ID code: '2GIO' 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' C A 3 alpha beta 73 93 79 76 109 C1' C A 4 alpha beta 104 124 110 107 140 C1' A A 5 alpha beta 135 157 141 138 173 C1' U A 6 alpha beta 168 188 174 171 203 C1' C A 7 alpha beta 198 218 204 201 234 C1' U A 8 alpha beta 229 249 235 232 264 C1' U A 9 alpha beta 259 279 265 262 294 C1' G A 10 alpha beta 289 312 295 292 328 C1' C A 11 alpha beta 323 343 329 326 359 C1' U A 12 alpha beta 354 374 360 357 389 C1' C A 13 alpha beta 384 404 390 387 420 C1' U A 14 alpha beta 415 435 421 418 450 C1' U A 15 alpha beta 445 465 451 448 480 C1' C A 16 alpha beta 475 495 481 478 511 C1' G A 17 alpha beta 506 529 512 509 545 C1' G A 18 alpha beta 540 563 546 543 579 C1' A A 19 alpha beta 574 596 580 577 612 C1' G A 20 alpha beta 607 630 613 610 646 C1' G A 21 alpha beta 641 664 647 644 680 C1' A A 22 alpha beta 675 697 681 678 713 C1' U A 23 alpha beta 708 728 714 711 743 C1' U A 24 alpha beta 738 758 744 741 773 C1' U A 25 alpha beta 768 788 774 771 803 C1' G A 26 alpha beta 798 821 804 801 837 C1' G A 27 alpha beta 832 855 838 835 871 C1' C A 28 alpha beta 866 886 872 869 902 C1' C A 29 alpha beta 897 918 903 900 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' C A 4 OK OK 109 105 122 108 138 C2' A A 5 OK OK 140 136 155 139 171 C2' U A 6 OK OK 173 169 186 172 201 C2' C A 7 OK OK 203 199 216 202 232 C2' U A 8 OK OK 234 230 247 233 262 C2' U A 9 OK OK 264 260 277 263 292 C2' G A 10 OK OK 294 290 310 293 326 C2' C A 11 OK OK 328 324 341 327 357 C2' U A 12 OK OK 359 355 372 358 387 C2' C A 13 OK OK 389 385 402 388 418 C2' U A 14 OK OK 420 416 433 419 448 C2' U A 15 OK OK 450 446 463 449 478 C2' C A 16 OK OK 480 476 493 479 509 C2' G A 17 OK OK 511 507 527 510 543 C2' G A 18 OK OK 545 541 561 544 577 C2' A A 19 OK OK 579 575 594 578 610 C2' G A 20 OK OK 612 608 628 611 644 C2' G A 21 OK OK 646 642 662 645 678 C2' A A 22 OK OK 680 676 695 679 711 C2' U A 23 OK OK 713 709 726 712 741 C2' U A 24 OK OK 743 739 756 742 771 C2' U A 25 OK OK 773 769 786 772 801 C2' G A 26 OK OK 803 799 819 802 835 C2' G A 27 OK OK 837 833 853 836 869 C2' C A 28 OK OK 871 867 884 870 900 C2' C A 29 OK OK 902 898 916 901 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' C A 4 OK OK 103 121 106 107 136 C3' A A 5 OK OK 134 154 137 138 169 C3' U A 6 OK OK 167 185 170 171 199 C3' C A 7 OK OK 197 215 200 201 230 C3' U A 8 OK OK 228 246 231 232 260 C3' U A 9 OK OK 258 276 261 262 290 C3' G A 10 OK OK 288 309 291 292 324 C3' C A 11 OK OK 322 340 325 326 355 C3' U A 12 OK OK 353 371 356 357 385 C3' C A 13 OK OK 383 401 386 387 416 C3' U A 14 OK OK 414 432 417 418 446 C3' U A 15 OK OK 444 462 447 448 476 C3' C A 16 OK OK 474 492 477 478 507 C3' G A 17 OK OK 505 526 508 509 541 C3' G A 18 OK OK 539 560 542 543 575 C3' A A 19 OK OK 573 593 576 577 608 C3' G A 20 OK OK 606 627 609 610 642 C3' G A 21 OK OK 640 661 643 644 676 C3' A A 22 OK OK 674 694 677 678 709 C3' U A 23 OK OK 707 725 710 711 739 C3' U A 24 OK OK 737 755 740 741 769 C3' U A 25 OK OK 767 785 770 771 799 C3' G A 26 OK OK 797 818 800 801 833 C3' G A 27 OK OK 831 852 834 835 867 C3' C A 28 OK OK 865 883 868 869 898 C3' C A 29 OK OK 896 914 899 900 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' C A 4 OK OK 105 120 102 104 134 C4' A A 5 OK OK 136 153 133 135 167 C4' U A 6 OK OK 169 184 166 168 197 C4' C A 7 OK OK 199 214 196 198 228 C4' U A 8 OK OK 230 245 227 229 258 C4' U A 9 OK OK 260 275 257 259 288 C4' G A 10 OK OK 290 308 287 289 322 C4' C A 11 OK OK 324 339 321 323 353 C4' U A 12 OK OK 355 370 352 354 383 C4' C A 13 OK OK 385 400 382 384 414 C4' U A 14 OK OK 416 431 413 415 444 C4' U A 15 OK OK 446 461 443 445 474 C4' C A 16 OK OK 476 491 473 475 505 C4' G A 17 OK OK 507 525 504 506 539 C4' G A 18 OK OK 541 559 538 540 573 C4' A A 19 OK OK 575 592 572 574 606 C4' G A 20 OK OK 608 626 605 607 640 C4' G A 21 OK OK 642 660 639 641 674 C4' A A 22 OK OK 676 693 673 675 707 C4' U A 23 OK OK 709 724 706 708 737 C4' U A 24 OK OK 739 754 736 738 767 C4' U A 25 OK OK 769 784 766 768 797 C4' G A 26 OK OK 799 817 796 798 831 C4' G A 27 OK OK 833 851 830 832 865 C4' C A 28 OK OK 867 882 864 866 896 C4' C A 29 OK OK 898 913 895 897 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' C A 4 OK OK 101 118 119 103 133 C5' A A 5 OK OK 132 151 152 134 166 C5' U A 6 OK OK 165 182 183 167 196 C5' C A 7 OK OK 195 212 213 197 227 C5' U A 8 OK OK 226 243 244 228 257 C5' U A 9 OK OK 256 273 274 258 287 C5' G A 10 OK OK 286 306 307 288 321 C5' C A 11 OK OK 320 337 338 322 352 C5' U A 12 OK OK 351 368 369 353 382 C5' C A 13 OK OK 381 398 399 383 413 C5' U A 14 OK OK 412 429 430 414 443 C5' U A 15 OK OK 442 459 460 444 473 C5' C A 16 OK OK 472 489 490 474 504 C5' G A 17 OK OK 503 523 524 505 538 C5' G A 18 OK OK 537 557 558 539 572 C5' A A 19 OK OK 571 590 591 573 605 C5' G A 20 OK OK 604 624 625 606 639 C5' G A 21 OK OK 638 658 659 640 673 C5' A A 22 OK OK 672 691 692 674 706 C5' U A 23 OK OK 705 722 723 707 736 C5' U A 24 OK OK 735 752 753 737 766 C5' U A 25 OK OK 765 782 783 767 796 C5' G A 26 OK OK 795 815 816 797 830 C5' G A 27 OK OK 829 849 850 831 864 C5' C A 28 OK OK 863 880 881 865 895 C5' C A 29 OK OK 894 911 912 896 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P C A 4 distorted distorted 75 99 100 101 129 P A A 5 distorted distorted 106 130 131 132 162 P U A 6 distorted distorted 137 163 164 165 192 P C A 7 distorted distorted 170 193 194 195 223 P U A 8 distorted distorted 200 224 225 226 253 P U A 9 distorted distorted 231 254 255 256 283 P G A 10 distorted distorted 261 284 285 286 317 P C A 11 distorted distorted 291 318 319 320 348 P U A 12 distorted distorted 325 349 350 351 378 P C A 13 distorted distorted 356 379 380 381 409 P U A 14 distorted distorted 386 410 411 412 439 P U A 15 distorted distorted 417 440 441 442 469 P C A 16 distorted distorted 447 470 471 472 500 P G A 17 distorted distorted 477 501 502 503 534 P G A 18 distorted distorted 508 535 536 537 568 P A A 19 distorted distorted 542 569 570 571 601 P G A 20 distorted distorted 576 602 603 604 635 P G A 21 distorted distorted 609 636 637 638 669 P A A 22 distorted distorted 643 670 671 672 702 P U A 23 distorted distorted 677 703 704 705 732 P U A 24 distorted distorted 710 733 734 735 762 P U A 25 distorted distorted 740 763 764 765 792 P G A 26 distorted distorted 770 793 794 795 826 P G A 27 distorted distorted 800 827 828 829 860 P C A 28 distorted distorted 834 861 862 863 891 P C A 29 distorted distorted 868 892 893 894 ---------------------------------------------------------------------------------