ID code: 2GYH 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 12 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 486 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 C01C1' 27 G02C1' 27 G02C1' 49 C03C1' 49 C03C1' 68 G04C1' 68 G04C1' 90 A05C1' 90 A05C1' 111 A06C1' 111 A06C1' 132 T07C1' 132 T07C1' 152 T08C1' 152 T08C1' 172 C09C1' 172 C09C1' 191 G10C1' 191 G10C1' 213 C11C1' 213 C11C1' 232 G12C1' 270 G14C1' 251 C13C1' 292 C15C1' 270 G14C1' 311 G16C1' 292 C15C1' 333 A17C1' 311 G16C1' 354 A18C1' 333 A17C1' 375 T19C1' 354 A18C1' 395 T20C1' 375 T19C1' 415 C21C1' 395 T20C1' 434 G22C1' 415 C21C1' 456 C23C1' 434 G22C1' 475 G24C1' 456 C23C1' 9 C01N1 28 G02N9 28 G02N9 50 C03N1 50 C03N1 69 G04N9 69 G04N9 91 A05N9 91 A05N9 112 A06N9 112 A06N9 133 T07N1 133 T07N1 153 T08N1 153 T08N1 173 C09N1 173 C09N1 192 G10N9 192 G10N9 214 C11N1 214 C11N1 233 G12N9 271 G14N9 252 C13N1 293 C15N1 271 G14N9 312 G16N9 293 C15N1 334 A17N9 312 G16N9 355 A18N9 334 A17N9 376 T19N1 355 A18N9 396 T20N1 376 T19N1 416 C21N1 396 T20N1 435 G22N9 416 C21N1 457 C23N1 435 G22N9 476 G24N9 457 C23N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.61203*S + -3.34391 Y = 0.33872*S + 10.46519 Z = 0.71462*S + -2.09652 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.61203*S + -3.34391 Y = 0.33872*S + 10.46519 Z = 0.71462*S + -2.09652 >>>>>> HELIX ROTATION: 33.373 DISPLACEMENT: 3.2273 STATISTICS: OVERALL STANDARD DEV.: 1.5145 SIGMA(X): 1.7548, SIGMA(Y): 1.6571, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.7782, SIGMA(ROTATION): 11.464 THERE ARE 10.79 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 = 12 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.09556 0.34231 0.93472 95.48 69.98 20.82 0.22888 -0.17868 0.95692 76.77 100.29 16.88 0.24651 -0.38519 0.88930 75.73 112.66 27.21 -0.08430 -0.24210 0.96658 94.84 104.01 14.85 0.03984 -0.35161 0.93530 87.72 110.59 20.72 0.02759 -0.10194 0.99441 88.42 95.85 6.06 0.13299 -0.08404 0.98755 82.36 94.82 9.05 0.23388 -0.02925 0.97183 76.47 91.68 13.63 0.29766 0.18432 0.93671 72.68 79.38 20.49 -0.07838 0.27648 0.95782 94.50 73.95 16.70 0.11132 0.28993 0.95055 83.61 73.15 18.09 0.08912 0.11695 0.98913 84.89 83.28 8.46 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.00002 -0.13338 0.99106 90.00 97.67 7.67 0.05331 -0.31286 0.94830 86.94 108.23 18.50 -0.00849 -0.15461 0.98794 90.49 98.89 8.91 0.12037 0.01321 0.99264 83.09 89.24 6.96 0.21129 0.18273 0.96019 77.80 79.47 16.22 0.14804 0.27795 0.94912 81.49 73.86 18.36 0.08691 0.29380 0.95191 85.01 72.91 17.84 0.09889 0.31285 0.94464 84.32 71.77 19.15 0.01248 0.11161 0.99367 89.28 83.59 6.45 -0.16035 -0.00197 0.98706 99.23 90.11 9.23 0.12265 0.07867 0.98933 82.95 85.49 8.38 -0.67792 -0.29970 0.67127 132.68 107.44 47.84 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.03831 0.04370 0.99831 87.80 87.50 3.33 0.14841 -0.26182 0.95364 81.47 105.18 17.51 0.12570 -0.23924 0.96279 82.78 103.84 15.68 -0.02383 -0.09670 0.99503 91.37 95.55 5.72 0.13546 -0.04411 0.98980 82.21 92.53 8.19 0.10392 0.13242 0.98573 84.04 82.39 9.69 0.10382 0.06032 0.99277 84.04 86.54 6.90 0.18114 0.10548 0.97778 79.56 83.95 12.10 0.10471 0.07691 0.99152 83.99 85.59 7.46 -0.09846 0.17108 0.98032 95.65 80.15 11.38 0.14430 0.14444 0.97894 81.70 81.70 11.78 -0.18478 -0.10954 0.97666 100.65 96.29 12.40 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 10 11 12 I= 1 0 18 17 8 7 6 3 9 4 10 8 15 I= 2 18 0 1 13 12 22 18 21 19 28 23 21 I= 3 17 1 0 12 11 21 17 20 18 27 22 19 I= 4 8 13 12 0 9 15 11 16 12 16 16 9 I= 5 7 12 11 9 0 10 6 8 7 18 10 18 I= 6 6 22 21 15 10 0 4 4 3 11 2 21 I= 7 3 18 17 11 6 4 0 5 0 13 5 19 I= 8 9 21 20 16 8 4 5 0 4 16 3 24 I= 9 4 19 18 12 7 3 0 4 0 12 4 19 I= 10 10 28 27 16 18 11 13 16 12 0 14 16 I= 11 8 23 22 16 10 2 5 3 4 14 0 23 I= 12 15 21 19 9 18 21 19 24 19 16 23 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 -17.68 10.63 33.02-16.41 0.00 -0.00 7.38 -2.07 10.55 -2.24****** 0.00 14.67 -8.16 10.35 5.93 0.00 0.00 18.01 4.12 -9.51 -2.26 0.00 0.00 26.18 6.91-21.13 0.04************ 5.59 6.91 2.94-11.85 0.00 0.00 -2.98 14.54 6.17 7.23 0.00 0.00 6.75 -1.65 6.54 -8.92 0.00 0.00 -5.34 19.96 8.73-11.46 -0.00 0.00 15.30 -5.26 0.75 -6.52 0.00 NaN -4.53 4.02 2.09 5.77 0.00 0.00 18.35 0.49 0.26 -3.61 0.00 0.00 -5.69 7.01 -0.15 6.59****** 0.00 16.35 6.96 0.61 1.14 0.00****** -11.15 7.75 3.54 12.37 0.00 0.00 7.81 17.37 -2.06-12.48 0.00 0.00 -12.71 15.80 22.57 2.93****** 0.00 1.44 6.28 9.18 -7.56************ 3.16 16.38-10.40 -3.42 0.00 0.00 9.20 0.65-17.00 -1.89 0.00 0.00 -16.09 8.05 9.71 -2.55****** 0.00 -8.26 -1.38 40.68 36.82 0.00****** -7.45 -3.98 0.00 0.00 0.00 0.00 23.79 38.45 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 18.87 -5.33 18.13 -0.59 37.97 2.55 -0.81 -1.44 -3.01 -4.92 18.25 -0.39 24.99 -25.33 -12.74 -0.15 -0.83 1.91 -0.30 -1.89 -0.07 26.11 3.75 0.79 -2.04 17.39 0.33 -1.81 -0.09 -12.76 -3.35 12.25 -1.23 -0.73 12.00 -4.01 -11.32 -0.07 34.35 4.06 -1.44 5.34 14.70 -4.08 -11.18 -0.18 -15.64 20.61 -0.51 0.32 -0.72 9.63 -1.82 9.45 -0.27 29.03 3.64 0.54 5.68 -0.63 -1.70 9.50 -0.12 -8.85 -9.83 -16.16 -1.25 -1.09 10.29 -8.63 5.62 -0.31 40.94 2.70 -0.96 5.23 6.29 -8.93 5.15 -0.22 21.59 -21.12 -25.01 -1.07 -1.05 4.15 0.67 -4.10 -0.88 33.45 3.11 -0.21 1.95 9.49 0.74 -4.07 -0.90 3.60 -22.89 -3.42 -2.25 -0.26 5.20 5.20 0.28 -0.30 40.63 2.91 0.73 6.33 2.73 5.14 0.04 -0.26 9.33 -22.04 0.18 -2.22 -0.13 4.74 -3.72 2.94 -0.79 22.63 3.79 -0.56 11.51 -3.67 -3.75 2.80 -0.67 -19.23 -19.03 9.51 -1.32 0.37 12.87 3.95 12.26 -0.33 23.80 3.61 1.34 6.15 -4.21 4.11 12.25 -0.19 -5.89 -14.27 -9.72 -2.17 -0.30 14.03 -6.97 -12.20 -0.68 37.76 3.70 -0.66 10.29 4.81 -6.71 -12.38 -0.78 6.13 -6.15 -15.61 -0.91 -0.43 23.99 9.71 22.04 -0.80 38.51 2.06 1.33 0.58 -11.77 12.08 21.05 -0.57 53.42 -7.92 -9.48 -2.28 -0.59 - - - - - - - 9.50 7.90 - - - - -34.70 43.94 -1.20 -0.29 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.