ID code: 1GLU, PDRC01 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 18 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 732 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 C-9C1' 27 A-8C1' 27 A-8C1' 48 G-7C1' 48 G-7C1' 70 A-6C1' 70 A-6C1' 91 A-5C1' 91 A-5C1' 112 C-4C1' 112 C-4C1' 131 A-3C1' 131 A-3C1' 152 T-2C1' 152 T-2C1' 172 C-1C1' 172 C-1C1' 191 G01C1' 191 G01C1' 213 A02C1' 213 A02C1' 234 T03C1' 234 T03C1' 254 G04C1' 254 G04C1' 276 T05C1' 276 T05C1' 296 T06C1' 296 T06C1' 316 C07C1' 316 C07C1' 335 T08C1' 335 T08C1' 355 G09C1' 393 A-8C1' 374 C-9C1' 414 G-7C1' 393 A-8C1' 436 A-6C1' 414 G-7C1' 457 A-5C1' 436 A-6C1' 478 C-4C1' 457 A-5C1' 497 A-3C1' 478 C-4C1' 518 T-2C1' 497 A-3C1' 538 C-1C1' 518 T-2C1' 557 G01C1' 538 C-1C1' 579 A02C1' 557 G01C1' 600 T03C1' 579 A02C1' 620 G04C1' 600 T03C1' 642 T05C1' 620 G04C1' 662 T06C1' 642 T05C1' 682 C07C1' 662 T06C1' 701 T08C1' 682 C07C1' 721 G09C1' 701 T08C1' 9 C-9N1 28 A-8N9 28 A-8N9 49 G-7N9 49 G-7N9 71 A-6N9 71 A-6N9 92 A-5N9 92 A-5N9 113 C-4N1 113 C-4N1 132 A-3N9 132 A-3N9 153 T-2N1 153 T-2N1 173 C-1N1 173 C-1N1 192 G01N9 192 G01N9 214 A02N9 214 A02N9 235 T03N1 235 T03N1 255 G04N9 255 G04N9 277 T05N1 277 T05N1 297 T06N1 297 T06N1 317 C07N1 317 C07N1 336 T08N1 336 T08N1 356 G09N9 394 A-8N9 375 C-9N1 415 G-7N9 394 A-8N9 437 A-6N9 415 G-7N9 458 A-5N9 437 A-6N9 479 C-4N1 458 A-5N9 498 A-3N9 479 C-4N1 519 T-2N1 498 A-3N9 539 C-1N1 519 T-2N1 558 G01N9 539 C-1N1 580 A02N9 558 G01N9 601 T03N1 580 A02N9 621 G04N9 601 T03N1 643 T05N1 621 G04N9 663 T06N1 643 T05N1 683 C07N1 663 T06N1 702 T08N1 683 C07N1 722 G09N9 702 T08N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.02261*S + -7.85707 Y = 0.12541*S + 0.20215 Z = 0.99185*S + 0.15353 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.02261*S + -7.85707 Y = 0.12541*S + 0.20215 Z = 0.99185*S + 0.15353 >>>>>> HELIX ROTATION: 34.112 DISPLACEMENT: 3.3017 STATISTICS: OVERALL STANDARD DEV.: 0.9910 SIGMA(X): 1.3817, SIGMA(Y): 1.3420, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.3374, SIGMA(ROTATION): 8.110 THERE ARE 10.55 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 = 18 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.29308 0.06424 0.95393 107.04 86.32 17.46 -0.22802 0.01466 0.97355 103.18 89.16 13.21 -0.22202 -0.16845 0.96038 102.83 99.70 16.18 -0.18177 -0.15487 0.97107 100.47 98.91 13.82 -0.16323 -0.22550 0.96047 99.39 103.03 16.16 0.10980 -0.20626 0.97232 83.70 101.90 13.51 0.10675 -0.05318 0.99286 83.87 93.05 6.85 0.11744 -0.00244 0.99308 83.26 90.14 6.75 0.25756 0.09989 0.96109 75.07 84.27 16.04 0.07298 0.07980 0.99414 85.81 85.42 6.21 0.05343 0.04577 0.99752 86.94 87.38 4.03 0.07441 0.00200 0.99723 85.73 89.89 4.27 0.05034 0.05791 0.99705 87.11 86.68 4.40 -0.18779 -0.03157 0.98170 100.82 91.81 10.98 -0.14090 -0.04561 0.98897 98.10 92.61 8.52 -0.15970 -0.04348 0.98621 99.19 92.49 9.53 -0.22796 0.01530 0.97355 103.18 89.12 13.21 -0.05487 -0.00774 0.99846 93.15 90.44 3.18 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.22932 -0.14293 0.96280 103.26 98.22 15.68 -0.09449 -0.18870 0.97748 95.42 100.88 12.18 0.01190 -0.09125 0.99576 89.32 95.24 5.28 0.08421 -0.18381 0.97935 85.17 100.59 11.66 0.05786 -0.09665 0.99364 86.68 95.55 6.47 0.03919 -0.00342 0.99923 87.75 90.20 2.25 0.17488 0.06897 0.98217 79.93 86.05 10.84 0.07934 0.08816 0.99294 85.45 84.94 6.81 0.11766 0.01841 0.99288 83.24 88.95 6.84 -0.09933 0.03285 0.99451 95.70 88.12 6.01 -0.03628 -0.04315 0.99841 92.08 92.47 3.23 -0.10338 -0.08263 0.99120 95.93 94.74 7.61 0.00966 -0.16366 0.98647 89.45 99.42 9.44 0.17962 -0.04189 0.98284 79.65 92.40 10.63 0.08654 0.00765 0.99622 85.04 89.56 4.98 0.00955 -0.02610 0.99961 89.45 91.50 1.59 0.08849 -0.00342 0.99607 84.92 90.20 5.08 -0.08658 0.01993 0.99605 94.97 88.86 5.10 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.27422 -0.03381 0.96107 105.92 91.94 16.04 -0.22763 -0.12505 0.96568 103.16 97.18 15.05 -0.16822 -0.21148 0.96280 99.68 102.21 15.68 -0.02719 -0.21903 0.97534 91.56 102.65 12.75 -0.01473 -0.17805 0.98391 90.84 100.26 10.29 0.04471 -0.08467 0.99541 87.44 94.86 5.49 0.09082 0.01530 0.99575 84.79 89.12 5.28 0.09904 0.03259 0.99455 84.32 88.13 5.98 0.15972 0.01403 0.98706 80.81 89.20 9.23 0.00552 0.03364 0.99942 89.68 88.07 1.95 -0.00104 -0.00628 0.99998 90.06 90.36 0.36 -0.00724 -0.03275 0.99944 90.42 91.88 1.92 0.08309 -0.01897 0.99636 85.23 91.09 4.89 -0.02019 0.01780 0.99964 91.16 88.98 1.54 -0.05717 0.02341 0.99809 93.28 88.66 3.54 -0.06150 -0.02297 0.99784 93.53 91.32 3.76 0.01194 -0.01590 0.99980 89.32 90.91 1.14 0.00039 0.05566 0.99845 89.98 86.81 3.19 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 I= 12 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 13 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 14 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 15 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 16 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 17 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 13 14 15 16 17 18 I= 1 0 5 11 17 17 18 21 21 25 16 15 15 20 15 13 12 16 16 I= 2 5 0 6 12 12 15 20 20 23 16 14 13 18 14 13 11 15 16 I= 3 11 6 0 8 9 14 19 20 23 17 15 13 18 15 15 12 15 18 I= 4 17 12 8 0 2 8 15 16 17 14 12 10 13 13 14 11 11 15 I= 5 17 12 9 2 0 6 12 13 14 12 9 8 10 11 11 9 9 13 I= 6 18 15 14 8 6 0 6 7 8 7 5 4 4 6 8 7 4 8 I= 7 21 20 19 15 12 6 0 1 3 5 5 6 2 6 8 9 4 5 I= 8 21 20 20 16 13 7 1 0 3 5 6 7 3 6 8 9 5 5 I= 9 25 23 23 17 14 8 3 3 0 8 9 9 4 10 12 12 8 9 I= 10 16 16 17 14 12 7 5 5 8 0 2 3 5 1 3 5 2 1 I= 11 15 14 15 12 9 5 5 6 9 2 0 1 4 1 3 3 0 3 I= 12 15 13 13 10 8 4 6 7 9 3 1 0 5 2 4 3 1 5 I= 13 20 18 18 13 10 4 2 3 4 5 4 5 0 6 8 8 4 6 I= 14 15 14 15 13 11 6 6 6 10 1 1 2 6 0 2 3 2 2 I= 15 13 13 15 14 11 8 8 8 12 3 3 4 8 2 0 2 4 3 I= 16 12 11 12 11 9 7 9 9 12 5 3 3 8 3 2 0 4 5 I= 17 16 15 15 11 9 4 4 5 8 2 0 1 4 2 4 4 0 4 I= 18 16 16 18 15 13 8 5 5 9 1 3 5 6 2 3 5 4 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 1.98 17.34 3.09 -3.52 0.00 -0.00 12.10 9.81 3.15 -7.55 0.00 -0.00 -4.99 12.20 9.16 5.20 0.00 0.00 8.54 8.63 -1.58 -8.14 0.00 0.00 -3.23 15.84 1.83 -1.60 0.00****** 3.96 3.49 5.87 3.31****** 0.00 -9.54 9.90 0.38 4.17 0.00 0.00 5.85 10.06 -0.67 -5.18 0.00 0.00 -14.23 7.51 12.49 9.66 0.00 0.00 0.54 6.45 2.77 -4.70****** 0.00 -7.25 11.34 8.44 -2.51 0.00 0.00 0.93 2.05 6.08 6.40 0.00 0.00 -3.77 5.71 2.48 1.63****** 0.00 2.70 10.48 3.02 -4.70 0.00 0.00 -3.57 5.72 -2.45 9.68 0.00 0.00 2.01 6.50 -4.24 -1.68 0.00 0.00 -11.50 11.02 10.36 -2.65 -0.00 0.00 -5.83 3.57 12.52 -0.96 0.00 0.50 -4.87 3.84 1.88 -1.23 0.00 0.00 5.32 2.78 -1.24 -5.53 0.00 0.00 -4.02 -0.28 1.67 -2.22****** 0.00 3.22 -0.30 3.78 2.37 0.00 0.00 -1.06 -4.13 -3.23 1.33 0.00 0.00 5.95 4.72 4.75 -6.41 0.00 0.00 -2.08 -3.88 -5.15 13.77****** 0.00 9.00 2.81 1.18-12.01****** 0.00 -8.27 7.17 2.78 0.35 0.00 0.00 10.09 -3.31 -5.74 -1.92 0.00 0.00 -8.29 1.95 -0.95 -0.52****** 0.00 4.98 -0.03 -4.82 0.12 0.00 0.00 -8.58 -4.11 0.05 -5.17 0.00 0.00 -0.56 1.49 3.91 2.62 0.00 0.00 -3.65-12.68 -1.29 9.97****** 0.00 1.55 4.84 1.31-10.09****** 0.00 0.76 -3.08 0.00 0.00 0.00 0.00 2.91 -4.18 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 5.88 -2.66 5.24 0.23 36.32 3.34 -0.74 14.38 6.96 -2.30 5.41 0.24 3.74 -10.16 -7.21 -2.53 -0.03 6.01 -0.04 6.01 -0.06 29.28 3.68 0.62 14.81 2.61 -0.31 6.01 -0.10 -8.86 -13.56 -3.47 -2.67 1.07 8.13 -2.90 7.60 -0.45 34.54 3.04 -0.53 15.66 0.71 -2.70 7.65 -0.44 12.39 -7.26 -12.34 -1.33 1.11 2.50 -2.24 1.13 -0.11 31.31 3.29 -0.40 12.75 -0.32 -2.20 1.09 -0.11 -1.39 -15.39 0.05 -1.31 0.74 6.38 -1.62 6.17 -0.45 34.47 3.42 -0.23 8.82 -5.26 -1.71 6.12 -0.35 -7.99 -14.77 -1.34 -1.48 0.78 6.31 1.48 6.14 -0.92 36.08 3.27 0.20 4.61 -2.98 1.02 6.24 -0.80 14.10 -8.22 -9.33 -1.50 0.86 1.10 -0.77 0.78 -0.66 23.68 3.49 -0.36 5.28 0.24 0.80 0.75 -0.64 -3.99 -6.48 4.77 -0.94 0.44 3.66 1.51 -3.34 -0.11 36.31 3.48 0.66 5.84 -1.30 1.40 -3.36 -0.11 -8.32 -5.58 0.78 -1.27 -0.11 8.94 -0.05 8.94 0.49 32.01 3.36 -0.38 4.26 -8.17 -0.15 8.94 0.62 6.48 -5.72 -7.54 -0.88 0.10 2.32 -1.87 1.37 -0.49 35.31 3.27 0.10 1.85 -0.62 -1.87 1.37 -0.47 1.04 -10.19 -1.06 -1.21 1.09 1.56 0.43 1.50 -1.00 32.52 3.15 0.38 -0.21 0.29 -0.38 1.51 -0.98 8.88 -7.24 -0.02 -0.45 1.06 5.24 -5.22 -0.43 -0.75 33.54 3.44 -0.58 -0.01 1.92 -5.19 -0.71 -0.71 -2.21 -7.03 8.86 0.34 0.07 6.29 3.21 -5.41 -0.16 37.92 3.74 -0.21 -4.07 2.70 3.06 -5.49 -0.14 -17.13 -11.13 6.65 -0.32 -0.59 2.15 0.18 -2.14 0.26 36.10 3.14 -0.07 -0.27 -1.52 0.03 -2.14 0.31 8.50 -18.44 -10.48 -0.77 -0.30 2.67 2.35 -1.26 -0.14 36.16 3.15 0.34 -1.60 -3.16 2.37 -1.24 -0.10 7.58 -13.28 -1.98 -0.89 0.56 4.23 3.24 2.72 -0.13 29.09 3.14 -0.33 -1.31 -3.53 2.95 3.03 -0.13 11.91 -8.03 5.61 -0.25 0.86 4.15 -0.59 4.11 0.39 41.91 3.63 0.66 0.95 -0.62 -0.67 4.10 0.35 -18.61 -5.29 17.51 -0.24 0.88 - - - - - - - 1.21 2.95 - - - - -2.16 -1.10 1.22 0.89 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.