ID code: 1RVA, PDE014 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 A02C1' 29 A03C1' 29 A03C1' 50 G04C1' 50 G04C1' 72 A05C1' 72 A05C1' 93 T06C1' 93 T06C1' 113 A07C1' 113 A07C1' 134 T08C1' 134 T08C1' 154 C09C1' 154 C09C1' 173 T10C1' 173 T10C1' 193 T11C1' 231 A03C1' 210 A02C1' 252 G04C1' 231 A03C1' 274 A05C1' 252 G04C1' 295 T06C1' 274 A05C1' 315 A07C1' 295 T06C1' 336 T08C1' 315 A07C1' 356 C09C1' 336 T08C1' 375 T10C1' 356 C09C1' 395 T11C1' 375 T10C1' 9 A02N9 30 A03N9 30 A03N9 51 G04N9 51 G04N9 73 A05N9 73 A05N9 94 T06N1 94 T06N1 114 A07N9 114 A07N9 135 T08N1 135 T08N1 155 C09N1 155 C09N1 174 T10N1 174 T10N1 194 T11N1 232 A03N9 211 A02N9 253 G04N9 232 A03N9 275 A05N9 253 G04N9 296 T06N1 275 A05N9 316 A07N9 296 T06N1 337 T08N1 316 A07N9 357 C09N1 337 T08N1 376 T10N1 357 C09N1 396 T11N1 376 T10N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.57791*S + -8.52270 Y = 0.56558*S + -7.44652 Z = 0.58833*S + -1.21318 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.57791*S + -8.52270 Y = 0.56558*S + -7.44652 Z = 0.58833*S + -1.21318 >>>>>> HELIX ROTATION: 28.095 DISPLACEMENT: 2.8708 STATISTICS: OVERALL STANDARD DEV.: 1.9093 SIGMA(X): 3.2966, SIGMA(Y): 3.0076, SIGMA(Z)=SIGMA(DISPLACEMENT): 1.0877, SIGMA(ROTATION): 8.826 THERE ARE 12.81 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 0.12214 -0.31685 0.94058 82.98 108.47 19.85 0.11885 -0.35458 0.92744 83.17 110.77 21.96 0.07109 -0.45755 0.88634 85.92 117.23 27.58 -0.04281 -0.41825 0.90732 92.45 114.72 24.86 0.08551 -0.43911 0.89435 85.09 116.05 26.57 0.04505 0.38401 0.92223 87.42 67.42 22.75 0.07522 0.42278 0.90311 85.69 64.99 25.43 0.32886 0.23127 0.91562 70.80 76.63 23.71 0.30009 0.42846 0.85227 72.54 64.63 31.54 0.10148 0.52423 0.84551 84.18 58.38 32.27 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.10924 -0.55816 0.82251 83.73 123.93 34.66 0.20563 -0.45120 0.86841 78.13 116.82 29.73 0.25857 -0.28816 0.92201 75.02 106.75 22.78 -0.02436 -0.41114 0.91125 91.40 114.28 24.32 -0.06394 -0.32653 0.94302 93.67 109.06 19.43 0.20326 0.41363 0.88747 78.27 65.57 27.44 0.09419 0.41400 0.90539 84.60 65.54 25.12 0.19418 0.45480 0.86917 78.80 62.95 29.64 0.16514 0.35058 0.92186 80.49 69.48 22.80 0.10150 0.26126 0.95992 84.17 74.85 16.28 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.18451 -0.44182 0.87792 79.37 116.22 28.61 0.18015 -0.40692 0.89552 79.62 114.01 26.42 0.14536 -0.40215 0.90396 81.64 113.71 25.32 -0.02565 -0.42078 0.90680 91.47 114.88 24.93 0.00391 -0.39653 0.91801 89.78 113.36 23.36 0.12667 0.41052 0.90301 82.72 65.76 25.44 0.09823 0.43037 0.89729 84.36 64.51 26.20 0.25868 0.38794 0.88464 75.01 67.17 27.79 0.25648 0.38408 0.88696 75.14 67.41 27.51 0.14988 0.39428 0.90668 81.38 66.78 24.95 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 2 3 12 10 50 51 49 48 49 I= 2 2 0 2 11 10 48 49 47 46 47 I= 3 3 2 0 9 8 47 49 47 46 46 I= 4 12 11 9 0 2 49 50 50 50 49 I= 5 10 10 8 2 0 48 49 48 48 47 I= 6 50 48 47 49 48 0 2 7 7 1 I= 7 51 49 49 50 49 2 0 9 9 3 I= 8 49 47 47 50 48 7 9 0 0 6 I= 9 48 46 46 50 48 7 9 0 0 6 I= 10 49 47 46 49 47 1 3 6 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 19.75 1.95 1.42 1.64****** 0.00 33.18 8.89 -0.54 -8.26****** 0.00 17.02 13.45 -1.44 6.35 0.00 0.00 24.72 15.45 1.01 -9.82 0.00 0.00 4.62 27.13 -5.59 -4.06****** 0.00 15.34 16.42-17.85 2.00 NaN 0.00 -17.83 16.75 3.70 6.48 0.00 0.00 -16.71 17.15 2.34 -4.82 0.00 0.00 -22.32 13.67 54.05 -8.87****** 0.00 -19.14 3.24 50.36 9.33****** 0.00 22.35 4.03 1.39 2.45 0.00 0.00 23.54 13.30 2.40 -5.78 0.00 0.00 18.31 17.02-18.48 -1.37****** 0.00 17.25 17.69 -3.56 5.07************ -14.90 18.00 2.56 11.20 0.00 0.00 -3.95 29.32 1.18 -6.10 0.00 0.00 -24.37 18.75 7.13 10.50 0.00 0.00 -15.12 16.66 5.73 -2.61****** 0.00 -26.53 17.02 0.00 0.00 0.00 0.00 -14.96 6.28 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 2.25 -1.30 -1.84 0.36 31.89 3.47 0.06 2.00 28.52 -1.22 -1.61 0.38 -4.55 -13.64 7.31 -4.26 -3.17 2.07 0.15 -2.06 -0.02 31.07 3.72 0.60 14.07 21.88 0.15 -2.01 -0.04 -12.68 -7.70 2.76 -3.79 -1.16 9.87 -2.28 -9.60 -0.72 39.49 3.37 -0.11 23.52 8.84 -1.84 -9.73 -0.83 10.22 -10.81 -9.92 -2.63 -0.61 2.28 0.43 2.24 -1.23 28.96 3.77 -0.17 17.53 -17.15 0.44 2.15 -1.22 -10.91 -1.12 0.29 -3.45 -0.44 48.19 0.23 48.19 -1.64 24.44 3.29 0.02 8.33 -21.66 0.56 54.71 -1.33 19.99 -3.21 -10.62 -5.15 -0.37 2.01 -1.08 1.70 -1.14 29.74 3.77 0.33 8.83 23.66 -1.07 1.67 -1.14 -8.81 -1.19 9.37 -5.15 -0.03 9.55 3.54 -8.87 -0.82 39.11 3.35 0.13 18.43 17.94 2.93 -9.09 -0.92 9.92 1.07 0.56 -3.39 0.15 0.29 0.25 0.14 -0.00 30.66 3.73 -0.64 26.23 -8.54 -0.23 0.11 -0.00 -13.64 -11.08 10.48 -2.79 0.17 6.24 3.28 5.31 0.48 28.55 3.58 -0.09 16.97 -20.97 3.56 5.00 0.55 -8.43 -9.27 -3.16 -4.18 0.76 - - - - - - - 9.64 -22.78 - - - - -11.75 -11.59 -4.78 2.71 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.