ID code: 1WPU 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 290 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: 49 G03C1' 72 A04C1' 72 A04C1' 94 G05C1' 217 A04C1' 194 G03C1' 239 G05C1' 217 A04C1' 50 G03N9 73 A04N9 73 A04N9 95 G05N9 218 A04N9 195 G03N9 240 G05N9 218 A04N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.03256*S + 61.10204 Y = -0.06378*S + 0.28089 Z = 0.99743*S + 2.01260 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.03256*S + 61.10204 Y = -0.06378*S + 0.28089 Z = 0.99743*S + 2.01260 >>>>>> HELIX ROTATION: -35.552 DISPLACEMENT: 1.6038 STATISTICS: OVERALL STANDARD DEV.: 5.3040 SIGMA(X): 6.4834, SIGMA(Y): 6.3570, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.1939, SIGMA(ROTATION): 22.699 THERE ARE 10.13 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 -0.84295 0.12458 0.52337 147.45 82.84 58.44 0.91843 -0.26245 0.29600 23.30 105.22 72.78 -0.36355 0.16554 0.91675 111.32 80.47 23.54 -0.63976 -0.61449 0.46164 129.77 127.91 62.51 -0.89905 -0.26976 0.34489 154.03 105.65 69.82 -0.09430 -0.52867 0.84357 95.41 121.92 32.48 -0.92841 0.00466 0.37153 158.19 89.73 68.19 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.55426 -0.75184 0.35712 123.66 138.75 69.08 -0.33797 0.41041 0.84696 109.75 65.77 32.12 -0.76570 -0.54577 0.34036 139.97 123.08 70.10 -0.89066 -0.10986 0.44120 152.96 96.31 63.82 -0.06795 -0.26829 0.96094 93.90 105.56 16.07 0.48321 0.85251 0.19935 61.11 31.51 78.50 -0.37635 -0.71216 0.59261 112.11 135.41 53.66 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.49013 -0.86809 0.07866 119.35 150.24 85.49 0.92743 0.25297 0.27548 21.96 75.35 74.01 0.25536 -0.95703 0.13742 75.21 163.14 82.10 0.88482 -0.33285 0.32604 27.77 109.44 70.97 -0.23321 0.93627 0.26269 103.49 20.56 74.77 0.82465 0.51288 0.23857 34.45 59.14 76.20 -0.98688 0.15319 0.05098 170.71 81.19 87.08 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 0 130 44 96 132 146 69 I= 2 130 0 88 34 84 16 149 I= 3 44 88 0 53 156 104 113 I= 4 96 34 53 0 115 50 155 I= 5 132 84 156 115 0 69 67 I= 6 146 16 104 50 69 0 136 I= 7 69 149 113 155 67 136 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 24.99 47.73-90.00-90.00 0.00 0.00 69.01 -1.62-53.37 60.24 0.00 0.00 -10.84-69.47-30.90 90.00 0.00 0.00 -12.10 29.25 67.69 29.42 0.00 0.00 -6.30 22.59 40.89 30.41 0.00 0.00 40.81 42.54-26.94 -1.00 NaN 0.00 19.33 55.38-25.51 1.44 0.00 0.00 -13.34 60.14 35.97-36.69 0.00 0.00 -36.18 46.87 54.21-13.78 0.00 0.00 5.46 15.06-10.02-90.00 0.00 0.00 2.71 32.34-36.56-52.26 0.00 0.00 14.09-71.66-90.00 90.00 0.00 0.00 -68.03 2.54 0.00 0.00 0.00 0.00 -19.77 46.97 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 130.73 -3.47-130.73 1.67 3.50 5.65 -1.76 -8.65 80.23 11.13 -90.00 1.11 108.31 59.27 -30.30 10.77 -6.83 88.13 2.25 88.12 -0.77 7.11 5.24 -4.73 -45.08 -40.56 48.78 90.00 -0.42-126.73 64.12 78.00 10.17 -2.75 53.89 -4.38 -53.76 2.97 5.04 -1.29 -3.43 -23.25 65.29 -52.46 -23.34 3.02 48.42 39.19 -48.73 6.21 0.22 115.62 4.16-115.60 3.54 12.11 1.23 2.97 -44.14 39.74 13.22 -90.00 3.15 46.07 -47.72 -0.31 3.36 0.69 69.48 -3.32 69.43 -0.74 6.54 6.85 2.73 -39.92 -46.10 -14.14 90.00 -0.60-126.65 -5.49 45.76 6.81 0.90 136.31 2.68-136.31 1.96 3.40 5.66 1.39 -45.29 41.44 -17.16 -90.00 1.32 111.55 24.78 -80.90 10.19 4.52 - - - - - - - -5.80 -83.50 - - - - 61.02 30.65 10.76 8.40 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.