Analysis for 6TNA.pdb Chain 1 1. Number of nucleotides in the molecule: --------------- 75 A. # Nucleotides that are stacked: 71 (94.6667%) B. # nucs. that are basedpaired --- 44 (58.6667%) 1. # stacked: ----- 44 (100%) 2. # unstacked = --- 0 (0%) C. # nucs. that do not form bp --- 31 (41.3333%) 1. # stacked: ----- 27 (87.0968%) 2. # unstacked = --- 4 (12.9032%) 2. Number of stacking interactions: ------------ 88 A. Of the nucleotides that are stacked: 1. # Consecutive nucleotides: ------ 54 (61.3636%) 2. # Cross-strand stacks: ---------- 19 (21.5909%) 3. # Not consecutive or X-strand: -- 15 (17.0455%) B. of the nucleotides that are stacked: 1. BB: 55 (62.5%) 2. BN: 6 (6.8182%) 3. NB: 6 (6.8182%) 4. NN: 21 (23.8636%) 3. Nucleotide stacking types total #/% |consectutive | cross strand | not cont | | | | or x-strand | TOTAL 88 | 54 (61.36%) | 19 (21.59%) | 15 (17.05%) | A vs _ 23/26.14% | | | | A: 2/ 2.27% ( 8.70%) | 2/ 2.27% | 0/ 0.00% | 0/ 0.00% | C: 5/ 5.68% (26.32%) | 3/ 3.41% | 0/ 0.00% | 2/ 2.27% | G: 12/13.64% (41.38%) | 6/ 6.82% | 2/ 2.27% | 4/ 4.55% | U: 4/ 4.55% (23.53%) | 3/ 3.41% | 1/ 1.14% | 0/ 0.00% | C vs _ 19/21.59% | | | | A: 6/ 6.82% (26.09%) | 4/ 4.55% | 2/ 2.27% | 0/ 0.00% | C: 3/ 3.41% (15.79%) | 2/ 2.27% | 1/ 1.14% | 0/ 0.00% | G: 5/ 5.68% (17.24%) | 4/ 4.55% | 1/ 1.14% | 0/ 0.00% | U: 5/ 5.68% (29.41%) | 4/ 4.55% | 0/ 0.00% | 1/ 1.14% | G vs _ 29/32.95% | | | | A: 11/12.50% (47.83%) | 7/ 7.95% | 3/ 3.41% | 1/ 1.14% | C: 7/ 7.95% (36.84%) | 5/ 5.68% | 1/ 1.14% | 1/ 1.14% | G: 7/ 7.95% (24.14%) | 2/ 2.27% | 3/ 3.41% | 2/ 2.27% | U: 4/ 4.55% (23.53%) | 2/ 2.27% | 1/ 1.14% | 1/ 1.14% | U vs _ 17/19.32% | | | | A: 1/ 1.14% ( 4.35%) | 0/ 0.00% | 1/ 1.14% | 0/ 0.00% | C: 7/ 7.95% (36.84%) | 4/ 4.55% | 1/ 1.14% | 2/ 2.27% | G: 6/ 6.82% (20.69%) | 3/ 3.41% | 2/ 2.27% | 1/ 1.14% | U: 3/ 3.41% (17.65%) | 3/ 3.41% | 0/ 0.00% | 0/ 0.00% | 4. Distribution of number of consecutive nucleotides that are stacked: Number of Consecutive Nucs--------Instances of this 2 1 15 1 26 1 ------------------------------------------------------------------------------------- Raw Data: CS NT1 NT2 1||2 2||1 Dist Angle BP-stat BP-1 BP-2 . 1 G 2 C 0.7900 1.0000 2.7498 16.22055 BB 72 C 71 G . 1 G 72 C 0.0000 0.1533 6.2573 14.11298 BB 72 C 1 G * 1 G 73 A 0.3700 0.9700 4.0716 15.09439 NB 72 C 0 . . 2 C 3 G 0.5800 0.4500 3.8254 7.47786 BB 71 G 70 C * 2 C 72 C 0.0067 0.0000 5.7112 7.38129 BB 71 G 1 G . 3 G 4 G 0.7150 0.5950 2.9541 19.70744 BB 70 C 69 U * 3 G 71 G 0.5550 0.6950 3.4594 5.15467 BB 70 C 2 C . 4 G 5 A 0.7750 0.7625 3.1907 5.20204 BB 69 U 68 U * 4 G 70 C 0.3450 0.5400 3.3720 4.79300 BB 69 U 3 G . 5 A 6 U 0.9063 1.0000 3.3236 2.02890 BB 68 U 67 A * 5 A 69 U 0.1313 0.2333 3.6879 3.63647 BB 68 U 4 G . 6 U 7 U 0.4933 0.2733 2.8478 22.60619 BB 67 A 66 A . 7 U 49 C 0.7200 0.4800 3.5280 5.83144 BB 66 A 65 G * 7 U 67 A 0.2667 0.1750 3.2275 8.03047 BB 66 A 6 U . 8 U 13 C 0.5333 0.4200 3.4789 17.65485 BN 0 . 22 G . 8 U 15 G 0.4667 0.0000 4.9704 27.14985 NN 0 . 0 . . 9 A 22 G 0.0000 0.1900 3.9263 21.16064 BN 0 . 13 C . 9 A 45 G 0.3850 0.5050 3.3996 13.49349 NN 0 . 0 . . 9 A 46 G 1.0000 0.5750 3.4630 15.81894 NN 0 . 0 . . 10 G 11 C 0.6600 1.0000 2.7095 12.25532 BB 25 C 24 G * 10 G 26 G 0.8200 0.4200 3.8022 8.07267 BB 25 C 44 A . 11 C 12 U 0.4733 0.5933 3.6661 6.54934 BB 24 G 23 A . 12 U 13 C 0.6267 0.8667 3.6883 8.52087 BB 23 A 22 G * 12 U 24 G 0.1267 0.1300 3.9161 7.44863 BB 23 A 11 C * 13 C 23 A 0.1667 0.0850 3.4796 3.37794 BB 22 G 12 U . 14 A 15 G 0.8850 0.7050 3.5215 13.90101 NN 0 . 0 . * 14 A 22 G 0.7150 0.5650 3.1011 6.64652 BN 0 . 13 C . 15 G 59 U 0.0400 0.2933 3.8688 17.06239 NN 0 . 0 . . 18 G 57 G 0.8050 0.8650 3.1613 7.57274 NN 0 . 0 . . 18 G 58 A 1.0000 0.9800 3.2696 5.40091 NN 0 . 0 . . 19 G 57 G 0.9000 0.5450 2.9731 25.59452 NN 0 . 0 . . 21 A 46 G 1.0000 0.9300 3.4447 9.02976 NN 0 . 0 . . 21 A 48 C 0.8900 1.0000 3.3357 13.47352 NN 0 . 0 . . 22 G 23 A 0.5750 0.4600 3.0833 2.16100 BB 13 C 12 U . 23 A 24 G 0.9100 0.6950 3.0957 13.43151 BB 12 U 11 C . 24 G 25 C 0.8800 1.0000 3.1710 4.75870 BB 11 C 10 G . 25 C 26 G 1.0000 0.3900 3.0805 12.36752 BB 10 G 44 A . 26 G 27 C 0.9300 1.0000 3.0274 19.24552 BB 44 A 43 G * 26 G 45 G 0.0000 0.0800 5.0178 28.02055 NB 44 A 0 . . 27 C 28 C 0.4933 0.3600 3.1517 9.45167 BB 43 G 42 G . 28 C 29 A 0.7467 0.2550 3.0761 11.84815 BB 42 G 41 U * 28 C 43 G 0.3000 0.2500 3.1289 6.93799 BB 42 G 27 C . 29 A 30 G 0.6200 0.6000 3.6610 10.66781 BB 41 U 40 C * 29 A 42 G 0.6050 0.5500 3.4110 5.25951 BB 41 U 28 C . 30 G 31 A 1.0000 1.0000 3.3290 10.09845 BB 40 C 39 U * 30 G 41 U 0.3400 0.5333 3.2626 8.64785 BB 40 C 29 A . 31 A 32 C 1.0000 1.0000 3.6032 13.88479 NB 39 U 0 . . 32 C 33 U 0.7800 0.9467 4.3670 16.73841 NN 0 . 0 . . 34 G 35 A 0.6950 0.7150 3.0780 8.50253 NN 0 . 0 . . 35 A 36 A 0.6550 0.6750 3.2876 9.11255 NN 0 . 0 . . 36 A 37 G 0.9000 0.4500 3.2454 8.80660 NN 0 . 0 . . 37 G 38 A 0.8950 0.9550 3.5228 4.37923 NN 0 . 0 . . 38 A 39 U 0.6700 1.0000 3.1657 23.25383 BN 0 . 31 A . 39 U 40 C 0.8600 0.4933 3.2029 7.98758 BB 31 A 30 G . 40 C 41 U 0.4067 0.1667 2.5842 13.72986 BB 30 G 29 A . 41 U 42 G 0.5067 0.2900 3.6953 2.95652 BB 29 A 28 C . 42 G 43 G 0.8000 0.8350 3.2362 1.36085 BB 28 C 27 C . 43 G 44 A 0.8350 0.8650 3.7504 3.28612 BB 27 C 26 G . 44 A 45 G 0.9750 0.8550 3.6070 13.56261 NB 26 G 0 . . 48 C 59 U 0.4133 0.3733 3.3243 13.51442 NN 0 . 0 . . 49 C 50 U 0.3733 0.2067 2.4959 10.33491 BB 65 G 64 A * 49 C 66 A 0.3533 0.2250 3.3487 1.87434 BB 65 G 7 U . 50 U 51 G 0.3133 0.1200 3.2277 5.86311 BB 64 A 63 C * 50 U 65 G 0.4867 0.2300 2.9926 8.42780 BB 64 A 49 C . 51 G 52 U 0.8500 1.0000 3.5444 4.55431 BB 63 C 62 A * 51 G 64 A 0.7350 0.7850 3.4835 12.99338 BB 63 C 50 U . 52 U 53 G 0.5600 0.3050 3.2260 3.68845 BB 62 A 61 C . 53 G 54 U 0.9800 1.0000 3.6184 6.42881 NB 61 C 0 . * 53 G 62 A 0.6000 0.5850 3.2452 3.25069 BB 61 C 52 U . 54 U 55 U 1.0000 1.0000 3.3895 23.37545 NN 0 . 0 . * 54 U 61 C 0.0000 0.0364 3.8183 6.32079 BN 0 . 53 G . 56 C 57 G 0.8933 0.3750 3.5350 12.75784 NN 0 . 0 . . 58 A 61 C 0.8200 0.8364 3.2004 10.96343 BN 0 . 53 G . 59 U 60 C 1.0000 0.9467 3.7986 21.63077 NN 0 . 0 . . 61 C 62 A 0.1182 0.0400 3.1325 2.62825 BB 53 G 52 U . 62 A 63 C 0.7950 1.0000 3.7094 7.41571 BB 52 U 51 G . 63 C 64 A 0.5800 0.0600 2.4522 18.00293 BB 51 G 50 U . 64 A 65 G 0.7900 0.7350 3.4527 6.60657 BB 50 U 49 C . 65 G 66 A 0.7750 0.6750 3.2162 4.56104 BB 49 C 7 U . 66 A 67 A 0.8300 0.8500 3.5108 2.66633 BB 7 U 6 U . 67 A 68 U 0.8750 1.0000 3.4070 12.00379 BB 6 U 5 A . 68 U 69 U 0.7867 0.5667 2.9014 10.79355 BB 5 A 4 G . 69 U 70 C 0.2267 0.1933 3.0444 6.36928 BB 4 G 3 G . 70 C 71 G 0.7600 0.1650 2.4615 15.60988 BB 3 G 2 C . 71 G 72 C 0.7600 1.0000 3.5037 5.42063 BB 2 C 1 G . 72 C 73 A 0.8933 0.3500 2.6651 19.40435 NB 1 G 0 . . 73 A 74 C 0.8750 1.0000 3.6294 6.48848 NN 0 . 0 . . 74 C 75 C 1.0000 1.0000 3.8372 18.66833 NN 0 . 0 .