ID code: 2L8U 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 9 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 418 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: 9 C01C1' 32 C02C1' 32 C02C1' 54 G03C1' 54 G03C1' 79 C04C1' 79 C04C1' 123 G06C1' 123 G06C1' 148 C07C1' 148 C07C1' 170 G08C1' 170 G08C1' 195 G09C1' 241 C11C1' 218 C10C1' 263 G12C1' 241 C11C1' 288 C13C1' 263 G12C1' 332 G15C1' 288 C13C1' 357 C16C1' 332 G15C1' 379 G17C1' 357 C16C1' 404 G18C1' 379 G17C1' 10 C01N1 33 C02N1 33 C02N1 55 G03N9 55 G03N9 80 C04N1 80 C04N1 124 G06N9 124 G06N9 149 C07N1 149 C07N1 171 G08N9 171 G08N9 196 G09N9 242 C11N1 219 C10N1 264 G12N9 242 C11N1 289 C13N1 264 G12N9 333 G15N9 289 C13N1 358 C16N1 333 G15N9 380 G17N9 358 C16N1 405 G18N9 380 G17N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.76314*S + -2.58204 Y = -0.59885*S + -5.56083 Z = -0.24289*S + 5.59789 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.76314*S + -2.58204 Y = -0.59885*S + -5.56083 Z = -0.24289*S + 5.59789 >>>>>> HELIX ROTATION: 34.153 DISPLACEMENT: 2.1363 STATISTICS: OVERALL STANDARD DEV.: 2.3404 SIGMA(X): 2.0819, SIGMA(Y): 1.9153, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.8816, SIGMA(ROTATION): 11.854 THERE ARE 10.54 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 = 9 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.53325 -0.00144 0.84595 122.23 90.08 32.23 -0.33374 -0.37296 0.86575 109.50 111.90 30.03 -0.12063 -0.47275 0.87290 96.93 118.21 29.20 -0.11159 -0.53714 0.83608 96.41 122.49 33.27 0.10183 -0.36689 0.92467 84.16 111.52 22.38 0.41082 -0.30289 0.85993 65.74 107.63 30.69 0.38173 -0.13739 0.91401 67.56 97.90 23.94 0.47733 -0.01003 0.87867 61.49 90.57 28.52 0.44779 0.12314 0.88562 63.40 82.93 27.67 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.20498 -0.37818 0.90275 101.83 112.22 25.48 -0.11037 -0.40257 0.90871 96.34 113.74 24.67 -0.07410 -0.20471 0.97601 94.25 101.81 12.57 0.16916 -0.52336 0.83515 80.26 121.56 33.37 0.48736 -0.43210 0.75879 60.83 115.60 40.64 0.71013 -0.08390 0.69905 44.75 94.81 45.65 0.57233 -0.04170 0.81896 55.09 92.39 35.02 0.48617 0.21682 0.84654 60.91 77.48 32.16 0.18195 0.43330 0.88269 79.52 64.32 28.03 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.30337 -0.21921 0.92731 107.66 102.66 21.98 -0.21474 -0.38150 0.89908 102.40 112.43 25.96 -0.12677 -0.38169 0.91555 97.28 112.44 23.72 0.06628 -0.44632 0.89242 86.20 116.51 26.82 0.27063 -0.42694 0.86283 74.30 115.27 30.36 0.53001 -0.19496 0.82528 57.99 101.24 34.38 0.52278 -0.06956 0.84962 58.48 93.99 31.83 0.47478 0.09372 0.87510 61.65 84.62 28.94 0.32653 0.23787 0.91476 70.94 76.24 23.83 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 I= 1 0 10 13 25 35 49 49 49 45 I= 2 10 0 5 16 28 45 47 49 48 I= 3 13 5 0 11 23 40 42 45 45 I= 4 25 16 11 0 11 30 34 39 42 I= 5 35 28 23 11 0 20 25 32 39 I= 6 49 45 40 30 20 0 7 17 28 I= 7 49 47 42 34 25 7 0 9 21 I= 8 49 49 45 39 32 17 9 0 12 I= 9 45 48 45 42 39 28 21 12 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 4.03 31.91 23.88 -6.77 0.00 -0.00 23.67 8.89 2.49 -5.02 0.00 -0.00 10.10 27.95 12.62 -5.02 0.00 0.00 17.78 16.54 -6.87 -9.30 0.00 0.00 8.36 27.76 0.97 3.60 0.00****** 2.54 12.31 16.33 16.61****** 0.00 -10.88 31.00 15.77 -1.48 0.00 0.00 5.22 32.85 18.44 5.60 0.00 0.00 -7.23 21.06 14.99 10.41 0.00 0.00 8.83 39.27 23.96 -4.42****** 0.00 -5.37 30.12 9.05 -3.40 0.00 0.00 13.53 42.51 0.91 -8.24 0.00 0.00 -13.43 19.43 3.93 8.26****** 0.00 -10.93 32.79 15.61 2.49 0.00 0.00 -21.61 17.68 5.00 6.03 0.00 0.00 -13.12 28.78 21.69 3.07 0.00 0.00 -25.54 9.94 0.00 0.00 -0.00 0.00 -7.59 26.81 0.00 0.00 0.00 0.50 BEST PLANE THROUGH BOTH BASES VALL VTIL VROL VSLI VTWI VRIS VSHF INCL TIP TILT ROLL SLIDE CUP PROP BUCK X DSP Y DSP 10.73 -2.59 10.42 -1.86 32.78 3.06 -0.18 15.82 14.86 -3.03 10.21 -1.70 10.81 -19.78 -21.51 -6.53 -2.42 5.13 -3.76 3.50 -2.51 27.89 3.41 -0.23 21.55 13.78 -3.68 3.45 -2.50 -4.99 -7.69 -10.70 -6.97 -1.00 11.76 1.74 11.63 -2.24 36.29 2.78 1.08 23.04 5.30 2.29 11.51 -2.11 17.08 5.83 -15.69 -7.16 -0.89 11.90 3.69 11.33 -2.14 22.82 3.05 -0.04 26.82 0.03 5.48 10.47 -1.99 17.02 -16.12 1.39 -6.00 0.53 20.16 3.35 19.89 -2.19 24.59 3.20 -0.01 30.33 -1.23 1.68 20.29 -2.00 -4.91 -16.27 18.41 -5.96 -0.08 7.34 -1.60 7.16 -1.32 34.77 3.20 -0.94 34.19 3.18 -1.74 7.00 -1.23 -0.36 -19.06 13.51 -6.07 -0.57 9.87 1.74 9.72 -1.72 30.69 3.28 0.50 29.11 -11.75 1.90 9.61 -1.64 -3.09 -2.63 13.15 -7.04 1.34 12.09 3.10 11.69 -1.84 32.26 3.15 0.50 22.38 -17.38 3.47 11.40 -1.69 5.20 -8.51 10.06 -6.30 2.30 - - - - - - - 15.85 -17.32 - - - - -18.03 15.26 -5.20 2.94 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.