ID code: 1DC1, PD0085 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 451 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 T02C1' 31 A03C1' 31 A03C1' 52 C04C1' 52 C04C1' 71 T05C1' 71 T05C1' 91 C06C1' 91 C06C1' 110 G07C1' 110 G07C1' 132 A08C1' 132 A08C1' 153 G09C1' 153 G09C1' 175 T10C1' 175 T10C1' 195 A11C1' 195 A11C1' 216 T12C1' 257 T03C1' 236 A02C1' 277 A04C1' 257 T03C1' 298 C05C1' 277 A04C1' 317 T06C1' 298 C05C1' 337 C07C1' 317 T06C1' 356 G08C1' 337 C07C1' 378 A09C1' 356 G08C1' 399 G10C1' 378 A09C1' 421 T11C1' 399 G10C1' 441 A12C1' 421 T11C1' 12 T02N1 32 A03N9 32 A03N9 53 C04N1 53 C04N1 72 T05N1 72 T05N1 92 C06N1 92 C06N1 111 G07N9 111 G07N9 133 A08N9 133 A08N9 154 G09N9 154 G09N9 176 T10N1 176 T10N1 196 A11N9 196 A11N9 217 T12N1 258 T03N1 237 A02N9 278 A04N9 258 T03N1 299 C05N1 278 A04N9 318 T06N1 299 C05N1 338 C07N1 318 T06N1 357 G08N9 338 C07N1 379 A09N9 357 G08N9 400 G10N9 379 A09N9 422 T11N1 400 G10N9 442 A12N9 422 T11N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.71764*S + 4.09237 Y = 0.68882*S + 1.98907 Z = -0.10258*S + 41.98743 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.71764*S + 4.09237 Y = 0.68882*S + 1.98907 Z = -0.10258*S + 41.98743 >>>>>> HELIX ROTATION: 32.404 DISPLACEMENT: 3.5711 STATISTICS: OVERALL STANDARD DEV.: 1.9297 SIGMA(X): 1.6863, SIGMA(Y): 1.5871, SIGMA(Z)=SIGMA(DISPLACEMENT): 1.0250, SIGMA(ROTATION): 14.786 THERE ARE 11.11 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 0.09094 0.07524 0.99301 84.78 85.68 6.78 -0.02845 -0.09600 0.99497 91.63 95.51 5.75 -0.33370 0.02894 0.94224 109.49 88.34 19.57 -0.19678 0.06607 0.97822 101.35 86.21 11.98 0.04374 0.30701 0.95070 87.49 72.12 18.07 0.28447 0.06735 0.95632 73.47 86.14 17.00 0.20311 -0.19055 0.96044 78.28 100.98 16.17 0.04055 -0.08957 0.99515 87.68 95.14 5.64 0.10547 -0.02975 0.99398 83.95 91.70 6.29 0.03852 0.04833 0.99809 87.79 87.23 3.54 -0.14511 0.09058 0.98526 98.34 84.80 9.85 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.06477 -0.01589 0.99777 93.71 90.91 3.82 0.08610 0.08354 0.99278 85.06 85.21 6.89 0.03311 0.12250 0.99192 88.10 82.96 7.29 0.18321 0.18282 0.96593 79.44 79.47 15.00 0.27888 -0.03592 0.95965 73.81 92.06 16.33 0.00887 -0.31399 0.94938 89.49 108.30 18.31 -0.19984 -0.04284 0.97889 101.53 92.46 11.79 -0.34806 -0.00023 0.93747 110.37 90.01 20.37 -0.03246 0.11703 0.99260 91.86 83.28 6.98 0.08467 0.05278 0.99501 85.14 86.97 5.73 0.12703 0.00060 0.99190 82.70 89.97 7.30 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.01623 0.01672 0.99973 89.07 89.04 1.34 0.01484 -0.01296 0.99981 89.15 90.74 1.13 -0.13734 0.02725 0.99015 97.89 88.44 8.05 -0.02735 0.10347 0.99426 91.57 84.06 6.14 0.18443 0.13488 0.97355 79.37 82.25 13.21 0.18766 -0.11534 0.97544 79.18 96.62 12.72 -0.01061 -0.07959 0.99677 90.61 94.57 4.61 -0.13556 -0.02046 0.99056 97.79 91.17 7.88 0.03645 0.03786 0.99862 87.91 87.83 3.01 0.05403 0.06205 0.99661 86.90 86.44 4.72 0.00866 0.06468 0.99787 89.50 86.29 3.74 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 1 8 5 11 12 5 8 1 3 2 I= 2 1 0 9 7 13 11 4 8 3 4 4 I= 3 8 9 0 7 19 20 9 2 10 11 8 I= 4 5 7 7 0 12 17 10 9 5 5 3 I= 5 11 13 19 12 0 14 16 20 10 8 10 I= 6 12 11 20 17 14 0 11 19 12 12 14 I= 7 5 4 9 10 16 11 0 7 7 8 8 I= 8 8 8 2 9 20 19 7 0 10 11 9 I= 9 1 3 10 5 10 12 7 10 0 1 2 I= 10 3 4 11 5 8 12 8 11 1 0 2 I= 11 2 4 8 3 10 14 8 9 2 2 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 -0.41 -6.77 1.86 11.90****** 0.00 -1.45 3.54 2.29-10.15****** 0.00 1.34 5.59-18.92 -3.47 0.00 0.00 1.88 -6.63 -3.43 -1.57 0.00 0.00 -19.00 -4.52 7.95 1.80****** 0.00 2.93 -6.67 9.26 0.98 NaN 0.00 -5.57-10.57 19.26 4.84 0.00 0.00 15.00 -0.36 -8.02 11.17 0.00 0.00 17.96 -1.93-13.83 13.97****** 0.00 1.97 16.21-16.19-15.62****** 0.00 -0.15 17.00-10.39-11.62 0.00 0.00 -17.88 -3.81 19.86 -2.37 0.00 0.00 -16.17 -0.14 11.00 0.78****** 0.00 6.77 -9.61 8.68 -1.80************ -3.12 -4.70 -4.35 2.60 0.00 0.00 20.09 -3.21-19.45 2.88 0.00 0.00 -4.37 -4.52 -0.25 5.90 0.00 0.00 -1.77 6.75 -2.39 -7.29****** 0.00 -3.53 -0.28 1.10 10.80 0.00 0.00 -5.23 -2.32 2.05 -3.26 0.00 0.00 -4.08 8.95 0.00 0.00****** 0.00 -0.97 -7.23 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 1.70 1.32 1.08 -0.69 23.90 3.90 0.56 -1.32 -0.23 1.28 1.12 -0.68 -22.52 1.04 10.30 -1.63 1.08 9.05 -0.66 -9.02 -0.95 38.78 3.43 -0.10 0.22 1.11 -0.49 -9.04 -1.04 10.21 -0.55 -12.21 -0.59 0.90 7.68 -1.13 7.59 -1.07 34.89 3.00 -0.84 -2.73 -7.57 -0.91 7.64 -1.01 12.06 -21.95 -2.00 -0.51 0.27 12.35 9.61 7.79 0.08 33.50 3.62 1.79 -5.38 2.95 9.57 7.75 0.13 7.72 -20.64 10.06 -1.44 0.06 14.38 0.24 -14.37 0.76 27.98 4.81 -0.04 8.35 10.16 0.22 -14.49 0.50 -38.21 16.19 17.78 1.03 0.24 11.63 -8.80 7.63 0.17 34.59 3.50 -1.79 8.90 -9.02 -8.76 7.57 0.21 11.07 18.08 -20.43 0.99 -0.43 7.93 0.10 7.93 -1.05 33.47 3.11 0.79 -3.77 -2.65 -0.34 7.94 -0.96 10.74 -23.00 -9.36 -1.52 -0.18 10.43 1.50 -10.32 -0.95 39.52 3.41 0.16 -2.40 7.50 1.25 -10.39 -1.04 9.88 -23.22 1.38 -0.72 -0.35 1.72 0.32 -1.69 -0.77 25.73 3.77 -0.52 0.82 -2.90 0.32 -1.68 -0.78 -13.31 -2.61 11.26 -0.82 -0.88 2.60 2.48 0.78 -0.42 26.64 3.78 -0.52 -0.57 -4.68 2.51 0.69 -0.41 -14.13 1.70 -2.05 -2.04 -1.04 - - - - - - - -0.02 -3.74 - - - - -3.16 -16.18 -3.15 -0.21 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.