ID code: 418D, DR0001 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 6 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 250 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' 52 G03C1' 52 G03C1' 75 C04C1' 75 C04C1' 95 A05C1' 95 A05C1' 117 C06C1' 177 G11C1' 134 G09C1' 200 C12C1' 177 G11C1' 220 A13C1' 200 C12C1' 242 C14C1' 220 A13C1' 10 G01N9 53 G03N9 53 G03N9 76 C04N1 76 C04N1 96 A05N9 96 A05N9 118 C06N1 178 G11N9 135 G09N9 201 C12N1 178 G11N9 221 A13N9 201 C12N1 243 C14N1 221 A13N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.79168*S + 4.95040 Y = -0.45923*S + 1.76624 Z = -0.40292*S + 7.71365 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.79168*S + 4.95040 Y = -0.45923*S + 1.76624 Z = -0.40292*S + 7.71365 >>>>>> HELIX ROTATION: 47.357 DISPLACEMENT: 3.1557 STATISTICS: OVERALL STANDARD DEV.: 3.3352 SIGMA(X): 1.7692, SIGMA(Y): 1.8403, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.4280, SIGMA(ROTATION): 23.416 THERE ARE 7.60 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 = 6 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.34096 -0.19487 0.91966 109.94 101.24 23.12 -0.31753 -0.21652 0.92320 108.51 102.50 22.60 -0.10698 -0.23638 0.96575 96.14 103.67 15.04 0.05896 -0.30157 0.95162 86.62 107.55 17.90 0.13680 0.19211 0.97179 82.14 78.92 13.64 0.22603 0.15826 0.96118 76.94 80.89 16.02 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.16608 -0.41562 0.89425 99.56 114.56 26.59 -0.17121 -0.22881 0.95830 99.86 103.23 16.61 -0.01405 -0.13719 0.99044 90.81 97.89 7.93 0.18497 0.08069 0.97943 79.34 85.37 11.64 0.36409 0.47073 0.80365 68.65 61.92 36.52 0.24360 0.48484 0.83999 75.90 61.00 32.86 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.27376 -0.31475 0.90884 105.89 108.35 24.65 -0.25854 -0.31490 0.91323 104.98 108.35 24.04 -0.03945 -0.22399 0.97379 92.26 102.94 13.15 0.14539 -0.10544 0.98374 81.64 96.05 10.35 0.25320 0.34732 0.90292 75.33 69.68 25.46 0.32464 0.39505 0.85939 71.06 66.73 30.75 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 I= 1 0 0 14 27 50 55 I= 2 0 0 14 26 49 54 I= 3 14 14 0 12 37 42 I= 4 27 26 12 0 27 31 I= 5 50 49 37 27 0 5 I= 6 55 54 42 31 5 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 -9.18 21.03 1.70 0.66 0.00****** 6.43 25.68 -4.20 -9.90 0.00 -0.00 -18.05 13.14 11.72 3.36 0.00 0.00 -9.39 13.57 9.87 -3.49 0.00 0.00 -12.28 8.55 4.06 9.42 0.00****** -4.71 6.36 17.15 -0.73 -1.85 0.00 -13.96 10.97 29.98 0.30 0.00 0.00 9.00 7.33 24.33 6.92 0.00 0.00 10.70 8.36 -4.02 3.72 0.00 0.00 26.98 22.66 3.80 -5.83 -3.59 0.00 -0.14 16.02 0.00 0.00 0.00 0.00 14.67 28.68 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 0.91 -0.35 0.84 -1.20 32.50 3.28 -1.09 24.56 -1.97 -0.31 0.81 -1.22 -4.71 -15.63 4.48 -1.38 1.81 14.06 -2.68 13.81 -1.42 32.76 3.10 -0.46 18.88 -14.33 -2.79 13.42 -1.37 -2.14 -8.68 -0.23 -2.28 0.53 12.62 2.92 12.28 -1.15 31.39 3.47 -0.08 9.93 -8.53 2.71 12.38 -1.05 -1.46 -7.56 -2.37 -3.28 0.01 27.32 1.58 27.28 -2.13 29.64 2.73 0.66 10.23 -1.56 2.34 27.62 -1.93 19.82 -22.97 -3.83 -3.60 0.26 5.52 5.35 1.37 -1.44 32.17 3.30 0.66 15.59 19.60 4.89 0.63 -1.46 -2.31 -16.44 15.99 -2.56 -0.74 - - - - - - - 29.58 7.65 - - - - -14.82 13.68 -1.87 -2.09 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.