ID code: 2VAL 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 306 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 C02C1' 32 C02C1' 52 G03C1' 52 G03C1' 75 G04C1' 75 G04C1' 98 G05C1' 98 G05C1' 121 A06C1' 121 A06C1' 143 A07C1' 185 C02C1' 162 G01C1' 205 G03C1' 185 C02C1' 228 G04C1' 205 G03C1' 251 G05C1' 228 G04C1' 274 A06C1' 251 G05C1' 296 A07C1' 274 A06C1' 10 G01N9 33 C02N1 33 C02N1 53 G03N9 53 G03N9 76 G04N9 76 G04N9 99 G05N9 99 G05N9 122 A06N9 122 A06N9 144 A07N9 186 C02N1 163 G01N9 206 G03N9 186 C02N1 229 G04N9 206 G03N9 252 G05N9 229 G04N9 275 A06N9 252 G05N9 297 A07N9 275 A06N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.34047*S + -20.64180 Y = 0.91683*S + 5.40251 Z = -0.20860*S + -9.94589 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.34047*S + -20.64180 Y = 0.91683*S + 5.40251 Z = -0.20860*S + -9.94590 >>>>>> HELIX ROTATION: -5.261 DISPLACEMENT: 2.4237 STATISTICS: OVERALL STANDARD DEV.: 5.4670 SIGMA(X): 13.1865, SIGMA(Y): 16.7501, SIGMA(Z)=SIGMA(DISPLACEMENT): 1.6569, SIGMA(ROTATION): 31.600 THERE ARE 68.42 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 0.32524 -0.40561 0.85422 71.02 113.93 31.33 0.40375 -0.45442 0.79403 66.19 117.03 37.44 0.47832 -0.24444 0.84348 61.42 104.15 32.49 0.47090 -0.14270 0.87057 61.91 98.20 29.48 0.41932 -0.05832 0.90596 65.21 93.34 25.05 0.33371 0.05327 0.94117 70.51 86.95 19.75 0.20265 0.09819 0.97432 78.31 84.37 13.01 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.13482 0.88446 0.44671 97.75 27.81 63.47 -0.24643 0.77939 0.57604 104.27 38.80 54.83 -0.20568 0.71159 0.67182 101.87 44.64 47.79 -0.17151 0.67084 0.72149 99.88 47.87 43.82 -0.10925 0.61471 0.78115 96.27 52.07 38.63 0.06261 0.57282 0.81728 86.41 55.05 35.19 0.18637 0.59618 0.78092 79.26 53.40 38.65 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.11207 -0.02691 0.99334 83.57 91.54 6.62 0.34559 0.38465 0.85593 69.78 67.38 31.14 0.24500 -0.05054 0.96821 75.82 92.90 14.49 0.34524 0.19237 0.91859 69.80 78.91 23.28 0.39058 0.27765 0.87770 67.01 73.88 28.63 0.31554 0.13495 0.93927 71.61 82.24 20.07 0.40483 0.31170 0.85963 66.12 71.84 30.73 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 28 7 18 24 15 27 I= 2 28 0 26 11 6 15 5 I= 3 7 26 0 15 21 11 23 I= 4 18 11 15 0 6 3 8 I= 5 24 6 21 6 0 9 2 I= 6 15 15 11 3 9 0 12 I= 7 27 5 23 8 2 12 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 -10.74 29.04 -4.62 2.60****** 0.00 44.09-34.22 -2.21 -8.53************ -15.65 33.01 5.57 11.57 0.00 0.00 39.05-31.38 -4.41 -1.07 0.00 0.00 -6.77 31.60 2.89 5.09 0.00 0.00 39.66-22.09 -2.77 -1.27 NaN****** -3.55 29.22 3.25 4.65 0.00 0.00 39.25-16.34 -3.76 -2.99 0.00 0.00 2.05 24.95 0.99 8.02 0.00****** 35.13-14.03 -7.29 -7.08****** 0.00 10.30 16.66 -4.95 6.22 0.00 0.00 33.51 -9.50 1.12 -7.15 0.00 0.00 11.01 6.85 0.00 0.00 0.00****** 37.14 -9.20 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 28.53 3.62 28.31 1.71 9.29 0.71 -1.41 6.34 1.91 23.74 14.40 1.77 -0.91 -76.15 -57.62 -1.67 1.23 26.63 0.21 -26.63 0.91 7.56 1.21 -1.96 10.14 29.09 -22.17 -13.83 0.97 10.77 -74.12 -58.53 -2.58 3.04 15.37 3.58 14.96 0.43 4.76 2.20 -0.72 14.47 0.68 15.21 0.80 0.58 8.30 -58.23 -47.76 -3.71 3.90 6.01 -2.29 5.56 -0.74 -4.05 3.09 -1.15 17.95 14.33 5.05 -2.29 -0.70 4.24 -51.73 -39.46 -3.82 3.98 9.90 -2.37 -9.61 -0.79 -11.85 3.90 0.19 18.64 20.92 -4.87 7.88 -0.98 10.58 -38.52 -35.23 -4.14 1.98 12.25 -0.41 12.25 -0.96 -10.50 4.20 1.50 13.78 14.30 -8.24 -7.85 -1.39 9.46 -24.94 -24.64 -2.91 -0.47 - - - - - - - 10.17 28.65 - - - - -27.22 -15.19 0.24 -2.47 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.