ID code: 1EZH 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 363 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 T01C1' 28 A02C1' 28 A02C1' 49 A03C1' 49 A03C1' 70 C04C1' 70 C04C1' 89 G05C1' 89 G05C1' 111 G06C1' 111 G06C1' 133 T07C1' 133 T07C1' 153 T08C1' 153 T08C1' 173 A09C1' 211 A11C1' 191 T10C1' 232 A12C1' 211 A11C1' 253 C13C1' 232 A12C1' 272 C14C1' 253 C13C1' 291 G15C1' 272 C14C1' 313 T16C1' 291 G15C1' 333 T17C1' 313 T16C1' 353 A18C1' 333 T17C1' 9 T01N1 29 A02N9 29 A02N9 50 A03N9 50 A03N9 71 C04N1 71 C04N1 90 G05N9 90 G05N9 112 G06N9 112 G06N9 134 T07N1 134 T07N1 154 T08N1 154 T08N1 174 A09N9 212 A11N9 192 T10N1 233 A12N9 212 A11N9 254 C13N1 233 A12N9 273 C14N1 254 C13N1 292 G15N9 273 C14N1 314 T16N1 292 G15N9 334 T17N1 314 T16N1 354 A18N9 334 T17N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.95121*S + -2.29451 Y = -0.14869*S + 23.96938 Z = 0.27035*S + 21.25629 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.95121*S + -2.29451 Y = -0.14869*S + 23.96938 Z = 0.27035*S + 21.25629 >>>>>> HELIX ROTATION: 32.545 DISPLACEMENT: 3.0812 STATISTICS: OVERALL STANDARD DEV.: 1.5776 SIGMA(X): 2.3718, SIGMA(Y): 2.3512, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.6743, SIGMA(ROTATION): 11.094 THERE ARE 11.06 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 0.00472 -0.49075 0.87129 89.73 119.39 29.39 0.12996 -0.52223 0.84284 82.53 121.48 32.56 0.04678 -0.49994 0.86480 87.32 120.00 30.14 0.15779 -0.24536 0.95650 80.92 104.20 16.96 0.10132 0.09984 0.98983 84.18 84.27 8.18 0.17805 0.08321 0.98050 79.74 85.23 11.33 0.28302 0.05318 0.95764 73.56 86.95 16.74 0.25698 0.24302 0.93536 75.11 75.94 20.71 0.12093 0.26574 0.95643 83.05 74.59 16.98 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.03035 -0.22429 0.97405 91.74 102.96 13.08 0.21349 -0.22343 0.95105 77.67 102.91 18.00 0.28395 -0.06713 0.95649 73.50 93.85 16.96 0.26086 -0.04378 0.96438 74.88 92.51 15.34 0.19953 0.22037 0.95479 78.49 77.27 17.29 0.03805 0.42053 0.90648 87.82 65.13 24.98 0.11152 0.34634 0.93146 83.60 69.74 21.34 0.00118 0.35582 0.93455 89.93 69.16 20.84 -0.00956 0.19226 0.98130 90.55 78.92 11.10 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.01383 -0.35357 0.93530 89.21 110.71 20.72 0.16193 -0.36697 0.91603 80.68 111.53 23.65 0.19236 -0.26299 0.94543 78.91 105.25 19.02 0.21431 -0.12925 0.96818 77.62 97.43 14.49 0.16398 0.16895 0.97189 80.56 80.27 13.62 0.11748 0.24345 0.96277 83.25 75.91 15.68 0.21770 0.19140 0.95707 77.43 78.97 16.85 0.15768 0.27527 0.94835 80.93 74.02 18.50 0.13177 0.16109 0.97810 82.43 80.73 12.01 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 8 11 17 31 35 33 37 30 I= 2 8 0 6 14 31 35 32 37 30 I= 3 11 6 0 7 25 29 26 31 24 I= 4 17 14 7 0 17 22 18 23 17 I= 5 31 31 25 17 0 5 3 6 1 I= 6 35 35 29 22 5 0 6 3 4 I= 7 33 32 26 18 3 6 0 5 5 I= 8 37 37 31 23 6 3 5 0 6 I= 9 30 30 24 17 1 4 5 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 13.43 25.62 5.78 4.64****** 0.00 4.44 12.28 12.82 5.80****** 0.00 15.16 28.05 -4.52 -1.98 0.00 0.00 15.33 9.21 5.35 -8.27 0.00 0.00 -12.33 27.03 14.70 -6.49****** 0.00 12.15 11.65 -0.07 -1.88 NaN 0.00 -8.19 14.75 19.06 -7.20 0.00 0.00 4.81 14.53 14.26 -6.52 0.00 0.00 5.05 6.42 -2.70 3.60****** 0.00 11.35 12.87 14.44 -3.61****** 0.00 -2.90 10.95 -5.99 1.83 0.00 0.00 17.33 17.41 -5.85 -1.28 0.00 0.00 -15.26 6.70 0.09 11.05****** 0.00 -1.67 21.27 6.21 1.35************ -19.91 5.47 5.02 6.12 0.00 0.00 -9.61 18.32 6.64 -6.67 0.00 0.00 -16.86 1.89 0.00 0.00 0.00 0.00 -9.20 6.15 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 8.60 -1.89 8.39 0.43 11.76 3.86 0.39 17.86 10.17 4.24 7.41 0.52 -5.06 9.07 -13.85 -3.60 0.27 6.44 -5.90 2.57 -0.08 42.51 3.23 -1.04 18.18 14.60 -5.64 2.62 -0.01 3.47 -0.19 -18.91 -2.34 0.18 7.88 -4.57 6.43 -0.98 30.02 3.03 -0.62 18.92 1.85 -4.81 6.11 -0.89 15.12 -24.71 -15.44 -2.54 0.91 17.40 -5.95 16.38 -0.38 33.24 3.13 -1.01 14.47 -0.77 -6.30 16.37 -0.23 6.94 -13.00 -0.32 -2.77 0.54 5.06 0.64 5.02 -0.56 33.05 3.62 0.18 10.47 8.61 -0.64 5.00 -0.49 0.53 -6.31 6.62 -3.06 1.33 6.48 0.54 -6.46 -0.13 35.51 3.28 -0.29 14.26 6.38 0.62 -6.45 -0.15 6.90 -20.26 7.15 -1.56 1.36 5.93 5.18 2.89 0.37 39.74 3.25 1.03 13.66 -9.67 5.21 2.80 0.46 -1.72 -13.72 14.05 -1.12 1.18 6.93 -3.88 5.74 0.69 32.96 3.63 -1.18 9.79 -15.53 -3.96 5.43 0.84 -8.08 -10.32 12.34 0.08 1.17 - - - - - - - -1.72 -11.88 - - - - -7.62 4.26 -1.18 2.00 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.