ID code: 1K82, PD0264 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 243 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 G01C1' 30 G02C1' 30 G02C1' 52 C03C1' 52 C03C1' 71 T04C1' 71 T04C1' 91 T05C1' 91 T05C1' 111 C06C1' 152 A29C1' 130 G28C1' 173 A30C1' 152 A29C1' 194 G31C1' 173 A30C1' 216 C32C1' 194 G31C1' 235 C33C1' 216 C32C1' 9 G01N9 31 G02N9 31 G02N9 53 C03N1 53 C03N1 72 T04N1 72 T04N1 92 T05N1 92 T05N1 112 C06N1 153 A29N9 131 G28N9 174 A30N9 153 A29N9 195 G31N9 174 A30N9 217 C32N1 195 G31N9 236 C33N1 217 C32N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.91800*S + 0.25269 Y = -0.38236*S + 9.03430 Z = 0.10520*S + 30.63078 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.91800*S + 0.25269 Y = -0.38236*S + 9.03431 Z = 0.10520*S + 30.63078 >>>>>> HELIX ROTATION: 35.514 DISPLACEMENT: 3.2265 STATISTICS: OVERALL STANDARD DEV.: 1.1365 SIGMA(X): 0.9163, SIGMA(Y): 0.8381, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.5235, SIGMA(ROTATION): 10.538 THERE ARE 10.14 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 -0.18194 -0.16490 0.96939 100.48 99.49 14.21 0.04459 -0.19417 0.97995 87.44 101.20 11.49 0.06067 -0.10080 0.99306 86.52 95.79 6.76 0.14540 -0.15359 0.97738 81.64 98.84 12.21 0.19055 -0.07692 0.97866 79.01 94.41 11.86 0.18075 0.19864 0.96326 79.59 78.54 15.58 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.11344 -0.14284 0.98322 83.49 98.21 10.51 0.19141 0.02853 0.98110 78.97 88.36 11.16 0.22086 -0.02415 0.97501 77.24 91.38 12.84 0.22452 0.17809 0.95806 77.03 79.74 16.65 0.25996 0.17972 0.94875 74.93 79.65 18.42 0.08585 0.09107 0.99214 85.08 84.77 7.19 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.05338 -0.20302 0.97772 93.06 101.71 12.12 0.11054 -0.10850 0.98793 83.65 96.23 8.91 0.18954 -0.08143 0.97849 79.07 94.67 11.91 0.21325 -0.01315 0.97691 77.69 90.75 12.34 0.22984 0.04945 0.97197 76.71 87.17 13.60 0.12379 0.11589 0.98552 82.89 83.35 9.76 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 10 15 18 21 21 I= 2 10 0 4 8 11 12 I= 3 15 4 0 4 7 11 I= 4 18 8 4 0 3 9 I= 5 21 11 7 3 0 7 I= 6 21 12 11 9 7 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 -8.49 11.31 12.80 3.17 0.00 0.00 7.95 6.83 5.58 -9.28 0.00 -0.00 -2.99 11.09 4.58 -2.93 0.00 0.00 10.50 3.73 -1.09 3.28 0.00 0.00 -3.81 5.57 -2.18 5.30 0.00****** 4.00 12.18 11.54 -1.72 0.54 0.00 -9.74 7.29 2.69 4.33 0.00 0.00 8.70 14.09 -0.86 1.84 0.00 0.00 -11.19 3.88 7.32 14.16 0.00 0.00 -4.43 17.85 6.84 -8.91 0.95 0.00 -6.64 14.03 0.00 0.00 0.00 0.00 -3.20 6.43 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 10.87 -3.99 10.12 -0.91 38.29 3.24 -1.03 12.09 -0.82 -4.30 10.00 -0.82 -2.73 -16.47 -4.50 -1.26 1.26 4.82 2.29 4.24 0.00 36.82 2.94 -0.12 8.50 2.66 2.30 4.20 0.03 13.84 -13.53 -7.23 -1.61 0.76 4.14 0.73 4.08 0.09 30.42 3.28 -0.20 11.90 0.27 0.69 4.09 0.11 0.15 -7.83 6.61 -1.01 1.11 3.72 2.51 2.75 0.44 41.27 3.17 0.79 12.14 -2.14 2.51 2.74 0.47 7.03 -18.48 6.76 -0.69 0.97 7.22 0.24 7.21 0.94 24.10 3.86 -0.61 10.87 -8.07 0.82 7.14 1.02 -21.44 -6.82 13.79 0.53 0.78 - - - - - - - 8.44 -4.88 - - - - -3.46 -7.65 -0.14 1.03 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.