ID code: 1O3T, PD0401 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 13 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 533 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: 11 A14C1' 32 T15C1' 32 T15C1' 52 C16C1' 52 C16C1' 71 G17C1' 71 G17C1' 93 C18C1' 93 C18C1' 112 A19C1' 112 A19C1' 133 T20C1' 133 T20C1' 153 T21C1' 153 T21C1' 173 T22C1' 173 T22C1' 193 T23C1' 193 T23C1' 213 T24C1' 213 T24C1' 233 C25C1' 233 C25C1' 252 G26C1' 293 G25C1' 274 C26C1' 315 A24C1' 293 G25C1' 336 A23C1' 315 A24C1' 357 A22C1' 336 A23C1' 378 A21C1' 357 A22C1' 399 A20C1' 378 A21C1' 420 T19C1' 399 A20C1' 440 G18C1' 420 T19C1' 462 C17C1' 440 G18C1' 481 G16C1' 462 C17C1' 503 A15C1' 481 G16C1' 524 T14C1' 503 A15C1' 12 A14N9 33 T15N1 33 T15N1 53 C16N1 53 C16N1 72 G17N9 72 G17N9 94 C18N1 94 C18N1 113 A19N9 113 A19N9 134 T20N1 134 T20N1 154 T21N1 154 T21N1 174 T22N1 174 T22N1 194 T23N1 194 T23N1 214 T24N1 214 T24N1 234 C25N1 234 C25N1 253 G26N9 294 G25N9 275 C26N1 316 A24N9 294 G25N9 337 A23N9 316 A24N9 358 A22N9 337 A23N9 379 A21N9 358 A22N9 400 A20N9 379 A21N9 421 T19N1 400 A20N9 441 G18N9 421 T19N1 463 C17N1 441 G18N9 482 G16N9 463 C17N1 504 A15N9 482 G16N9 525 T14N1 504 A15N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.98325*S + -1.74173 Y = 0.17788*S + 3.72363 Z = 0.03964*S + 26.49505 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.98325*S + -1.74173 Y = 0.17788*S + 3.72363 Z = 0.03964*S + 26.49505 >>>>>> HELIX ROTATION: 33.629 DISPLACEMENT: 3.4132 STATISTICS: OVERALL STANDARD DEV.: 2.2740 SIGMA(X): 2.8703, SIGMA(Y): 2.8628, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.8206, SIGMA(ROTATION): 22.834 THERE ARE 10.71 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 = 13 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.59711 0.55491 0.57925 126.66 56.30 54.60 -0.60720 0.24783 0.75491 127.39 75.65 40.98 -0.73677 -0.10629 0.66773 137.46 96.10 48.11 0.06842 0.03579 0.99701 86.08 87.95 4.43 0.20985 -0.22040 0.95257 77.89 102.73 17.72 0.12629 0.00126 0.99199 82.74 89.93 7.26 -0.00670 -0.07338 0.99728 90.38 94.21 4.23 0.07852 -0.16210 0.98365 85.50 99.33 10.38 0.10311 -0.19230 0.97591 84.08 101.09 12.60 0.28726 -0.24843 0.92508 73.31 104.38 22.32 0.32516 -0.08563 0.94177 71.02 94.91 19.65 0.41603 -0.09625 0.90424 65.42 95.52 25.28 NaN NaN NaN NaN NaN NaN STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.29235 0.20508 0.93406 107.00 78.17 20.92 -0.38872 0.10479 0.91538 112.87 83.98 23.74 -0.62986 0.44446 0.63697 129.04 63.61 50.43 -0.23570 -0.13588 0.96228 103.63 97.81 15.79 0.16791 -0.08124 0.98245 80.33 94.66 10.75 0.02249 0.09926 0.99481 88.71 84.30 5.84 0.05930 0.09137 0.99405 86.60 84.76 6.25 0.12312 -0.34216 0.93154 82.93 110.01 21.32 0.10627 -0.15764 0.98176 83.90 99.07 10.96 -0.05559 -0.04158 0.99759 93.19 92.38 3.98 -0.04197 -0.18028 0.98272 92.41 100.39 10.67 0.09685 -0.18789 0.97740 84.44 100.83 12.20 NaN NaN NaN NaN NaN NaN BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.52674 0.40390 0.74794 121.79 66.18 41.59 -0.57355 0.18785 0.79734 125.00 79.17 37.12 -0.67696 0.27696 0.68192 132.61 73.92 47.01 -0.05046 -0.08808 0.99483 92.89 95.05 5.83 0.18693 -0.05816 0.98065 79.23 93.33 11.29 0.11390 0.01019 0.99344 83.46 89.42 6.57 0.10350 -0.01534 0.99451 84.06 90.88 6.01 0.06287 -0.25473 0.96497 86.40 104.76 15.21 0.08175 -0.23173 0.96934 85.31 103.40 14.22 0.15211 -0.19188 0.96956 81.25 101.06 14.17 0.19568 -0.14381 0.97006 78.72 98.27 14.05 0.18814 -0.16241 0.96862 79.16 99.35 14.39 NaN NaN NaN NaN NaN NaN 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= NaN LS= NaN PL= NaN 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 10 11 12 13 I= 1 0 13 11 42 52 46 46 54 53 55 55 55**** I= 2 13 0 10 36 48 43 43 46 46 49 50 50**** I= 3 11 10 0 46 58 52 52 56 57 59 60 60**** I= 4 42 36 46 0 13 10 9 11 11 13 14 14**** I= 5 52 48 58 13 0 5 5 13 11 7 4 6**** I= 6 46 43 52 10 5 0 1 15 14 11 10 10**** I= 7 46 43 52 9 5 1 0 14 12 10 9 9**** I= 8 54 46 56 11 13 15 14 0 1 6 9 8**** I= 9 53 46 57 11 11 14 12 1 0 4 8 7**** I= 10 55 49 59 13 7 11 10 6 4 0 3 2**** I= 11 55 50 60 14 4 10 9 9 8 3 0 1**** I= 12 55 50 60 14 6 10 9 8 7 2 1 0**** I= 13 **************************************************** 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 -26.63 42.91 17.88 -0.70****** 0.00 -8.85 18.80 6.14 5.10****** 0.00 -28.20 27.05 13.14 17.51 0.00 0.00 -14.67 18.24-24.59 1.06 0.00 0.00 -33.38 30.09 35.08-35.56****** 0.00 -50.42 -0.83 41.08 14.22 NaN 0.00 3.31 -2.94 8.63 14.55 0.00 0.00 -11.28 10.90 23.67 -3.92 0.00 0.00 9.98 14.48 2.20-13.52****** 0.00 8.82 6.09 -2.05-13.24****** 0.00 4.67 5.54 -6.85 -5.45 0.00 0.00 5.21 -2.63 0.38 2.12 0.00 0.00 -4.23 0.08 -6.04 3.65****** 0.00 5.58 2.81-25.91 -1.88************ -10.36 -0.57 -2.22 -0.27 0.00 0.00 -21.04 -3.34 8.05 6.97 0.00 0.00 -9.75 -7.91-10.76 -2.70 0.00 0.00 -9.14 -5.99 9.63 6.20****** 0.00 -13.00-17.82 -6.86 6.72 0.00 0.00 3.64 -1.62 3.61 -7.14 0.00 0.00 -7.02-18.26 -0.76 -5.19****** 0.00 9.81 -4.14 -1.64 -7.82 0.00 -0.00 6.72-24.25 NaN NaN 0.00 0.00 11.10 -5.01 NaN NaN 0.00 0.00 NaN NaN 0.00 0.00 0.00 0.00 NaN NaN 0.00 0.00 -0.00 NaN BEST PLANE THROUGH BOTH BASES VALL VTIL VROL VSLI VTWI VRIS VSHF INCL TIP TILT ROLL SLIDE CUP PROP BUCK X DSP Y DSP 13.01 2.06 12.84 -0.19 29.38 3.13 -0.44 35.90 -18.12 1.78 12.64 -0.13 17.52 -17.80 -29.07 3.94 2.20 10.26 3.52 -9.64 2.43 33.04 3.87 1.39 26.63 -23.84 2.21 -7.52 2.32 -17.25 -13.36 -11.55 2.53 -1.49 46.52 1.83 46.49 1.71 21.68 3.59 -0.04 8.66 -45.71 -3.69 46.24 1.98 42.73 15.57 -28.80 0.40 -1.64 13.77 2.26 13.58 -0.21 22.91 3.74 -0.14 5.61 -1.58 -2.18 13.66 -0.12 -22.34 14.69 13.92 -1.34 0.02 5.78 -5.52 -1.71 0.84 40.87 3.38 -0.81 4.95 10.12 -5.49 -1.67 0.84 0.25 1.26 -8.42 -1.20 0.05 1.58 -0.02 -1.58 -0.93 33.23 3.38 -0.19 4.66 4.61 0.00 -1.58 -0.99 10.91 -0.58 -8.17 -1.06 1.45 14.05 -5.01 -13.14 -0.56 36.16 3.58 0.14 6.00 -0.23 -5.29 -12.98 -0.71 -5.70 -9.83 2.74 -0.51 0.60 1.72 1.72 0.08 -0.96 38.37 3.05 0.42 -3.93 -14.67 1.70 0.13 -0.92 4.89 10.66 -2.96 -0.68 0.18 4.63 2.58 -3.85 -0.26 34.86 2.80 -0.17 -10.50 -9.49 2.48 -3.92 -0.23 14.55 -0.59 1.93 -0.84 0.14 3.72 0.91 -3.60 -0.33 40.21 3.10 -0.22 -12.76 -6.07 0.98 -3.59 -0.27 -2.45 -16.78 16.48 -1.03 1.05 1.15 -0.09 1.15 1.41 37.99 3.43 0.09 -14.05 0.06 0.14 1.14 1.45 5.08 -16.97 14.03 -0.31 2.00 NaN NaN NaN NaN NaN NaN NaN -10.36 9.88 NaN NaN -4.87 NaN -4.27 19.11 2.11 3.64 - - - - - - - NaN NaN - - - - NaN NaN NaN NaN 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.