ID code: 2V6W 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 292 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 G01C1' 32 G02C1' 32 G02C1' 55 A03C1' 55 A03C1' 77 G04C1' 77 G04C1' 100 A05C1' 145 A07C1' 122 G06C1' 184 C67C1' 145 A07C1' 224 C69C1' 184 C67C1' 264 C71C1' 224 C69C1' 284 C72C1' 264 C71C1' 10 G01N9 33 G02N9 33 G02N9 56 A03N9 56 A03N9 78 G04N9 78 G04N9 101 A05N9 146 A07N9 123 G06N9 185 C67N1 146 A07N9 225 C69N1 185 C67N1 265 C71N1 225 C69N1 285 C72N1 265 C71N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.61562*S + 2.25177 Y = 0.46814*S + 4.34087 Z = -0.63392*S + 1.01890 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.61562*S + 2.25177 Y = 0.46814*S + 4.34087 Z = -0.63392*S + 1.01890 >>>>>> HELIX ROTATION: 25.710 DISPLACEMENT: 1.9334 STATISTICS: OVERALL STANDARD DEV.: 6.2981 SIGMA(X): 3.4041, SIGMA(Y): 2.8797, SIGMA(Z)=SIGMA(DISPLACEMENT): 1.9263, SIGMA(ROTATION): 31.322 THERE ARE 14.00 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 0.31683 0.34161 0.88483 71.53 70.03 27.77 0.33689 0.31964 0.88563 70.31 71.36 27.67 0.35788 0.45565 0.81505 69.03 62.89 35.41 0.33499 0.55189 0.76367 70.43 56.50 40.21 0.23548 0.59438 0.76894 76.38 53.53 39.74 0.16822 0.62507 0.76222 80.32 51.31 40.34 0.01787 0.63000 0.77639 88.98 50.95 39.07 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.45991 0.32394 0.82677 62.62 71.10 34.23 0.50167 0.49319 0.71069 59.89 60.45 44.71 0.36114 0.50773 0.78217 68.83 59.49 38.54 0.20035 0.70736 0.67787 78.44 44.98 47.32 0.12025 0.64145 0.75768 83.09 50.10 40.74 -0.09365 0.56686 0.81847 95.37 55.47 35.07 -0.15197 0.48680 0.86019 98.74 60.87 30.66 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.37460 0.34520 0.86053 68.00 69.81 30.62 0.39013 0.40875 0.82506 67.04 65.87 34.41 0.35905 0.48272 0.79879 68.96 61.14 36.99 0.27021 0.61767 0.73856 74.32 51.85 42.39 0.17596 0.61931 0.76517 79.87 51.73 40.08 0.05739 0.59780 0.79959 86.71 53.29 36.91 -0.04798 0.55454 0.83077 92.75 56.32 33.82 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 4 8 18 20 23 27 I= 2 4 0 4 14 17 22 26 I= 3 8 4 0 9 13 18 23 I= 4 18 14 9 0 5 12 19 I= 5 20 17 13 5 0 7 13 I= 6 23 22 18 12 7 0 6 I= 7 27 26 23 19 13 6 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 27.65 2.33 -0.90 1.45 0.00 0.00 32.54 9.47 10.03 -0.30 0.00 0.00 21.73 16.28 7.20 3.27 0.00 0.00 34.64 24.49 2.98 -7.55 0.00 0.00 16.22 30.51 4.47 3.50****** 0.00 19.02 32.07 14.49 3.21 0.00 0.00 2.32 40.12 6.18 0.65 0.00 0.00 13.87 44.03 3.27 -4.97 0.00 0.00 -19.69 32.91 3.15 2.83****** 0.00 -13.41 37.59 13.09 -0.41 0.00 0.50 -34.17 18.78 5.00 7.04 0.00 0.00 -19.60 27.80 5.68 -0.12 0.00 0.00 -38.22 6.90 0.00 0.00 0.00 0.00 -26.22 14.75 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 4.26 0.14 4.26 -1.98 31.79 3.19 -0.29 4.83 30.16 -0.12 3.75 -1.90 3.52 -4.94 7.42 -6.76 -1.86 4.84 -0.44 4.82 -1.34 30.52 3.43 -0.33 18.56 27.83 -0.57 4.57 -1.26 -8.79 -13.10 10.94 -6.16 -1.27 9.89 2.77 9.50 -2.07 26.67 3.12 1.00 31.29 17.68 2.88 8.83 -1.98 3.31 -2.80 2.15 -5.63 -0.67 5.61 -1.75 5.34 -1.64 34.45 3.21 -0.91 41.40 7.54 -1.50 5.19 -1.56 -2.03 -11.57 5.47 -4.44 -1.26 7.19 0.76 7.15 -1.36 31.39 3.17 0.15 35.34 -16.43 0.86 6.87 -1.28 2.55 -6.29 3.43 -6.37 -0.34 6.77 3.30 5.91 -1.51 33.29 3.21 0.57 22.41 -27.65 3.30 5.64 -1.42 0.52 -14.58 5.98 -7.27 1.09 - - - - - - - 9.66 -32.05 - - - - -11.99 6.51 -7.33 2.81 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.