ID code: 476D, BD0018 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 10 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 404 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 G02C1' 30 C03C1' 30 C03C1' 49 G04C1' 49 G04C1' 71 A05C1' 71 A05C1' 92 A06C1' 92 A06C1' 113 T07C1' 113 T07C1' 133 T08C1' 133 T08C1' 153 C09C1' 153 C09C1' 172 G10C1' 172 G10C1' 194 C11C1' 232 C15C1' 210 G14C1' 251 G16C1' 232 C15C1' 273 A17C1' 251 G16C1' 294 A18C1' 273 A17C1' 315 T19C1' 294 A18C1' 335 T20C1' 315 T19C1' 355 C21C1' 335 T20C1' 374 G22C1' 355 C21C1' 396 C23C1' 374 G22C1' 9 G02N9 31 C03N1 31 C03N1 50 G04N9 50 G04N9 72 A05N9 72 A05N9 93 A06N9 93 A06N9 114 T07N1 114 T07N1 134 T08N1 134 T08N1 154 C09N1 154 C09N1 173 G10N9 173 G10N9 195 C11N1 233 C15N1 211 G14N9 252 G16N9 233 C15N1 274 A17N9 252 G16N9 295 A18N9 274 A17N9 316 T19N1 295 A18N9 336 T20N1 316 T19N1 356 C21N1 336 T20N1 375 G22N9 356 C21N1 397 C23N1 375 G22N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.04518*S + 33.03734 Y = 0.06049*S + 10.21609 Z = 0.99715*S + 0.87714 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.04518*S + 33.03734 Y = 0.06049*S + 10.21610 Z = 0.99715*S + 0.87714 >>>>>> HELIX ROTATION: 34.052 DISPLACEMENT: 3.3480 STATISTICS: OVERALL STANDARD DEV.: 0.7913 SIGMA(X): 0.8789, SIGMA(Y): 0.8691, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.3921, SIGMA(ROTATION): 5.670 THERE ARE 10.57 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 = 10 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.01267 0.07226 0.99731 89.27 85.86 4.21 -0.09396 0.01274 0.99549 95.39 89.27 5.44 0.02081 -0.16097 0.98674 88.81 99.26 9.34 0.08423 -0.11095 0.99025 85.17 96.37 8.01 0.05909 -0.07043 0.99577 86.61 94.04 5.27 0.15056 -0.05927 0.98682 81.34 93.40 9.31 0.16962 0.05830 0.98378 80.23 86.66 10.33 0.16144 0.06580 0.98469 80.71 86.23 10.04 0.02089 -0.04119 0.99893 88.80 92.36 2.65 -0.03690 -0.05620 0.99774 92.11 93.22 3.85 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.05030 -0.19687 0.97914 87.12 101.35 11.72 -0.11867 -0.11787 0.98591 96.82 96.77 9.63 -0.01112 0.15655 0.98761 90.64 80.99 9.03 -0.05709 0.18300 0.98145 93.27 79.46 11.05 -0.14668 0.12668 0.98104 98.43 82.72 11.18 -0.14510 0.03961 0.98862 98.34 87.73 8.65 -0.13396 0.01801 0.99082 97.70 88.97 7.77 -0.10441 0.01302 0.99445 95.99 89.25 6.04 0.05446 0.03437 0.99792 86.88 88.03 3.69 0.07339 0.06085 0.99545 85.79 86.51 5.47 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.04790 -0.07502 0.99603 87.25 94.30 5.11 -0.09798 -0.08488 0.99156 95.62 94.87 7.45 -0.02244 -0.02839 0.99934 91.29 91.63 2.07 -0.01187 0.06286 0.99795 90.68 86.40 3.67 -0.05674 0.05304 0.99698 93.25 86.96 4.45 0.03671 -0.01877 0.99915 87.90 91.08 2.36 0.05579 0.02344 0.99817 86.80 88.66 3.47 0.01737 0.00904 0.99981 89.00 89.48 1.12 0.01313 -0.01223 0.99984 89.25 90.70 1.03 0.00347 0.01613 0.99986 89.80 89.08 0.95 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 10 I= 1 0 8 4 8 9 3 5 5 4 5 I= 2 8 0 5 9 8 8 10 8 7 8 I= 3 4 5 0 5 5 3 5 3 2 2 I= 4 8 9 5 0 2 5 4 3 4 2 I= 5 9 8 5 2 0 6 6 4 5 4 I= 6 3 8 3 5 6 0 2 1 1 2 I= 7 5 10 5 4 6 2 0 2 3 3 I= 8 5 8 3 3 4 1 2 0 1 0 I= 9 4 7 2 4 5 1 3 1 0 1 I= 10 5 8 2 2 4 2 3 0 1 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 -0.24 -4.20 -6.27 3.14 0.00 0.00 5.40 10.37 -9.52 -4.95 0.00 -0.00 -4.73 -2.69 -0.80 11.99 0.00 0.00 -8.86 3.73 14.59 -8.81 0.00 0.00 -6.34 6.83 3.98 2.36 0.00****** 6.50 -6.24 0.47 -3.00****** 0.00 -6.09 5.17 2.63 -0.74 0.00 0.00 10.35 -3.84 -1.69 -5.83 0.00 0.00 -5.26 0.37 -3.87 3.60 0.00 0.00 10.88 -2.54 -3.01 -3.99****** 0.00 -9.30 -0.38 -0.97 6.77 0.00 0.00 8.63 -0.58 -0.66 -1.23 0.00 0.00 -10.33 0.29 0.12 0.62****** 0.00 7.04 3.28 -1.19 -1.24 0.00 0.00 -8.20 -5.76 8.24 5.93 0.00 0.00 2.60 5.45 -3.83 -8.38 0.00 0.00 2.36 -1.21 -0.01 3.42 0.00 0.00 -1.98 -3.11 -1.19 -1.44 0.00 0.50 1.85 3.38 0.00 0.00 0.00 0.00 -1.11 -5.36 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 8.39 -0.06 -8.39 0.69 35.22 3.59 0.79 3.56 3.66 0.20 -8.41 0.58 -8.16 -5.69 14.59 0.62 -0.91 5.42 0.08 5.42 0.68 28.28 3.84 -0.22 2.42 -7.04 0.05 5.41 0.72 -19.51 4.13 6.43 0.75 -0.92 5.27 -1.35 5.09 -0.16 36.65 3.14 -0.29 0.05 -2.07 -1.31 5.10 -0.08 4.06 -12.92 -13.08 -0.14 -0.41 2.63 -2.63 0.19 -0.30 39.00 3.04 -0.14 -0.88 3.56 -2.63 0.17 -0.27 6.10 -16.49 -9.02 -0.64 -0.25 6.76 -0.11 -6.76 -0.48 34.88 3.17 0.04 -0.85 4.37 -0.18 -6.77 -0.53 2.71 -16.14 -2.92 -0.68 -0.05 2.66 2.44 -1.06 -0.41 36.43 3.04 0.13 -0.33 -2.34 2.44 -1.05 -0.40 3.19 -17.93 -0.21 -0.64 -0.16 2.35 0.68 2.25 -0.26 39.97 3.10 0.42 0.33 -3.45 0.66 2.26 -0.21 8.22 -17.37 2.98 -0.75 -0.14 1.24 -0.11 1.24 0.31 32.48 3.63 0.09 -0.56 -0.97 -0.12 1.24 0.32 -13.11 -10.85 11.21 -0.47 0.05 1.72 0.15 -1.71 -0.25 28.18 3.57 -0.44 -0.76 0.70 0.12 -1.71 -0.29 -6.83 4.34 -1.91 -0.19 0.62 - - - - - - - -0.61 -0.72 - - - - 2.97 -8.74 -0.36 0.53 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.