ID code: 1O3Z, AR0046 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 7 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 295 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' 69 G04C1' 69 G04C1' 92 C05C1' 92 C05C1' 132 G07C1' 132 G07C1' 155 C17C1' 197 G19C1' 175 A18C1' 220 C20C1' 197 G19C1' 240 A21C1' 220 C20C1' 262 A22C1' 240 A21C1' 284 G23C1' 262 A22C1' 10 C01N1 70 G04N9 70 G04N9 93 C05N1 93 C05N1 133 G07N9 133 G07N9 156 C17N1 198 G19N9 176 A18N9 221 C20N1 198 G19N9 241 A21N9 221 C20N1 263 A22N9 241 A21N9 285 G23N9 263 A22N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.83396*S + 34.84183 Y = -0.04418*S + 17.04492 Z = -0.55005*S + 51.45718 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.83396*S + 34.84183 Y = -0.04418*S + 17.04493 Z = -0.55005*S + 51.45718 >>>>>> HELIX ROTATION: 48.278 DISPLACEMENT: 1.2298 STATISTICS: OVERALL STANDARD DEV.: 4.3281 SIGMA(X): 2.8740, SIGMA(Y): 3.1293, SIGMA(Z)=SIGMA(DISPLACEMENT): 1.6657, SIGMA(ROTATION): 21.698 THERE ARE 7.46 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 = 7 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.54448 -0.48647 0.68330 57.01 119.11 46.90 0.76734 -0.25154 0.58984 39.88 104.57 53.85 0.80892 -0.02171 0.58752 36.01 91.24 54.02 0.75403 0.17598 0.63283 41.06 79.86 50.74 0.69961 0.19977 0.68603 45.60 78.48 46.68 0.52454 0.42453 0.73799 58.36 64.88 42.44 0.28765 0.35153 0.89089 73.28 69.42 27.01 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.74025 0.00603 0.67231 42.25 89.65 47.75 0.81047 0.09306 0.57835 35.86 84.66 54.67 0.74960 0.23715 0.61795 41.44 76.28 51.83 0.67250 0.41260 0.61441 47.74 65.63 52.09 0.50295 0.43780 0.74523 59.80 64.04 41.82 0.31560 0.45686 0.83167 71.60 62.82 33.73 0.12962 0.18881 0.97342 82.55 79.12 13.24 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.65918 -0.26280 0.70457 48.76 105.24 45.21 0.75854 -0.04741 0.64989 40.66 92.72 49.47 0.76273 0.10040 0.63887 40.29 84.24 50.29 0.72044 0.29014 0.62991 43.91 73.13 50.96 0.59185 0.37349 0.71430 53.71 68.07 44.41 0.44507 0.41408 0.79401 63.57 65.54 37.44 0.23039 0.27716 0.93279 76.68 73.91 21.13 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 I= 1 0 13 22 32 37 41 42 I= 2 13 0 8 19 26 33 39 I= 3 22 8 0 11 19 27 36 I= 4 32 19 11 0 10 19 33 I= 5 37 26 19 10 0 9 25 I= 6 41 33 27 19 9 0 16 I= 7 42 39 36 33 25 16 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 27.66 34.30 18.89 -0.48 0.00 0.00 47.10 6.11 6.38 -0.68****** 0.00 19.40 47.40 13.51 0.17 0.00 0.00 37.99 32.37 7.59 -4.81 0.00 0.00 -5.72 53.42 11.79 1.08****** 0.00 9.43 50.26 11.03 -0.56 0.00 0.00 -30.46 35.82 3.28 -0.92 0.00 0.00 -17.58 46.79 8.46 -5.05 0.00 0.00 -43.78 13.00 9.28 13.58 0.00 0.00 -29.13 27.11 10.71 1.73 0.00 0.50 -41.63 6.80 13.34 5.20 0.00 0.00 -29.80 14.33 18.21 -5.37 0.00 0.00 -26.92 -2.07 0.00 0.00****** 0.00 -13.24 0.06 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 13.98 -4.95 13.09 -1.52 35.03 2.82 -0.57 21.09 37.71 -4.70 12.86 -1.36 15.29 -20.46 -23.07 -7.59 -1.99 8.50 -1.24 8.41 -1.42 32.33 3.09 -0.13 36.29 28.48 -1.16 8.42 -1.27 5.20 -18.47 -7.78 -7.05 0.23 11.17 2.60 10.86 -1.96 31.52 3.02 0.30 50.25 1.51 1.59 11.09 -1.84 9.00 -15.15 -2.58 -5.21 2.20 10.04 -1.15 9.97 -1.22 31.90 3.18 -0.43 41.14 -24.38 -0.98 8.76 -1.13 3.58 -12.92 6.42 -3.55 2.23 9.86 2.42 9.56 -1.24 33.25 3.20 0.28 23.25 -35.31 2.83 8.28 -1.13 -3.84 -15.11 10.00 -4.34 2.00 16.67 1.71 16.59 -1.49 29.26 3.21 0.62 8.49 -36.14 1.53 14.67 -1.32 -3.93 -11.77 6.15 -4.89 2.41 - - - - - - - -1.80 -21.04 - - - - -13.68 2.23 -4.71 3.00 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.