ID code: '1ULL' 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' --------------------------------------------------------------------------------- 8 C1' G A 1 alpha beta 3 24 9 6 40 C1' G A 2 alpha beta 35 58 41 38 74 C1' C A 3 alpha beta 69 89 75 72 105 C1' U A 4 alpha beta 100 120 106 103 135 C1' G A 5 alpha beta 130 153 136 133 169 C1' G A 6 alpha beta 164 187 170 167 203 C1' A A 7 alpha beta 198 220 204 201 236 C1' C A 8 alpha beta 231 251 237 234 267 C1' U A 9 alpha beta 262 282 268 265 297 C1' C A 10 alpha beta 292 312 298 295 328 C1' G A 11 alpha beta 323 346 329 326 362 C1' U A 12 alpha beta 357 377 363 360 392 C1' A A 13 alpha beta 387 409 393 390 425 C1' C A 14 alpha beta 420 440 426 423 456 C1' U A 15 alpha beta 451 471 457 454 486 C1' U A 16 alpha beta 481 501 487 484 516 C1' C A 17 alpha beta 511 531 517 514 547 C1' G A 18 alpha beta 542 565 548 545 581 C1' G A 19 alpha beta 576 599 582 579 615 C1' U A 20 alpha beta 610 630 616 613 645 C1' A A 21 alpha beta 640 662 646 643 678 C1' C A 22 alpha beta 673 693 679 676 709 C1' U A 23 alpha beta 704 724 710 707 739 C1' G A 24 alpha beta 734 757 740 737 773 C1' G A 25 alpha beta 768 791 774 771 807 C1' A A 26 alpha beta 802 824 808 805 840 C1' G A 27 alpha beta 835 858 841 838 874 C1' A A 28 alpha beta 869 891 875 872 907 C1' A A 29 alpha beta 902 924 908 905 940 C1' A A 30 alpha beta 935 957 941 938 973 C1' C A 31 alpha beta 968 988 974 971 1004 C1' A A 32 alpha beta 999 1021 1005 1002 1037 C1' G A 33 alpha beta 1032 1055 1038 1035 1071 C1' C A 34 alpha beta 1066 1086 1072 1069 1102 C1' C A 35 alpha beta 1097 1117 1103 1100 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6 C2' G A 1 OK OK 8 4 22 7 38 C2' G A 2 OK OK 40 36 56 39 72 C2' C A 3 OK OK 74 70 87 73 103 C2' U A 4 OK OK 105 101 118 104 133 C2' G A 5 OK OK 135 131 151 134 167 C2' G A 6 OK OK 169 165 185 168 201 C2' A A 7 OK OK 203 199 218 202 234 C2' C A 8 OK OK 236 232 249 235 265 C2' U A 9 OK OK 267 263 280 266 295 C2' C A 10 OK OK 297 293 310 296 326 C2' G A 11 OK OK 328 324 344 327 360 C2' U A 12 OK OK 362 358 375 361 390 C2' A A 13 OK OK 392 388 407 391 423 C2' C A 14 OK OK 425 421 438 424 454 C2' U A 15 OK OK 456 452 469 455 484 C2' U A 16 OK OK 486 482 499 485 514 C2' C A 17 OK OK 516 512 529 515 545 C2' G A 18 OK OK 547 543 563 546 579 C2' G A 19 OK OK 581 577 597 580 613 C2' U A 20 OK OK 615 611 628 614 643 C2' A A 21 OK OK 645 641 660 644 676 C2' C A 22 OK OK 678 674 691 677 707 C2' U A 23 OK OK 709 705 722 708 737 C2' G A 24 OK OK 739 735 755 738 771 C2' G A 25 OK OK 773 769 789 772 805 C2' A A 26 OK OK 807 803 822 806 838 C2' G A 27 OK OK 840 836 856 839 872 C2' A A 28 OK OK 874 870 889 873 905 C2' A A 29 OK OK 907 903 922 906 938 C2' A A 30 OK OK 940 936 955 939 971 C2' C A 31 OK OK 973 969 986 972 1002 C2' A A 32 OK OK 1004 1000 1019 1003 1035 C2' G A 33 OK OK 1037 1033 1053 1036 1069 C2' C A 34 OK OK 1071 1067 1084 1070 1100 C2' C A 35 OK OK 1102 1098 1115 1101 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4 C3' G A 1 OK OK 2 21 5 6 36 C3' G A 2 OK OK 34 55 37 38 70 C3' C A 3 OK OK 68 86 71 72 101 C3' U A 4 OK OK 99 117 102 103 131 C3' G A 5 OK OK 129 150 132 133 165 C3' G A 6 OK OK 163 184 166 167 199 C3' A A 7 OK OK 197 217 200 201 232 C3' C A 8 OK OK 230 248 233 234 263 C3' U A 9 OK OK 261 279 264 265 293 C3' C A 10 OK OK 291 309 294 295 324 C3' G A 11 OK OK 322 343 325 326 358 C3' U A 12 OK OK 356 374 359 360 388 C3' A A 13 OK OK 386 406 389 390 421 C3' C A 14 OK OK 419 437 422 423 452 C3' U A 15 OK OK 450 468 453 454 482 C3' U A 16 OK OK 480 498 483 484 512 C3' C A 17 OK OK 510 528 513 514 543 C3' G A 18 OK OK 541 562 544 545 577 C3' G A 19 OK OK 575 596 578 579 611 C3' U A 20 OK OK 609 627 612 613 641 C3' A A 21 OK OK 639 659 642 643 674 C3' C A 22 OK OK 672 690 675 676 705 C3' U A 23 OK OK 703 721 706 707 735 C3' G A 24 OK OK 733 754 736 737 769 C3' G A 25 OK OK 767 788 770 771 803 C3' A A 26 OK OK 801 821 804 805 836 C3' G A 27 OK OK 834 855 837 838 870 C3' A A 28 OK OK 868 888 871 872 903 C3' A A 29 OK OK 901 921 904 905 936 C3' A A 30 OK OK 934 954 937 938 969 C3' C A 31 OK OK 967 985 970 971 1000 C3' A A 32 OK OK 998 1018 1001 1002 1033 C3' G A 33 OK OK 1031 1052 1034 1035 1067 C3' C A 34 OK OK 1065 1083 1068 1069 1098 C3' C A 35 OK OK 1096 1114 1099 1100 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2 C4' G A 1 OK OK 4 20 1 3 34 C4' G A 2 OK OK 36 54 33 35 68 C4' C A 3 OK OK 70 85 67 69 99 C4' U A 4 OK OK 101 116 98 100 129 C4' G A 5 OK OK 131 149 128 130 163 C4' G A 6 OK OK 165 183 162 164 197 C4' A A 7 OK OK 199 216 196 198 230 C4' C A 8 OK OK 232 247 229 231 261 C4' U A 9 OK OK 263 278 260 262 291 C4' C A 10 OK OK 293 308 290 292 322 C4' G A 11 OK OK 324 342 321 323 356 C4' U A 12 OK OK 358 373 355 357 386 C4' A A 13 OK OK 388 405 385 387 419 C4' C A 14 OK OK 421 436 418 420 450 C4' U A 15 OK OK 452 467 449 451 480 C4' U A 16 OK OK 482 497 479 481 510 C4' C A 17 OK OK 512 527 509 511 541 C4' G A 18 OK OK 543 561 540 542 575 C4' G A 19 OK OK 577 595 574 576 609 C4' U A 20 OK OK 611 626 608 610 639 C4' A A 21 OK OK 641 658 638 640 672 C4' C A 22 OK OK 674 689 671 673 703 C4' U A 23 OK OK 705 720 702 704 733 C4' G A 24 OK OK 735 753 732 734 767 C4' G A 25 OK OK 769 787 766 768 801 C4' A A 26 OK OK 803 820 800 802 834 C4' G A 27 OK OK 836 854 833 835 868 C4' A A 28 OK OK 870 887 867 869 901 C4' A A 29 OK OK 903 920 900 902 934 C4' A A 30 OK OK 936 953 933 935 967 C4' C A 31 OK OK 969 984 966 968 998 C4' A A 32 OK OK 1000 1017 997 999 1031 C4' G A 33 OK OK 1033 1051 1030 1032 1065 C4' C A 34 OK OK 1067 1082 1064 1066 1096 C4' C A 35 OK OK 1098 1113 1095 1097 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1 C5' G A 1 2 33 C5' G A 2 OK OK 32 52 53 34 67 C5' C A 3 OK OK 66 83 84 68 98 C5' U A 4 OK OK 97 114 115 99 128 C5' G A 5 OK OK 127 147 148 129 162 C5' G A 6 OK OK 161 181 182 163 196 C5' A A 7 OK OK 195 214 215 197 229 C5' C A 8 OK OK 228 245 246 230 260 C5' U A 9 OK OK 259 276 277 261 290 C5' C A 10 OK OK 289 306 307 291 321 C5' G A 11 OK OK 320 340 341 322 355 C5' U A 12 OK OK 354 371 372 356 385 C5' A A 13 OK OK 384 403 404 386 418 C5' C A 14 OK OK 417 434 435 419 449 C5' U A 15 OK OK 448 465 466 450 479 C5' U A 16 OK OK 478 495 496 480 509 C5' C A 17 OK OK 508 525 526 510 540 C5' G A 18 OK OK 539 559 560 541 574 C5' G A 19 OK OK 573 593 594 575 608 C5' U A 20 OK OK 607 624 625 609 638 C5' A A 21 OK OK 637 656 657 639 671 C5' C A 22 OK OK 670 687 688 672 702 C5' U A 23 OK OK 701 718 719 703 732 C5' G A 24 OK OK 731 751 752 733 766 C5' G A 25 OK OK 765 785 786 767 800 C5' A A 26 OK OK 799 818 819 801 833 C5' G A 27 OK OK 832 852 853 834 867 C5' A A 28 OK OK 866 885 886 868 900 C5' A A 29 OK OK 899 918 919 901 933 C5' A A 30 OK OK 932 951 952 934 966 C5' C A 31 OK OK 965 982 983 967 997 C5' A A 32 OK OK 996 1015 1016 998 1030 C5' G A 33 OK OK 1029 1049 1050 1031 1064 C5' C A 34 OK OK 1063 1080 1081 1065 1095 C5' C A 35 OK OK 1094 1111 1112 1096 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P G A 2 distorted distorted 5 30 31 32 63 P C A 3 distorted distorted 37 64 65 66 94 P U A 4 distorted distorted 71 95 96 97 124 P G A 5 distorted distorted 102 125 126 127 158 P G A 6 distorted distorted 132 159 160 161 192 P A A 7 distorted distorted 166 193 194 195 225 P C A 8 distorted distorted 200 226 227 228 256 P U A 9 distorted distorted 233 257 258 259 286 P C A 10 distorted distorted 264 287 288 289 317 P G A 11 distorted distorted 294 318 319 320 351 P U A 12 distorted distorted 325 352 353 354 381 P A A 13 distorted distorted 359 382 383 384 414 P C A 14 distorted distorted 389 415 416 417 445 P U A 15 distorted distorted 422 446 447 448 475 P U A 16 distorted distorted 453 476 477 478 505 P C A 17 distorted distorted 483 506 507 508 536 P G A 18 distorted distorted 513 537 538 539 570 P G A 19 distorted distorted 544 571 572 573 604 P U A 20 distorted distorted 578 605 606 607 634 P A A 21 distorted distorted 612 635 636 637 667 P C A 22 distorted distorted 642 668 669 670 698 P U A 23 distorted distorted 675 699 700 701 728 P G A 24 distorted distorted 706 729 730 731 762 P G A 25 distorted distorted 736 763 764 765 796 P A A 26 distorted distorted 770 797 798 799 829 P G A 27 distorted distorted 804 830 831 832 863 P A A 28 distorted distorted 837 864 865 866 896 P A A 29 distorted distorted 871 897 898 899 929 P A A 30 distorted distorted 904 930 931 932 962 P C A 31 distorted distorted 937 963 964 965 993 P A A 32 distorted distorted 970 994 995 996 1026 P G A 33 distorted distorted 1001 1027 1028 1029 1060 P C A 34 distorted distorted 1034 1061 1062 1063 1091 P C A 35 distorted distorted 1068 1092 1093 1094 ---------------------------------------------------------------------------------