ID code: 2GXP 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 12 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 486 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 C01C1' 27 G02C1' 27 G02C1' 49 C03C1' 49 C03C1' 68 G04C1' 68 G04C1' 90 A05C1' 90 A05C1' 111 A06C1' 111 A06C1' 132 T07C1' 132 T07C1' 152 T08C1' 152 T08C1' 172 C09C1' 172 C09C1' 191 G10C1' 191 G10C1' 213 C11C1' 213 C11C1' 232 G12C1' 270 G14C1' 251 C13C1' 292 C15C1' 270 G14C1' 311 G16C1' 292 C15C1' 333 A17C1' 311 G16C1' 354 A18C1' 333 A17C1' 375 T19C1' 354 A18C1' 395 T20C1' 375 T19C1' 415 C21C1' 395 T20C1' 434 G22C1' 415 C21C1' 456 C23C1' 434 G22C1' 475 G24C1' 456 C23C1' 9 C01N1 28 G02N9 28 G02N9 50 C03N1 50 C03N1 69 G04N9 69 G04N9 91 A05N9 91 A05N9 112 A06N9 112 A06N9 133 T07N1 133 T07N1 153 T08N1 153 T08N1 173 C09N1 173 C09N1 192 G10N9 192 G10N9 214 C11N1 214 C11N1 233 G12N9 271 G14N9 252 C13N1 293 C15N1 271 G14N9 312 G16N9 293 C15N1 334 A17N9 312 G16N9 355 A18N9 334 A17N9 376 T19N1 355 A18N9 396 T20N1 376 T19N1 416 C21N1 396 T20N1 435 G22N9 416 C21N1 457 C23N1 435 G22N9 476 G24N9 457 C23N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.18629*S + 11.92063 Y = -0.21513*S + 27.67866 Z = 0.95865*S + 3.89493 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.18629*S + 11.92063 Y = -0.21513*S + 27.67866 Z = 0.95865*S + 3.89494 >>>>>> HELIX ROTATION: 32.440 DISPLACEMENT: 3.4387 STATISTICS: OVERALL STANDARD DEV.: 1.7076 SIGMA(X): 1.6986, SIGMA(Y): 1.5905, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.6724, SIGMA(ROTATION): 14.805 THERE ARE 11.10 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 = 12 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.53091 0.03071 0.84687 57.93 88.24 32.13 0.26213 0.16506 0.95081 74.80 80.50 18.05 0.12159 0.10218 0.98731 83.02 84.14 9.14 -0.10706 -0.20318 0.97327 96.15 101.72 13.28 -0.03522 -0.05886 0.99765 92.02 93.37 3.93 -0.26974 0.02062 0.96271 105.65 88.82 15.70 -0.19470 -0.00413 0.98085 101.23 90.24 11.23 -0.14892 -0.14344 0.97839 98.56 98.25 11.93 -0.14816 -0.10826 0.98302 98.52 96.22 10.57 0.07138 -0.09607 0.99281 85.91 95.51 6.87 0.22325 -0.00896 0.97472 77.10 90.51 12.91 0.08187 -0.03235 0.99612 85.30 91.85 5.05 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.35926 0.15501 0.92027 68.95 81.08 23.03 0.23027 0.03599 0.97246 76.69 87.94 13.48 -0.02182 -0.03597 0.99911 91.25 92.06 2.41 0.00604 -0.33224 0.94317 89.65 109.40 19.41 0.13956 -0.12205 0.98266 81.98 97.01 10.68 0.14016 -0.07259 0.98746 81.94 94.16 9.08 0.06829 0.01836 0.99750 86.08 88.95 4.06 0.28731 0.02982 0.95737 73.30 88.29 16.79 0.28989 -0.05978 0.95519 73.15 93.43 17.22 -0.02787 0.05502 0.99810 91.60 86.85 3.54 -0.11021 0.13972 0.98404 96.33 81.97 10.25 -0.42026 0.19978 0.88514 114.85 78.48 27.73 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.41856 0.08851 0.90387 65.26 84.92 25.33 0.27035 0.09763 0.95780 74.32 84.40 16.70 0.09518 -0.02373 0.99518 84.54 91.36 5.63 0.00787 -0.24633 0.96915 89.55 104.26 14.27 0.04464 -0.11167 0.99274 87.44 96.41 6.91 -0.02134 -0.06142 0.99788 91.22 93.52 3.73 -0.07851 -0.02936 0.99648 94.50 91.68 4.81 -0.02008 -0.02691 0.99944 91.15 91.54 1.92 0.11241 -0.04930 0.99244 83.55 92.83 7.05 0.06833 -0.01079 0.99760 86.08 90.62 3.97 0.03089 0.07330 0.99683 88.23 85.80 4.56 -0.16587 0.10126 0.98094 99.55 84.19 11.21 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 I= 10 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 11 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 11 12 I= 1 0 9 20 30 25 27 30 26 19 21 23 34 I= 2 9 0 12 24 17 19 21 18 12 13 14 25 I= 3 20 12 0 13 5 7 9 6 1 1 6 16 I= 4 30 24 13 0 8 10 13 12 12 14 18 22 I= 5 25 17 5 8 0 4 8 6 5 5 10 17 I= 6 27 19 7 10 4 0 3 1 7 5 8 12 I= 7 30 21 9 13 8 3 0 3 11 8 8 9 I= 8 26 18 6 12 6 1 3 0 7 5 6 11 I= 9 19 12 1 12 5 7 11 7 0 3 8 18 I= 10 21 13 1 14 5 5 8 5 3 0 5 14 I= 11 23 14 6 18 10 8 8 6 8 5 0 11 I= 12 34 25 16 22 17 12 9 11 18 14 11 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 -31.68 -4.81 12.22 12.32 0.00 0.00 -22.59 4.26 9.22 -4.10****** 0.00 -18.04 -0.17 7.84 4.10 0.00 0.00 -12.31 -5.41 12.27 8.83 0.00 0.00 -7.96 -4.45 20.77 8.09****** 0.00 2.37 0.44 16.18 -5.99 0.00 0.00 12.60 4.11 -7.23 -5.79 0.00 0.00 19.06 -3.51-10.20-10.08 0.00 0.00 1.56 3.61-13.70 4.15****** 0.00 10.40 -2.42 -1.63 -2.32 0.00 0.50 -15.18 3.91 4.38 1.18 0.00 0.00 8.98 1.32 -4.40 -4.98 0.00 0.00 -10.85 -2.86 -1.89 8.21****** 0.00 4.05 0.07 11.14 5.95 0.00 0.00 -11.90 -0.84 1.94 -0.57 0.00 0.00 12.38 11.16 -4.85 1.69 0.00 0.00 -6.35 -8.42 0.02 12.70****** 0.00 -3.15 16.91 7.56-18.13****** 0.00 -6.44 2.39 -0.95 10.04 0.00 0.00 3.47 -0.65 6.70 -1.05 0.00 0.00 -11.02 6.64 7.51 -3.36****** 0.00 9.73 3.20 18.37 -1.20 0.00 0.00 -4.64 -1.98 0.00 0.00 0.00 0.00 24.49 12.20 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 9.06 3.83 8.22 1.20 20.40 3.79 0.27 -0.19 -25.33 3.21 7.90 1.29 -14.19 -9.18 9.04 1.82 -3.24 12.42 3.59 11.90 -0.25 36.28 3.03 1.51 -3.68 -16.27 3.59 11.75 -0.10 10.08 -5.75 -5.15 -0.24 -2.12 13.81 1.43 13.74 -0.42 11.37 3.78 -0.59 -5.59 -0.66 1.49 13.75 -0.28 -12.60 -10.34 4.93 -0.42 -1.77 8.12 -3.81 -7.17 0.23 45.17 3.31 -0.55 -2.80 13.98 -3.70 -7.11 0.21 1.68 -6.42 -7.67 -0.90 -1.74 4.76 -0.07 -4.76 -0.34 35.37 3.37 0.16 1.65 6.71 -0.13 -4.76 -0.36 3.32 -8.87 -5.99 -1.75 -0.44 3.76 -1.75 -3.32 -1.09 35.11 3.15 0.10 3.73 -0.01 -1.65 -3.37 -1.11 5.59 -24.17 -2.67 -1.50 0.02 3.36 1.65 2.92 -1.00 31.79 2.93 0.23 0.37 -4.79 1.61 2.94 -0.92 9.08 -14.92 2.92 -1.64 -0.29 7.72 7.55 1.60 0.20 40.87 3.50 -0.13 0.18 -1.92 7.65 1.07 0.29 13.29 -24.46 12.00 -1.77 -0.35 3.37 -2.23 2.53 -0.38 17.25 3.88 0.15 6.50 -2.72 -2.40 2.34 -0.41 -28.35 -3.38 25.29 -1.74 0.96 5.28 1.13 5.15 -0.18 40.23 3.28 -0.50 3.59 -1.69 1.03 5.18 -0.14 -0.41 -9.92 -3.06 -1.50 0.73 11.44 -1.46 11.35 -0.96 34.86 2.81 0.59 4.48 0.84 -1.32 11.38 -0.85 18.21 -20.76 -3.47 -1.28 1.35 - - - - - - - 6.07 9.38 - - - - -29.35 14.74 0.19 0.51 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.