ID code: 1BW7, 1BW7 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 A04C1' 68 A04C1' 89 T05C1' 89 T05C1' 109 T06C1' 109 T06C1' 129 G07C1' 129 G07C1' 151 T08C1' 151 T08C1' 171 T09C1' 171 T09C1' 191 A10C1' 191 A10C1' 212 C11C1' 212 C11C1' 231 C12C1' 269 G02C1' 247 G01C1' 291 T03C1' 269 G02C1' 311 A04C1' 291 T03C1' 332 A05C1' 311 A04C1' 353 C06C1' 332 A05C1' 372 A07C1' 353 C06C1' 393 A08C1' 372 A07C1' 414 T09C1' 393 A08C1' 434 G10C1' 414 T09C1' 456 C11C1' 434 G10C1' 475 G12C1' 456 C11C1' 9 C01N1 28 G02N9 28 G02N9 50 C03N1 50 C03N1 69 A04N9 69 A04N9 90 T05N1 90 T05N1 118 T06N1 118 T06N1 130 G07N9 130 G07N9 152 T08N1 152 T08N1 172 T09N1 172 T09N1 192 A10N9 192 A10N9 213 C11N1 213 C11N1 237 C12N1 270 G02N9 248 G01N9 292 T03N1 270 G02N9 312 A04N9 292 T03N1 333 A05N9 312 A04N9 354 C06N1 333 A05N9 373 A07N9 354 C06N1 394 A08N9 373 A07N9 415 T09N1 394 A08N9 435 G10N9 415 T09N1 457 C11N1 435 G10N9 480 G12N9 457 C11N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.00154*S + -0.18664 Y = 0.08376*S + -1.70450 Z = 0.99649*S + 0.14298 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.00154*S + -0.18664 Y = 0.08376*S + -1.70450 Z = 0.99649*S + 0.14298 >>>>>> HELIX ROTATION: 36.224 DISPLACEMENT: 2.9890 STATISTICS: OVERALL STANDARD DEV.: 0.6649 SIGMA(X): 0.8874, SIGMA(Y): 0.8740, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.2452, SIGMA(ROTATION): 4.508 THERE ARE 9.94 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 -0.02105 -0.22513 0.97410 91.21 103.01 13.07 0.06533 -0.01305 0.99778 86.25 90.75 3.82 0.11709 -0.03374 0.99255 83.28 91.93 7.00 0.00587 0.02107 0.99976 89.66 88.79 1.25 0.16959 0.09714 0.98072 80.24 84.43 11.27 -0.01855 0.19255 0.98111 91.06 78.90 11.15 -0.10939 -0.05835 0.99228 96.28 93.35 7.12 -0.19538 -0.05613 0.97912 101.27 93.22 11.73 -0.16386 -0.19021 0.96797 99.43 100.97 14.54 0.09049 -0.01134 0.99583 84.81 90.65 5.23 0.14060 -0.13164 0.98128 81.92 97.56 11.11 -0.02130 -0.17715 0.98395 91.22 100.20 10.28 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.06395 -0.04730 0.99683 86.33 92.71 4.56 -0.03867 0.00820 0.99922 92.22 89.53 2.27 -0.02634 0.02957 0.99922 91.51 88.31 2.27 -0.16480 -0.01774 0.98617 99.49 91.02 9.54 -0.15465 -0.05648 0.98635 98.90 93.24 9.48 -0.07776 -0.11494 0.99032 94.46 96.60 7.98 -0.03900 -0.10751 0.99344 92.23 96.17 6.57 0.03371 0.01163 0.99936 88.07 89.33 2.04 0.03953 -0.02910 0.99879 87.73 91.67 2.81 0.11346 0.14988 0.98217 83.49 81.38 10.84 0.06771 0.09503 0.99317 86.12 84.55 6.70 0.03722 0.09403 0.99487 87.87 84.60 5.80 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.06977 -0.13367 0.98857 86.00 97.68 8.67 0.05281 0.01787 0.99844 86.97 88.98 3.20 0.06024 0.03516 0.99756 86.55 87.99 4.00 -0.10674 0.02947 0.99385 96.13 88.31 6.36 -0.02716 0.08892 0.99567 91.56 84.90 5.33 -0.12387 0.07099 0.98976 97.12 85.93 8.21 -0.10276 -0.10044 0.98962 95.90 95.76 8.26 -0.13132 -0.05712 0.98969 97.55 93.27 8.23 -0.10024 -0.10271 0.98965 95.75 95.90 8.25 0.14597 0.04224 0.98839 81.61 87.58 8.74 0.09811 -0.00851 0.99514 84.37 90.49 5.65 0.09089 0.02022 0.99566 84.79 88.84 5.34 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 8 9 13 13 16 10 12 9 11 7 8 I= 2 8 0 1 9 6 10 11 11 11 5 3 2 I= 3 9 1 0 9 5 10 12 12 12 4 3 1 I= 4 13 9 9 0 5 2 7 5 7 14 11 11 I= 5 13 6 5 5 0 5 11 10 11 10 9 7 I= 6 16 10 10 2 5 0 9 7 10 15 13 12 I= 7 10 11 12 7 11 9 0 2 0 16 12 13 I= 8 12 11 12 5 10 7 2 0 3 16 13 13 I= 9 9 11 12 7 11 10 0 3 0 16 12 13 I= 10 11 5 4 14 10 15 16 16 16 0 4 3 I= 11 7 3 3 11 9 13 12 13 12 4 0 1 I= 12 8 2 1 11 7 12 13 13 13 3 1 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 -13.07 -0.25 10.96 7.33 0.00 0.00 -2.43 3.86 4.31 -5.12 0.00 0.00 -2.40 2.97 -3.00 1.11 0.00 0.00 1.45 -1.74 0.30 1.38 0.00 0.00 -6.96 0.76 6.68 2.46****** 0.00 2.04 0.99 7.63 -3.52 0.00 0.00 -0.59 1.10-10.31 -1.39 0.00 0.00 9.48 1.08 0.71 -2.18 0.00 0.00 -10.52 -4.00 -0.20 12.18****** 0.00 8.14 4.81 1.08 -5.43 0.00 0.50 -11.00 1.81 12.07 9.54 0.00 0.00 6.89 4.00 0.30 -2.24 0.00 0.00 -0.30 7.12 -3.73 3.23 0.00 0.00 4.18 5.06 -1.53 -7.87 0.00 0.00 -9.00 7.46 2.33 7.56 0.00 0.00 1.50 -1.39 0.49 2.31 0.00 0.00 -12.19 7.80 18.08 -1.16 0.00 0.00 1.70 2.24 9.00 -6.56 0.00 0.00 3.11 4.20 -5.15 5.42 0.00 0.00 10.76 -1.22 -3.94 -1.13 0.00 0.00 -6.84 8.70 -0.04 -9.68 0.00 0.00 5.77 3.40 0.41 -1.70 0.00 0.00 -7.80 -6.65 0.00 0.00 0.00 0.00 3.31 4.77 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 8.76 0.78 8.73 -0.72 31.90 3.15 -0.01 4.56 -7.36 0.81 8.73 -0.68 -8.72 -10.67 4.00 -0.91 -0.30 1.08 1.02 0.35 -0.15 39.91 2.98 0.05 3.16 -0.50 1.02 0.35 -0.17 4.93 -3.85 -4.71 -1.40 -0.55 9.59 -1.12 9.52 -1.08 34.96 2.92 -0.24 3.18 -2.43 -1.32 9.53 -1.02 -0.20 -9.00 0.21 -1.55 0.18 5.69 0.50 -5.67 -0.64 37.98 3.02 -0.23 2.99 5.60 0.41 -5.69 -0.72 8.77 -10.07 0.01 -1.67 -0.03 5.65 4.78 3.00 -0.28 35.10 3.11 0.74 4.44 -2.96 4.54 3.35 -0.30 -6.67 -18.77 8.78 -1.78 0.20 9.91 1.07 9.85 -0.99 34.09 3.05 0.14 7.38 -3.58 1.97 9.75 -0.94 -4.15 -17.93 2.11 -0.95 0.45 2.97 -0.77 -2.87 0.05 35.74 3.31 -0.49 8.02 1.97 -0.73 -2.88 -0.02 -6.86 -4.48 -2.04 -0.83 -0.40 3.16 2.49 1.95 -0.46 39.84 2.90 0.23 6.03 -5.59 2.48 1.96 -0.46 3.24 -10.52 -8.90 -1.60 -0.03 16.43 -0.28 16.42 -1.24 29.77 2.77 0.25 4.01 -7.20 0.26 16.60 -1.13 0.30 -13.91 -5.66 -1.58 0.37 4.02 -1.33 -3.79 -0.08 38.63 3.12 -0.26 4.39 7.55 -1.33 -3.77 -0.12 0.05 -7.70 -5.36 -1.28 -0.26 1.70 -0.01 1.70 -0.96 38.42 2.78 0.72 5.65 -0.01 0.04 1.70 -0.96 16.70 -12.62 -5.32 -1.34 0.23 - - - - - - - 4.98 -1.92 - - - - -11.24 11.39 -0.67 -0.35 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.