 6 9 13 13 17 18 16 16 15 13 13 15 14 I= 7 16 14 12 9 8 6 0 3 8 9 14 17 16 15 13 11 11 13 11 I= 8 15 12 11 9 10 9 3 0 5 6 12 16 15 14 11 9 9 11 10 I= 9 12 7 10 11 14 13 8 5 0 1 8 13 13 11 8 6 6 7 6 I= 10 10 6 9 10 14 13 9 6 1 0 6 11 12 10 7 5 5 6 5 I= 11 5 1 6 11 17 17 14 12 8 6 0 6 7 5 2 4 3 1 3 I= 12 1 7 4 11 17 18 17 16 13 11 6 0 2 2 4 6 6 5 6 I= 13 1 8 3 9 16 16 16 15 13 12 7 2 0 1 4 6 6 6 6 I= 14 0 6 2 9 15 16 15 14 11 10 5 2 1 0 3 5 4 4 5 I= 15 3 3 3 9 15 15 13 11 8 7 2 4 4 3 0 2 1 1 1 I= 16 5 4 3 8 13 13 11 9 6 5 4 6 6 5 2 0 0 2 0 I= 17 5 4 3 8 14 13 11 9 6 5 3 6 6 4 1 0 0 2 0 I= 18 4 2 4 10 16 15 13 11 7 6 1 5 6 4 1 2 2 0 1 I= 19 5 3 4 8 14 14 11 10 6 5 3 6 6 5 1 0 0 1 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 4.17 5.81 -5.29 5.98 0.00 0.00 6.16 0.37 -5.17 -0.14 0.00 -0.00 -6.80 11.27 13.46 -4.04 0.00 0.00 -0.06 2.13 2.69 0.64 0.00 0.00 2.15 5.59 5.02 -2.59 0.00****** 1.20 3.12 7.36 -3.51 -0.00 0.00 4.33 4.79 2.07 -1.38 0.00 0.00 7.37 1.98 7.41 5.85 0.00 0.00 2.44 5.83 4.54 2.57 0.00 0.00 9.30 14.45 -0.54 -8.12 -0.00 0.00 2.80 10.15 2.93 -2.82 0.00 0.00 2.98 9.16 1.85 -7.56 0.00 0.00 -0.58 7.87 0.30 5.52****** 0.00 0.66 2.38 3.00 0.25 0.00 0.00 -6.20 11.71 6.73 -4.33 0.00 0.00 2.04 3.59 2.19 0.15 0.00 0.00 -4.16 3.56 1.70 -0.25 0.00 0.00 1.61 4.87 -1.15 -0.70 0.00 0.50 -3.78 0.76 6.09 -2.44 0.00 0.00 -2.41 3.84 5.36 -0.22 0.00 0.00 2.93 -2.11 -0.92 2.42 -0.00 0.00 1.11 3.15 6.84 5.10 0.00 0.00 1.91 2.24 0.25 0.62 0.00 0.00 3.53 10.28 3.48 -4.84 0.00 0.00 0.78 3.52 -4.56 -2.45 -0.00 0.00 2.74 6.64 -0.45 0.78 -0.00 0.00 -5.10 -0.61 1.08 0.21 0.00 0.00 -2.76 7.47 1.24 -3.26 0.00 0.00 -2.74 -3.01 1.17 4.77 -0.00 0.00 -4.40 1.62 5.94 -1.33 0.00 0.00 -0.82 0.85 -0.13 5.62 0.00 0.00 1.54 -0.69 -0.70 -7.52 0.00 0.00 -2.86 5.54 4.15 -2.64 -0.00 0.00 3.07 -7.05 3.28 -0.37 -0.00 0.00 -0.58 1.93 2.88 6.34 0.00 0.00 9.56 -3.81 -6.94 -3.76 0.00 0.00 -1.71 7.97 0.00 0.00 -0.00 0.00 4.72 -2.41 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 6.66 0.09 -6.66 -0.45 35.01 3.52 0.13 3.67 5.09 0.12 -6.67 -0.49 -3.76 -2.00 -5.42 -0.63 0.02 7.45 0.30 7.45 -0.39 32.81 3.24 0.19 4.00 -4.32 0.33 7.46 -0.30 6.71 -6.79 -9.18 -0.59 -0.40 6.37 -1.49 6.19 -0.13 32.63 3.37 -0.22 3.42 1.25 -1.51 6.19 -0.06 -0.32 0.95 -2.47 -0.77 -0.57 6.76 1.63 6.56 -0.18 41.90 3.01 -0.24 3.85 5.56 1.75 6.46 -0.12 11.54 -3.05 -2.79 -1.06 -0.35 1.75 -1.02 1.41 -0.24 28.88 3.61 -0.20 10.37 7.13 -1.10 1.35 -0.27 -9.73 -6.88 8.75 -1.09 -0.09 6.45 -2.99 5.72 0.23 38.76 3.17 -0.44 11.93 2.75 -2.85 5.78 0.21 -4.50 -0.18 -0.98 -1.12 -0.49 3.09 1.26 2.82 -0.31 31.84 3.43 0.23 10.08 0.98 -1.39 2.75 -0.33 -2.69 -1.24 -5.48 -1.64 0.11 5.32 -1.28 5.16 -0.33 35.55 3.14 -0.57 8.63 -1.47 -1.12 5.20 -0.29 9.47 -8.26 -8.17 -1.38 0.08 1.49 -0.58 1.37 -0.59 36.03 3.26 0.35 6.52 -0.93 -0.61 1.35 -0.60 1.77 -5.78 1.30 -1.90 0.39 6.85 -1.20 6.74 -0.24 32.74 3.30 -0.16 4.59 -3.11 1.29 6.74 -0.25 2.18 -1.38 3.07 -1.38 0.51 6.15 0.08 6.15 0.42 40.10 3.25 0.10 5.24 1.02 0.10 6.16 0.42 2.79 1.83 5.26 -1.22 0.78 2.22 -1.28 1.81 -0.38 27.39 3.42 -0.15 6.84 3.16 -1.19 1.87 -0.40 -4.92 -1.62 8.05 -0.18 1.41 1.70 -1.47 -0.86 0.22 39.12 3.21 -0.26 6.72 1.70 -1.46 -0.86 0.17 4.94 -1.96 3.12 0.30 0.58 3.32 -3.07 1.26 0.65 37.77 3.56 0.11 4.61 -3.25 -3.11 1.13 0.63 -3.43 -2.35 8.06 0.26 0.25 2.27 0.58 2.20 0.16 35.68 3.41 -0.40 -0.83 -3.21 0.58 2.20 0.20 -6.17 1.66 4.63 0.41 0.60 0.28 -0.20 -0.20 0.36 36.88 3.52 -0.48 -1.32 -0.21 -0.20 -0.19 0.40 -11.05 -2.36 -1.54 0.28 0.64 2.19 -1.71 1.36 -0.70 31.29 3.18 0.76 -1.43 0.50 -1.74 1.32 -0.64 6.83 -5.97 -12.59 0.30 0.92 1.60 0.77 -1.40 0.41 43.93 3.40 -0.03 -2.24 2.94 0.83 -1.36 0.48 -4.62 -10.16 -5.76 1.39 -0.16 - - - - - - - 0.61 2.09 - - - - -6.46 -10.38 1.19 -0.71 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.