ID code: 3GLP 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 8 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 400 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' 32 C02C1' 32 C02C1' 72 G04C1' 72 G04C1' 95 C05C1' 95 C05C1' 135 G07C1' 135 G07C1' 158 C08C1' 158 C08C1' 177 G01C1' 212 C02C1' 211 C02C1' 281 G04C1' 212 C02C1' 315 C05C1' 281 G04C1' 316 C05C1' 315 C05C1' 369 G07C1' 316 C05C1' 392 C08C1' 369 G07C1' 10 G01N9 33 C02N1 33 C02N1 73 G04N9 73 G04N9 96 C05N1 96 C05N1 136 G07N9 136 G07N9 159 C08N1 159 C08N1 178 G01N9 214 C02N1 213 C02N1 282 G04N9 214 C02N1 317 C05N1 282 G04N9 318 C05N1 317 C05N1 370 G07N9 318 C05N1 393 C08N1 370 G07N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.48706*S + 12.57811 Y = -0.34481*S + 13.93650 Z = 0.80242*S + -1.64608 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.48706*S + 12.57811 Y = -0.34481*S + 13.93650 Z = 0.80242*S + -1.64608 >>>>>> HELIX ROTATION: 37.394 DISPLACEMENT: 1.8999 STATISTICS: OVERALL STANDARD DEV.: 4.6661 SIGMA(X): 3.7350, SIGMA(Y): 3.2156, SIGMA(Z)=SIGMA(DISPLACEMENT): 1.9935, SIGMA(ROTATION): 24.898 THERE ARE 9.63 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 = 8 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.32475 0.45272 0.83041 71.05 63.08 33.86 0.48922 0.49855 0.71562 60.71 60.10 44.31 0.18548 0.69785 0.69182 79.31 45.75 46.23 NaN NaN NaN NaN NaN NaN -0.08991 0.70498 0.70350 95.16 45.17 45.29 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN -0.24222 0.27837 0.92943 104.02 73.84 21.65 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.27351 0.51844 0.81019 74.13 58.77 35.89 0.09421 0.63380 0.76774 84.59 50.67 39.85 -0.06876 0.67288 0.73655 93.94 47.71 42.56 0.00364 0.07559 0.99713 89.79 85.67 4.34 -0.14137 0.50700 0.85027 98.13 59.54 31.76 0.22589 0.11762 0.96703 76.94 83.25 14.75 0.52826 0.30265 0.79331 58.11 72.38 37.50 -0.14190 0.30359 0.94218 98.16 72.33 19.58 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.31983 0.47704 0.81862 71.35 61.51 35.05 0.26761 0.56795 0.77835 74.48 55.39 38.89 0.01247 0.66209 0.74932 89.29 48.54 41.47 0.00364 0.07559 0.99713 89.79 85.67 4.34 -0.10540 0.58959 0.80080 96.05 53.87 36.79 0.22589 0.11762 0.96703 76.94 83.25 14.75 0.52826 0.30265 0.79331 58.11 72.38 37.50 -0.18731 0.29866 0.93580 100.80 72.62 20.64 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 I= 1 0 6 21 31 25 23 15 31 I= 2 6 0 15 34 21 28 21 32 I= 3 21 15 0 37 8 36 36 26 I= 4 31 34 37 0 32 13 35 17 I= 5 25 21 8 32 0 34 40 19 I= 6 23 28 36 13 34 0 22 26 I= 7 15 21 36 35 40 22 0 42 I= 8 31 32 26 17 19 26 42 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 31.93 10.08 1.47 9.72 0.00****** 35.20 6.12 7.82 -9.44 0.00 -0.00 26.03 32.92 20.94 -3.73 0.00 0.00 38.22 9.59 8.34 -4.82 0.00 0.00 12.15 43.69 NaN NaN 0.00****** 24.42 32.37-22.47-27.69****** 0.00 NaN NaN NaN NaN 0.00 0.00 0.01 4.34 1.54 27.02 0.00 0.00 -18.56 39.45 NaN NaN 0.00 0.00 -9.51 29.98 4.53-31.96****** 0.00 NaN NaN NaN NaN 0.00 0.00 -9.39-11.28-15.12-13.89 0.00 0.00 NaN NaN NaN NaN****** 0.00 -10.04-35.69-16.44 37.41 0.00 0.00 -21.63 1.04 0.00 0.00 0.00 0.00 -19.05 -4.38 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 6.44 -2.63 5.88 -0.77 26.18 3.72 -0.15 9.39 33.41 -2.34 5.54 -0.70 -17.43 -3.31 -3.63 -8.36 -2.79 15.72 -7.36 13.93 -1.29 45.53 2.78 -1.20 19.35 32.23 -6.18 14.46 -1.10 12.52 -12.17 -21.06 -7.24 -1.18 37.13 -36.21 -8.81 -2.84 23.28 2.66 0.00 34.69 19.79 -29.95 -17.94 -1.94 NaN -12.23 -8.54 -6.42 2.48 32.58 -32.54 -1.61 -3.12 30.85 2.39 -0.12 4.34 0.01 31.64 -1.69 -2.26 NaN NaN NaN -4.94 1.67 34.92 -33.62 10.01 -2.20 44.49 2.48 -1.20 33.25 -13.95 -33.52 9.57 -1.34 NaN -9.14 -11.22 -4.38 0.81 22.77 -18.37 -13.68 -3.03 32.49 1.97 -0.29 -11.28 -9.39 -13.89 -15.12 -1.37 NaN NaN NaN -5.47 2.23 42.79 -40.18 -15.99 -3.03 27.87 2.59 -0.17 -35.69 -10.04 40.60 -17.32 -1.96 NaN NaN NaN -5.53 2.66 - - - - - - - -2.15 -20.52 - - - - -2.59 -5.38 -5.26 2.91 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.