ID code: '1T28' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' C A 4 alpha beta 103 123 109 106 139 C1' A A 5 alpha beta 134 156 140 137 172 C1' U A 6 alpha beta 167 187 173 170 202 C1' C A 7 alpha beta 197 217 203 200 233 C1' G A 8 alpha beta 228 251 234 231 267 C1' U A 9 alpha beta 262 282 268 265 297 C1' U A 10 alpha beta 292 312 298 295 327 C1' G A 11 alpha beta 322 345 328 325 361 C1' A A 12 alpha beta 356 378 362 359 394 C1' G A 13 alpha beta 389 412 395 392 428 C1' A A 14 alpha beta 423 445 429 426 461 C1' A A 15 alpha beta 456 478 462 459 494 C1' A A 16 alpha beta 489 511 495 492 527 C1' A A 17 alpha beta 522 544 528 525 560 C1' C A 18 alpha beta 555 575 561 558 591 C1' G A 19 alpha beta 586 609 592 589 625 C1' A A 20 alpha beta 620 642 626 623 658 C1' A A 21 alpha beta 653 675 659 656 691 C1' A A 22 alpha beta 686 708 692 689 724 C1' C A 23 alpha beta 719 739 725 722 755 C1' A A 24 alpha beta 750 772 756 753 788 C1' G A 25 alpha beta 783 806 789 786 822 C1' A A 26 alpha beta 817 839 823 820 855 C1' C A 27 alpha beta 850 870 856 853 886 C1' G A 28 alpha beta 881 904 887 884 920 C1' G A 29 alpha beta 915 938 921 918 954 C1' U A 30 alpha beta 949 969 955 952 984 C1' G A 31 alpha beta 979 1002 985 982 1018 C1' G A 32 alpha beta 1013 1036 1019 1016 1052 C1' C A 33 alpha beta 1047 1067 1053 1050 1083 C1' C A 34 alpha beta 1078 1099 1084 1081 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' C A 4 OK OK 108 104 121 107 137 C2' A A 5 OK OK 139 135 154 138 170 C2' U A 6 OK OK 172 168 185 171 200 C2' C A 7 OK OK 202 198 215 201 231 C2' G A 8 OK OK 233 229 249 232 265 C2' U A 9 OK OK 267 263 280 266 295 C2' U A 10 OK OK 297 293 310 296 325 C2' G A 11 OK OK 327 323 343 326 359 C2' A A 12 OK OK 361 357 376 360 392 C2' G A 13 OK OK 394 390 410 393 426 C2' A A 14 OK OK 428 424 443 427 459 C2' A A 15 OK OK 461 457 476 460 492 C2' A A 16 OK OK 494 490 509 493 525 C2' A A 17 OK OK 527 523 542 526 558 C2' C A 18 OK OK 560 556 573 559 589 C2' G A 19 OK OK 591 587 607 590 623 C2' A A 20 OK OK 625 621 640 624 656 C2' A A 21 OK OK 658 654 673 657 689 C2' A A 22 OK OK 691 687 706 690 722 C2' C A 23 OK OK 724 720 737 723 753 C2' A A 24 OK OK 755 751 770 754 786 C2' G A 25 OK OK 788 784 804 787 820 C2' A A 26 OK OK 822 818 837 821 853 C2' C A 27 OK OK 855 851 868 854 884 C2' G A 28 OK OK 886 882 902 885 918 C2' G A 29 OK OK 920 916 936 919 952 C2' U A 30 OK OK 954 950 967 953 982 C2' G A 31 OK OK 984 980 1000 983 1016 C2' G A 32 OK OK 1018 1014 1034 1017 1050 C2' C A 33 OK OK 1052 1048 1065 1051 1081 C2' C A 34 OK OK 1083 1079 1097 1082 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' C A 4 OK OK 102 120 105 106 135 C3' A A 5 OK OK 133 153 136 137 168 C3' U A 6 OK OK 166 184 169 170 198 C3' C A 7 OK OK 196 214 199 200 229 C3' G A 8 OK OK 227 248 230 231 263 C3' U A 9 OK OK 261 279 264 265 293 C3' U A 10 OK OK 291 309 294 295 323 C3' G A 11 OK OK 321 342 324 325 357 C3' A A 12 OK OK 355 375 358 359 390 C3' G A 13 OK OK 388 409 391 392 424 C3' A A 14 OK OK 422 442 425 426 457 C3' A A 15 OK OK 455 475 458 459 490 C3' A A 16 OK OK 488 508 491 492 523 C3' A A 17 OK OK 521 541 524 525 556 C3' C A 18 OK OK 554 572 557 558 587 C3' G A 19 OK OK 585 606 588 589 621 C3' A A 20 OK OK 619 639 622 623 654 C3' A A 21 OK OK 652 672 655 656 687 C3' A A 22 OK OK 685 705 688 689 720 C3' C A 23 OK OK 718 736 721 722 751 C3' A A 24 OK OK 749 769 752 753 784 C3' G A 25 OK OK 782 803 785 786 818 C3' A A 26 OK OK 816 836 819 820 851 C3' C A 27 OK OK 849 867 852 853 882 C3' G A 28 OK OK 880 901 883 884 916 C3' G A 29 OK OK 914 935 917 918 950 C3' U A 30 OK OK 948 966 951 952 980 C3' G A 31 OK OK 978 999 981 982 1014 C3' G A 32 OK OK 1012 1033 1015 1016 1048 C3' C A 33 OK OK 1046 1064 1049 1050 1079 C3' C A 34 OK OK 1077 1095 1080 1081 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' C A 4 OK OK 104 119 101 103 133 C4' A A 5 OK OK 135 152 132 134 166 C4' U A 6 OK OK 168 183 165 167 196 C4' C A 7 OK OK 198 213 195 197 227 C4' G A 8 OK OK 229 247 226 228 261 C4' U A 9 OK OK 263 278 260 262 291 C4' U A 10 OK OK 293 308 290 292 321 C4' G A 11 OK OK 323 341 320 322 355 C4' A A 12 OK OK 357 374 354 356 388 C4' G A 13 OK OK 390 408 387 389 422 C4' A A 14 OK OK 424 441 421 423 455 C4' A A 15 OK OK 457 474 454 456 488 C4' A A 16 OK OK 490 507 487 489 521 C4' A A 17 OK OK 523 540 520 522 554 C4' C A 18 OK OK 556 571 553 555 585 C4' G A 19 OK OK 587 605 584 586 619 C4' A A 20 OK OK 621 638 618 620 652 C4' A A 21 OK OK 654 671 651 653 685 C4' A A 22 OK OK 687 704 684 686 718 C4' C A 23 OK OK 720 735 717 719 749 C4' A A 24 OK OK 751 768 748 750 782 C4' G A 25 OK OK 784 802 781 783 816 C4' A A 26 OK OK 818 835 815 817 849 C4' C A 27 OK OK 851 866 848 850 880 C4' G A 28 OK OK 882 900 879 881 914 C4' G A 29 OK OK 916 934 913 915 948 C4' U A 30 OK OK 950 965 947 949 978 C4' G A 31 OK OK 980 998 977 979 1012 C4' G A 32 OK OK 1014 1032 1011 1013 1046 C4' C A 33 OK OK 1048 1063 1045 1047 1077 C4' C A 34 OK OK 1079 1094 1076 1078 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' C A 4 OK OK 100 117 118 102 132 C5' A A 5 OK OK 131 150 151 133 165 C5' U A 6 OK OK 164 181 182 166 195 C5' C A 7 OK OK 194 211 212 196 226 C5' G A 8 OK OK 225 245 246 227 260 C5' U A 9 OK OK 259 276 277 261 290 C5' U A 10 OK OK 289 306 307 291 320 C5' G A 11 OK OK 319 339 340 321 354 C5' A A 12 OK OK 353 372 373 355 387 C5' G A 13 OK OK 386 406 407 388 421 C5' A A 14 OK OK 420 439 440 422 454 C5' A A 15 OK OK 453 472 473 455 487 C5' A A 16 OK OK 486 505 506 488 520 C5' A A 17 OK OK 519 538 539 521 553 C5' C A 18 OK OK 552 569 570 554 584 C5' G A 19 OK OK 583 603 604 585 618 C5' A A 20 OK OK 617 636 637 619 651 C5' A A 21 OK OK 650 669 670 652 684 C5' A A 22 OK OK 683 702 703 685 717 C5' C A 23 OK OK 716 733 734 718 748 C5' A A 24 OK OK 747 766 767 749 781 C5' G A 25 OK OK 780 800 801 782 815 C5' A A 26 OK OK 814 833 834 816 848 C5' C A 27 OK OK 847 864 865 849 879 C5' G A 28 OK OK 878 898 899 880 913 C5' G A 29 OK OK 912 932 933 914 947 C5' U A 30 OK OK 946 963 964 948 977 C5' G A 31 OK OK 976 996 997 978 1011 C5' G A 32 OK OK 1010 1030 1031 1012 1045 C5' C A 33 OK OK 1044 1061 1062 1046 1076 C5' C A 34 OK OK 1075 1092 1093 1077 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P C A 4 distorted distorted 75 98 99 100 128 P A A 5 distorted distorted 105 129 130 131 161 P U A 6 distorted distorted 136 162 163 164 191 P C A 7 distorted distorted 169 192 193 194 222 P G A 8 distorted distorted 199 223 224 225 256 P U A 9 distorted distorted 230 257 258 259 286 P U A 10 distorted distorted 264 287 288 289 316 P G A 11 distorted distorted 294 317 318 319 350 P A A 12 distorted distorted 324 351 352 353 383 P G A 13 distorted distorted 358 384 385 386 417 P A A 14 distorted distorted 391 418 419 420 450 P A A 15 distorted distorted 425 451 452 453 483 P A A 16 distorted distorted 458 484 485 486 516 P A A 17 distorted distorted 491 517 518 519 549 P C A 18 distorted distorted 524 550 551 552 580 P G A 19 distorted distorted 557 581 582 583 614 P A A 20 distorted distorted 588 615 616 617 647 P A A 21 distorted distorted 622 648 649 650 680 P A A 22 distorted distorted 655 681 682 683 713 P C A 23 distorted distorted 688 714 715 716 744 P A A 24 distorted distorted 721 745 746 747 777 P G A 25 distorted distorted 752 778 779 780 811 P A A 26 distorted distorted 785 812 813 814 844 P C A 27 distorted distorted 819 845 846 847 875 P G A 28 distorted distorted 852 876 877 878 909 P G A 29 distorted distorted 883 910 911 912 943 P U A 30 distorted distorted 917 944 945 946 973 P G A 31 distorted distorted 951 974 975 976 1007 P G A 32 distorted distorted 981 1008 1009 1010 1041 P C A 33 distorted distorted 1015 1042 1043 1044 1072 P C A 34 distorted distorted 1049 1073 1074 1075 ---------------------------------------------------------------------------------