ID code: 4BDP, PDE0133 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 11 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 445 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 G19C1' 30 C20C1' 30 C20C1' 49 A21C1' 49 A21C1' 70 T22C1' 70 T22C1' 90 C23C1' 90 C23C1' 109 A24C1' 109 A24C1' 130 T25C1' 130 T25C1' 150 G26C1' 150 G26C1' 172 C27C1' 172 C27C1' 191 A28C1' 191 A28C1' 212 A29C1' 250 T05C1' 230 T04C1' 270 G06C1' 250 T05C1' 292 C07C1' 270 G06C1' 311 A08C1' 292 C07C1' 332 T09C1' 311 A08C1' 352 G10C1' 332 T09C1' 374 A11C1' 352 G10C1' 395 T12C1' 374 A11C1' 415 G13C1' 395 T12C1' 437 C14C1' 415 G13C1' 9 G19N9 31 C20N1 31 C20N1 50 A21N9 50 A21N9 71 T22N1 71 T22N1 91 C23N1 91 C23N1 110 A24N9 110 A24N9 131 T25N1 131 T25N1 151 G26N9 151 G26N9 173 C27N1 173 C27N1 192 A28N9 192 A28N9 213 A29N9 251 T05N1 231 T04N1 271 G06N9 251 T05N1 293 C07N1 271 G06N9 312 A08N9 293 C07N1 333 T09N1 312 A08N9 353 G10N9 333 T09N1 375 A11N9 353 G10N9 396 T12N1 375 A11N9 416 G13N9 396 T12N1 438 C14N1 416 G13N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.58387*S + 38.32871 Y = 0.71580*S + 16.85992 Z = 0.38306*S + 26.91667 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.58387*S + 38.32871 Y = 0.71580*S + 16.85993 Z = 0.38306*S + 26.91667 >>>>>> HELIX ROTATION: 34.922 DISPLACEMENT: 3.3332 STATISTICS: OVERALL STANDARD DEV.: 1.3976 SIGMA(X): 2.1761, SIGMA(Y): 2.1364, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.4356, SIGMA(ROTATION): 10.026 THERE ARE 10.31 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 = 11 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.01909 -0.02567 0.99949 91.09 91.47 1.83 -0.07637 0.09747 0.99230 94.38 84.41 7.11 -0.11801 -0.01797 0.99285 96.78 91.03 6.86 -0.21508 -0.04647 0.97549 102.42 92.66 12.71 -0.04869 -0.10367 0.99342 92.79 95.95 6.58 0.08979 -0.08598 0.99224 84.85 94.93 7.14 0.10900 -0.00763 0.99401 83.74 90.44 6.27 0.15359 0.24271 0.95786 81.17 75.95 16.69 0.11507 0.20716 0.97152 83.39 78.04 13.71 -0.14143 0.25762 0.95584 98.13 75.07 17.09 -0.36598 0.30019 0.88088 111.47 72.53 28.25 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.25220 -0.06252 0.96565 104.61 93.58 15.06 -0.18748 -0.03586 0.98161 100.81 92.05 11.00 -0.02807 -0.11562 0.99290 91.61 96.64 6.83 0.05437 -0.14400 0.98808 86.88 98.28 8.85 0.08905 -0.02864 0.99562 84.89 91.64 5.37 0.23249 0.12689 0.96429 76.56 82.71 15.36 0.22732 0.07234 0.97113 76.86 85.85 13.80 0.17516 0.06447 0.98243 79.91 86.30 10.76 -0.12339 0.14195 0.98215 97.09 81.84 10.84 -0.25977 -0.05027 0.96436 105.06 92.88 15.34 -0.15898 -0.15984 0.97426 99.15 99.20 13.03 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.14860 -0.05972 0.98709 98.55 93.42 9.22 -0.15013 0.01046 0.98861 98.63 89.40 8.66 -0.06794 -0.08428 0.99412 93.90 94.83 6.21 -0.09776 -0.08438 0.99163 95.61 94.84 7.42 0.02941 -0.06489 0.99746 88.31 93.72 4.09 0.16510 0.05239 0.98488 80.50 87.00 9.97 0.15157 0.03022 0.98799 81.28 88.27 8.89 0.15744 0.15121 0.97588 80.94 81.30 12.61 -0.00845 0.17281 0.98492 90.48 80.05 9.96 -0.20388 0.14126 0.96875 101.76 81.88 14.36 -0.25322 0.07442 0.96454 104.67 85.73 15.30 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 10 11 I= 1 0 4 4 3 10 19 18 21 15 12 9 I= 2 4 0 7 6 11 18 17 19 12 8 7 I= 3 4 7 0 1 5 15 14 18 15 15 14 I= 4 3 6 1 0 7 17 15 20 15 14 12 I= 5 10 11 5 7 0 10 8 14 13 17 18 I= 6 19 18 15 17 10 0 1 5 12 21 24 I= 7 18 17 14 15 8 1 0 6 12 21 23 I= 8 21 19 18 20 14 5 6 0 9 20 24 I= 9 15 12 15 15 13 12 12 9 0 11 15 I= 10 12 8 15 14 17 21 21 20 11 0 4 I= 11 9 7 14 12 18 24 23 24 15 4 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 1.75 0.55 -7.05 3.34****** 0.00 8.19 12.55 -1.56 -3.70****** 0.00 -6.77 2.19 3.99 5.80 0.00 0.00 -1.77 10.86 9.08 -4.76 0.00 0.00 -4.58 5.09 -4.52 3.63****** 0.00 2.96 6.15 4.99 -0.30 NaN 0.00 -11.90 4.40 9.09 4.45 0.00 0.00 4.26 7.75 2.80 -6.32 0.00 0.00 -5.13 4.10 6.16 5.12****** 0.00 3.86 3.73 12.21 -0.06****** 0.00 -2.06 6.84 4.63 0.08 0.00 0.00 12.62 8.61 -3.11 0.40 0.00 0.00 -0.85 6.21 12.94 6.92****** 0.00 3.27 13.39 0.50 -2.98************ 6.72 15.21 0.61 -2.94 0.00 0.00 -2.48 10.46 16.72 -6.38 0.00 0.00 -2.69 13.43 15.07 1.52 0.00 0.00 9.24 5.62 6.78-11.77****** 0.00 6.58 15.70 10.80 7.52 0.00 0.00 15.28 -1.35 -2.69 -8.12 0.00 0.00 6.35 27.40 0.00 0.00****** 0.00 12.90 -1.80 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 4.02 -0.05 -4.02 0.23 39.13 3.47 0.18 6.92 6.06 0.12 -4.02 0.18 -3.45 -6.47 12.08 0.55 1.54 7.20 -0.73 7.16 -0.19 30.26 3.50 -0.53 7.89 -3.53 -0.66 7.17 -0.13 -7.58 -5.02 8.62 1.55 0.47 1.71 0.71 -1.56 -0.04 31.03 3.23 -0.52 6.21 0.06 0.66 -1.58 -0.05 2.20 -7.54 1.05 0.81 -0.76 7.38 0.01 7.38 -0.44 34.29 3.34 0.22 5.59 -4.86 -0.20 7.39 -0.36 -3.62 -16.17 3.24 -0.44 -1.27 10.31 0.75 10.29 0.38 36.77 3.26 0.30 4.08 -0.13 1.11 10.27 0.50 2.33 -8.99 -0.38 -1.22 -1.46 1.50 -0.53 -1.40 -0.59 30.49 3.14 0.47 7.09 6.98 -0.47 -1.41 -0.58 5.24 -14.68 1.95 -1.32 -0.47 6.98 2.63 6.47 -0.56 29.36 3.70 0.75 8.81 1.15 2.48 6.50 -0.50 -12.01 -4.13 7.19 -0.97 -0.92 9.61 -4.74 8.37 -0.42 37.89 3.50 -0.26 12.41 2.22 -4.54 8.48 -0.32 -2.88 9.21 -4.82 -0.75 -1.70 11.40 -2.76 11.06 -1.80 22.92 3.56 -0.55 9.33 3.46 -2.84 11.05 -1.72 -9.09 -11.96 -7.70 -2.10 -1.78 4.77 -2.44 4.10 -1.08 30.91 3.66 0.11 9.28 10.86 -2.33 4.15 -1.02 -12.17 -8.92 -16.79 -3.21 -3.04 - - - - - - - 12.25 9.03 - - - - -6.80 -28.96 -4.07 -2.79 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.