ID code: 1EO4, PD0130 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 9 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 369 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: 11 A03C1' 32 G04C1' 32 G04C1' 54 A05C1' 54 A05C1' 95 A07C1' 95 A07C1' 116 T08C1' 116 T08C1' 136 C09C1' 136 C09C1' 155 T10C1' 155 T10C1' 175 T11C1' 216 A03C1' 195 A02C1' 237 G04C1' 216 A03C1' 259 A05C1' 237 G04C1' 300 A07C1' 259 A05C1' 321 T08C1' 300 A07C1' 341 C09C1' 321 T08C1' 360 T10C1' 341 C09C1' 12 A03N9 33 G04N9 33 G04N9 55 A05N9 55 A05N9 96 A07N9 96 A07N9 117 T08N1 117 T08N1 137 C09N1 137 C09N1 156 T10N1 156 T10N1 176 T11N1 217 A03N9 196 A02N9 238 G04N9 217 A03N9 260 A05N9 238 G04N9 301 A07N9 260 A05N9 322 T08N1 301 A07N9 342 C09N1 322 T08N1 361 T10N1 342 C09N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.56277*S + -8.34621 Y = -0.41177*S + -7.77674 Z = -0.71676*S + -2.08541 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.56277*S + -8.34621 Y = -0.41177*S + -7.77674 Z = -0.71676*S + -2.08541 >>>>>> HELIX ROTATION: 30.963 DISPLACEMENT: 2.6963 STATISTICS: OVERALL STANDARD DEV.: 3.0482 SIGMA(X): 3.3411, SIGMA(Y): 3.2414, SIGMA(Z)=SIGMA(DISPLACEMENT): 1.6707, SIGMA(ROTATION): 15.383 THERE ARE 11.63 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 = 9 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.14972 -0.45249 0.87911 81.39 116.90 28.46 0.16902 -0.56881 0.80491 80.27 124.67 36.40 0.04329 -0.51678 0.85503 87.52 121.12 31.24 0.28205 -0.59832 0.74997 73.62 126.75 41.41 0.16107 0.38021 0.91077 80.73 67.65 24.39 0.26147 0.37045 0.89129 74.84 68.26 26.96 0.46680 0.19407 0.86280 62.17 78.81 30.37 0.57204 0.28244 0.77007 55.11 73.59 39.64 0.49548 0.35161 0.79428 60.30 69.41 37.41 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.42006 -0.56475 0.71036 65.16 124.38 44.74 0.44135 -0.42957 0.78783 63.81 115.44 38.02 -0.01211 -0.39657 0.91792 90.69 113.36 23.38 -0.05872 -0.38864 0.91952 93.37 112.87 23.14 0.39202 0.36022 0.84650 66.92 68.89 32.17 0.28229 0.38819 0.87728 73.60 67.16 28.68 0.34674 0.34918 0.87054 69.71 69.56 29.48 0.27279 0.26141 0.92588 74.17 74.85 22.20 0.26266 0.07009 0.96234 74.77 85.98 15.77 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.31498 -0.52527 0.79049 71.64 121.69 37.77 0.28102 -0.50907 0.81356 73.68 120.60 35.56 0.04421 -0.51959 0.85327 87.47 121.30 31.43 0.08939 -0.51628 0.85174 84.87 121.08 31.60 0.28957 0.38121 0.87797 73.17 67.59 28.60 0.28850 0.39217 0.87348 73.23 66.91 29.13 0.40080 0.29418 0.86765 66.37 72.89 29.81 0.45953 0.28078 0.84262 62.64 73.69 32.58 0.44495 0.21537 0.86927 63.58 77.56 29.63 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 I= 1 0 2 15 13 54 54 48 48 44 I= 2 2 0 13 11 53 53 48 47 43 I= 3 15 13 0 2 55 56 52 53 49 I= 4 13 11 2 0 54 55 51 52 48 I= 5 54 53 55 54 0 0 8 11 13 I= 6 54 53 56 55 0 0 8 11 13 I= 7 48 48 52 51 8 8 0 3 5 I= 8 48 47 53 52 11 11 3 0 4 I= 9 44 43 49 48 13 13 5 4 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 24.88 12.94 3.13 6.00****** 0.00 43.93 6.81 -1.26 -7.76****** 0.00 17.25 30.93 -6.66 -4.08 0.00 0.00 31.94 18.38-26.27 -5.96 0.00 0.00 -13.47 27.60 6.47 13.05****** 0.00 -12.56 19.38 -1.58 -2.20 NaN 0.00 -24.11 31.35 62.64-25.35 0.00 0.00 -21.95 6.99 58.63 10.77 0.00 0.00 22.34 9.28 -2.84 5.04****** 0.00 21.11 23.09 4.02 -5.10****** 0.00 9.81 24.85-15.70 -0.43 0.00 0.00 10.03 26.57 -4.28 0.59 0.00 0.00 -22.85 18.88 -5.24 5.90****** 0.00 -13.16 25.86 3.46 -5.60************ -38.91 6.40 1.63 5.69 0.00 0.00 -19.57 10.07 6.30 -9.04 0.00 0.00 -37.08 -4.32 0.00 0.00 0.00 0.00 -13.95 -7.22 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 2.53 -0.33 -2.51 -0.24 32.60 3.38 0.84 9.35 36.19 -0.28 -2.14 -0.24 -5.66 -19.06 -3.91 -5.97 -2.69 13.80 -2.50 -13.58 -0.42 39.33 3.46 -0.05 25.46 23.06 -1.54 -13.62 -0.59 1.21 -14.81 -9.58 -4.46 -1.05 2.60 1.67 1.99 -1.31 29.92 3.84 -0.13 27.79 -13.51 1.68 1.98 -1.33 -16.62 -0.81 -8.37 -4.53 0.27 54.77 -1.19 54.76 -1.76 25.40 3.00 -0.06 18.14 -24.93 -5.63 66.11 -1.43 38.74 -2.40 -24.98 -5.79 0.40 0.68 0.20 0.65 -1.22 31.63 3.77 0.09 16.84 22.40 0.20 0.60 -1.24 -12.01 1.26 13.76 -5.68 0.66 8.55 -0.39 -8.55 -0.57 35.95 3.41 -0.23 27.04 10.03 -0.31 -8.57 -0.66 3.93 -0.21 1.75 -4.03 0.84 3.74 -0.30 -3.73 -0.00 35.21 3.39 -1.02 23.56 -17.20 -0.27 -3.44 -0.03 -3.59 -9.74 5.68 -3.70 1.38 4.13 -2.87 2.97 0.36 31.69 3.32 -0.50 8.12 -31.31 -2.74 2.69 0.41 -3.54 -19.35 2.09 -4.85 3.04 - - - - - - - -8.14 -28.27 - - - - -23.16 -1.45 -5.00 5.73 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.