ID code: '4ENA' 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' --------------------------------------------------------------------------------- 21 C1' GTP A 1 beta 16 22 19 44 C1' G A 2 beta 39 45 42 67 C1' G A 3 beta 62 68 65 90 C1' C A 4 beta 85 91 88 110 C1' G A 5 beta 105 111 108 133 C1' A A 6 beta 128 134 131 155 C1' U A 7 beta 150 156 153 175 C1' G A 8 beta 170 176 173 198 C1' A A 9 beta 193 199 196 220 C1' G A 10 beta 215 221 218 243 C1' G A 11 beta 238 244 241 266 C1' C A 12 beta 261 267 264 286 C1' C A 13 beta 281 287 284 306 C1' C A 14 beta 301 307 304 326 C1' G A 15 beta 321 327 324 349 C1' C A 16 beta 344 350 347 369 C1' C A 17 beta 364 370 367 389 C1' C A 18 beta 384 390 387 409 C1' A A 19 beta 404 410 407 431 C1' A A 20 beta 426 432 429 453 C1' A A 21 beta 448 454 451 475 C1' C A 22 beta 470 476 473 495 C1' U A 23 beta 490 496 493 515 C1' G A 24 beta 510 516 513 538 C1' C A 25 beta 533 539 536 558 C1' C A 26 beta 553 559 556 578 C1' C A 27 beta 573 579 576 598 C1' U A 28 beta 593 599 596 618 C1' G A 29 beta 613 619 616 641 C1' A A 30 beta 636 642 639 663 C1' A A 31 beta 658 664 661 685 C1' A A 32 beta 680 686 683 707 C1' A A 33 beta 702 708 705 729 C1' G A 34 beta 724 730 727 752 C1' G A 35 beta 747 753 750 775 C1' G A 36 beta 770 776 773 798 C1' C A 37 beta 793 799 796 818 C1' U A 38 beta 813 819 816 838 C1' G A 39 beta 833 839 836 861 C1' A A 40 beta 856 862 859 883 C1' U A 41 beta 878 884 881 903 C1' G A 42 beta 898 904 901 926 C1' G A 43 beta 921 927 924 949 C1' C A 44 beta 944 950 947 969 C1' C A 45 beta 964 970 967 989 C1' U A 46 beta 984 990 987 1009 C1' C A 47 beta 1004 1010 1007 1029 C1' U A 48 beta 1024 1030 1027 1049 C1' A A 49 beta 1044 1050 1047 1071 C1' C A 50 beta 1066 1072 1069 1091 C1' U A 51 beta 1086 1092 1089 1111 C1' G A 52 beta 1106 1112 1109 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 19 C2' GTP A 1 OK 21 17 20 42 C2' G A 2 OK 44 40 43 65 C2' G A 3 OK 67 63 66 88 C2' C A 4 OK 90 86 89 108 C2' G A 5 OK 110 106 109 131 C2' A A 6 OK 133 129 132 153 C2' U A 7 OK 155 151 154 173 C2' G A 8 OK 175 171 174 196 C2' A A 9 OK 198 194 197 218 C2' G A 10 OK 220 216 219 241 C2' G A 11 OK 243 239 242 264 C2' C A 12 OK 266 262 265 284 C2' C A 13 OK 286 282 285 304 C2' C A 14 OK 306 302 305 324 C2' G A 15 OK 326 322 325 347 C2' C A 16 OK 349 345 348 367 C2' C A 17 OK 369 365 368 387 C2' C A 18 OK 389 385 388 407 C2' A A 19 OK 409 405 408 429 C2' A A 20 OK 431 427 430 451 C2' A A 21 OK 453 449 452 473 C2' C A 22 OK 475 471 474 493 C2' U A 23 OK 495 491 494 513 C2' G A 24 OK 515 511 514 536 C2' C A 25 OK 538 534 537 556 C2' C A 26 OK 558 554 557 576 C2' C A 27 OK 578 574 577 596 C2' U A 28 OK 598 594 597 616 C2' G A 29 OK 618 614 617 639 C2' A A 30 OK 641 637 640 661 C2' A A 31 OK 663 659 662 683 C2' A A 32 OK 685 681 684 705 C2' A A 33 OK 707 703 706 727 C2' G A 34 OK 729 725 728 750 C2' G A 35 OK 752 748 751 773 C2' G A 36 OK 775 771 774 796 C2' C A 37 OK 798 794 797 816 C2' U A 38 OK 818 814 817 836 C2' G A 39 OK 838 834 837 859 C2' A A 40 OK 861 857 860 881 C2' U A 41 OK 883 879 882 901 C2' G A 42 OK 903 899 902 924 C2' G A 43 OK 926 922 925 947 C2' C A 44 OK 949 945 948 967 C2' C A 45 OK 969 965 968 987 C2' U A 46 OK 989 985 988 1007 C2' C A 47 OK 1009 1005 1008 1027 C2' U A 48 OK 1029 1025 1028 1047 C2' A A 49 OK 1049 1045 1048 1069 C2' C A 50 OK 1071 1067 1070 1089 C2' U A 51 OK 1091 1087 1090 1109 C2' G A 52 OK 1111 1107 1110 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 17 C3' GTP A 1 OK 15 18 19 40 C3' G A 2 OK 38 41 42 63 C3' G A 3 OK 61 64 65 86 C3' C A 4 OK 84 87 88 106 C3' G A 5 OK 104 107 108 129 C3' A A 6 OK 127 130 131 151 C3' U A 7 OK 149 152 153 171 C3' G A 8 OK 169 172 173 194 C3' A A 9 OK 192 195 196 216 C3' G A 10 OK 214 217 218 239 C3' G A 11 OK 237 240 241 262 C3' C A 12 OK 260 263 264 282 C3' C A 13 OK 280 283 284 302 C3' C A 14 OK 300 303 304 322 C3' G A 15 OK 320 323 324 345 C3' C A 16 OK 343 346 347 365 C3' C A 17 OK 363 366 367 385 C3' C A 18 OK 383 386 387 405 C3' A A 19 OK 403 406 407 427 C3' A A 20 OK 425 428 429 449 C3' A A 21 OK 447 450 451 471 C3' C A 22 OK 469 472 473 491 C3' U A 23 OK 489 492 493 511 C3' G A 24 OK 509 512 513 534 C3' C A 25 OK 532 535 536 554 C3' C A 26 OK 552 555 556 574 C3' C A 27 OK 572 575 576 594 C3' U A 28 OK 592 595 596 614 C3' G A 29 OK 612 615 616 637 C3' A A 30 OK 635 638 639 659 C3' A A 31 OK 657 660 661 681 C3' A A 32 OK 679 682 683 703 C3' A A 33 OK 701 704 705 725 C3' G A 34 OK 723 726 727 748 C3' G A 35 OK 746 749 750 771 C3' G A 36 OK 769 772 773 794 C3' C A 37 OK 792 795 796 814 C3' U A 38 OK 812 815 816 834 C3' G A 39 OK 832 835 836 857 C3' A A 40 OK 855 858 859 879 C3' U A 41 OK 877 880 881 899 C3' G A 42 OK 897 900 901 922 C3' G A 43 OK 920 923 924 945 C3' C A 44 OK 943 946 947 965 C3' C A 45 OK 963 966 967 985 C3' U A 46 OK 983 986 987 1005 C3' C A 47 OK 1003 1006 1007 1025 C3' U A 48 OK 1023 1026 1027 1045 C3' A A 49 OK 1043 1046 1047 1067 C3' C A 50 OK 1065 1068 1069 1087 C3' U A 51 OK 1085 1088 1089 1107 C3' G A 52 OK 1105 1108 1109 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 15 C4' GTP A 1 OK 17 14 16 38 C4' G A 2 OK 40 37 39 61 C4' G A 3 OK 63 60 62 84 C4' C A 4 OK 86 83 85 104 C4' G A 5 OK 106 103 105 127 C4' A A 6 OK 129 126 128 149 C4' U A 7 OK 151 148 150 169 C4' G A 8 OK 171 168 170 192 C4' A A 9 OK 194 191 193 214 C4' G A 10 OK 216 213 215 237 C4' G A 11 OK 239 236 238 260 C4' C A 12 OK 262 259 261 280 C4' C A 13 OK 282 279 281 300 C4' C A 14 OK 302 299 301 320 C4' G A 15 OK 322 319 321 343 C4' C A 16 OK 345 342 344 363 C4' C A 17 OK 365 362 364 383 C4' C A 18 OK 385 382 384 403 C4' A A 19 OK 405 402 404 425 C4' A A 20 OK 427 424 426 447 C4' A A 21 OK 449 446 448 469 C4' C A 22 OK 471 468 470 489 C4' U A 23 OK 491 488 490 509 C4' G A 24 OK 511 508 510 532 C4' C A 25 OK 534 531 533 552 C4' C A 26 OK 554 551 553 572 C4' C A 27 OK 574 571 573 592 C4' U A 28 OK 594 591 593 612 C4' G A 29 OK 614 611 613 635 C4' A A 30 OK 637 634 636 657 C4' A A 31 OK 659 656 658 679 C4' A A 32 OK 681 678 680 701 C4' A A 33 OK 703 700 702 723 C4' G A 34 OK 725 722 724 746 C4' G A 35 OK 748 745 747 769 C4' G A 36 OK 771 768 770 792 C4' C A 37 OK 794 791 793 812 C4' U A 38 OK 814 811 813 832 C4' G A 39 OK 834 831 833 855 C4' A A 40 OK 857 854 856 877 C4' U A 41 OK 879 876 878 897 C4' G A 42 OK 899 896 898 920 C4' G A 43 OK 922 919 921 943 C4' C A 44 OK 945 942 944 963 C4' C A 45 OK 965 962 964 983 C4' U A 46 OK 985 982 984 1003 C4' C A 47 OK 1005 1002 1004 1023 C4' U A 48 OK 1025 1022 1024 1043 C4' A A 49 OK 1045 1042 1044 1065 C4' C A 50 OK 1067 1064 1066 1085 C4' U A 51 OK 1087 1084 1086 1105 C4' G A 52 OK 1107 1104 1106 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 14 C5' GTP A 1 13 15 37 C5' G A 2 36 38 60 C5' G A 3 59 61 83 C5' C A 4 82 84 103 C5' G A 5 102 104 126 C5' A A 6 125 127 148 C5' U A 7 147 149 168 C5' G A 8 167 169 191 C5' A A 9 190 192 213 C5' G A 10 212 214 236 C5' G A 11 235 237 259 C5' C A 12 258 260 279 C5' C A 13 278 280 299 C5' C A 14 298 300 319 C5' G A 15 318 320 342 C5' C A 16 341 343 362 C5' C A 17 361 363 382 C5' C A 18 381 383 402 C5' A A 19 401 403 424 C5' A A 20 423 425 446 C5' A A 21 445 447 468 C5' C A 22 467 469 488 C5' U A 23 487 489 508 C5' G A 24 507 509 531 C5' C A 25 530 532 551 C5' C A 26 550 552 571 C5' C A 27 570 572 591 C5' U A 28 590 592 611 C5' G A 29 610 612 634 C5' A A 30 633 635 656 C5' A A 31 655 657 678 C5' A A 32 677 679 700 C5' A A 33 699 701 722 C5' G A 34 721 723 745 C5' G A 35 744 746 768 C5' G A 36 767 769 791 C5' C A 37 790 792 811 C5' U A 38 810 812 831 C5' G A 39 830 832 854 C5' A A 40 853 855 876 C5' U A 41 875 877 896 C5' G A 42 895 897 919 C5' G A 43 918 920 942 C5' C A 44 941 943 962 C5' C A 45 961 963 982 C5' U A 46 981 983 1002 C5' C A 47 1001 1003 1022 C5' U A 48 1021 1023 1042 C5' A A 49 1041 1043 1064 C5' C A 50 1063 1065 1084 C5' U A 51 1083 1085 1104 C5' G A 52 1103 1105 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 18 34 35 36 56 P G A 3 distorted distorted 41 57 58 59 79 P C A 4 distorted distorted 64 80 81 82 99 P G A 5 distorted distorted 87 100 101 102 122 P A A 6 distorted distorted 107 123 124 125 144 P U A 7 distorted distorted 130 145 146 147 164 P G A 8 distorted distorted 152 165 166 167 187 P A A 9 distorted distorted 172 188 189 190 209 P G A 10 distorted distorted 195 210 211 212 232 P G A 11 distorted distorted 217 233 234 235 255 P C A 12 distorted distorted 240 256 257 258 275 P C A 13 distorted distorted 263 276 277 278 295 P C A 14 distorted distorted 283 296 297 298 315 P G A 15 distorted distorted 303 316 317 318 338 P C A 16 distorted distorted 323 339 340 341 358 P C A 17 distorted distorted 346 359 360 361 378 P C A 18 distorted distorted 366 379 380 381 398 P A A 19 distorted distorted 386 399 400 401 420 P A A 20 distorted distorted 406 421 422 423 442 P A A 21 distorted distorted 428 443 444 445 464 P C A 22 distorted distorted 450 465 466 467 484 P U A 23 distorted distorted 472 485 486 487 504 P G A 24 distorted distorted 492 505 506 507 527 P C A 25 distorted distorted 512 528 529 530 547 P C A 26 distorted distorted 535 548 549 550 567 P C A 27 distorted distorted 555 568 569 570 587 P U A 28 distorted distorted 575 588 589 590 607 P G A 29 distorted distorted 595 608 609 610 630 P A A 30 distorted distorted 615 631 632 633 652 P A A 31 distorted distorted 638 653 654 655 674 P A A 32 distorted distorted 660 675 676 677 696 P A A 33 distorted distorted 682 697 698 699 718 P G A 34 distorted distorted 704 719 720 721 741 P G A 35 distorted distorted 726 742 743 744 764 P G A 36 distorted distorted 749 765 766 767 787 P C A 37 distorted distorted 772 788 789 790 807 P U A 38 distorted distorted 795 808 809 810 827 P G A 39 distorted distorted 815 828 829 830 850 P A A 40 distorted distorted 835 851 852 853 872 P U A 41 distorted distorted 858 873 874 875 892 P G A 42 distorted distorted 880 893 894 895 915 P G A 43 distorted distorted 900 916 917 918 938 P C A 44 distorted distorted 923 939 940 941 958 P C A 45 distorted distorted 946 959 960 961 978 P U A 46 distorted distorted 966 979 980 981 998 P C A 47 distorted distorted 986 999 1000 1001 1018 P U A 48 distorted distorted 1006 1019 1020 1021 1038 P A A 49 distorted distorted 1026 1039 1040 1041 1060 P C A 50 distorted distorted 1046 1061 1062 1063 1080 P U A 51 distorted distorted 1068 1081 1082 1083 1100 P G A 52 distorted distorted 1088 1101 1102 1103 ---------------------------------------------------------------------------------