ID code: '2RQJ' 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' A A 3 alpha beta 73 95 79 76 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' G A 5 alpha beta 140 163 146 143 179 C1' A A 6 alpha beta 174 196 180 177 212 C1' G A 7 alpha beta 207 230 213 210 246 C1' G A 8 alpha beta 241 264 247 244 280 C1' A A 9 alpha beta 275 297 281 278 313 C1' G A 10 alpha beta 308 331 314 311 347 C1' G A 11 alpha beta 342 365 348 345 381 C1' A A 12 alpha beta 376 399 382 379 413 C1' G B 13 alpha beta 408 431 414 411 448 C1' G B 14 alpha beta 443 466 449 446 482 C1' A B 15 alpha beta 477 499 483 480 515 C1' G B 16 alpha beta 510 533 516 513 549 C1' G B 17 alpha beta 544 567 550 547 583 C1' A B 18 alpha beta 578 600 584 581 616 C1' G B 19 alpha beta 611 634 617 614 650 C1' G B 20 alpha beta 645 668 651 648 684 C1' A B 21 alpha beta 679 701 685 682 717 C1' G B 22 alpha beta 712 735 718 715 751 C1' G B 23 alpha beta 746 769 752 749 785 C1' A B 24 alpha beta 780 803 786 783 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 C2' G A 4 OK OK 111 107 127 110 143 C2' G A 5 OK OK 145 141 161 144 177 C2' A A 6 OK OK 179 175 194 178 210 C2' G A 7 OK OK 212 208 228 211 244 C2' G A 8 OK OK 246 242 262 245 278 C2' A A 9 OK OK 280 276 295 279 311 C2' G A 10 OK OK 313 309 329 312 345 C2' G A 11 OK OK 347 343 363 346 379 C2' A A 12 OK OK 381 377 397 380 411 C2' G B 13 OK OK 413 409 429 412 446 C2' G B 14 OK OK 448 444 464 447 480 C2' A B 15 OK OK 482 478 497 481 513 C2' G B 16 OK OK 515 511 531 514 547 C2' G B 17 OK OK 549 545 565 548 581 C2' A B 18 OK OK 583 579 598 582 614 C2' G B 19 OK OK 616 612 632 615 648 C2' G B 20 OK OK 650 646 666 649 682 C2' A B 21 OK OK 684 680 699 683 715 C2' G B 22 OK OK 717 713 733 716 749 C2' G B 23 OK OK 751 747 767 750 783 C2' A B 24 OK OK 785 781 801 784 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 C3' G A 4 OK OK 105 126 108 109 141 C3' G A 5 OK OK 139 160 142 143 175 C3' A A 6 OK OK 173 193 176 177 208 C3' G A 7 OK OK 206 227 209 210 242 C3' G A 8 OK OK 240 261 243 244 276 C3' A A 9 OK OK 274 294 277 278 309 C3' G A 10 OK OK 307 328 310 311 343 C3' G A 11 OK OK 341 362 344 345 377 C3' A A 12 OK OK 375 395 378 379 409 C3' G B 13 OK OK 407 428 410 411 444 C3' G B 14 OK OK 442 463 445 446 478 C3' A B 15 OK OK 476 496 479 480 511 C3' G B 16 OK OK 509 530 512 513 545 C3' G B 17 OK OK 543 564 546 547 579 C3' A B 18 OK OK 577 597 580 581 612 C3' G B 19 OK OK 610 631 613 614 646 C3' G B 20 OK OK 644 665 647 648 680 C3' A B 21 OK OK 678 698 681 682 713 C3' G B 22 OK OK 711 732 714 715 747 C3' G B 23 OK OK 745 766 748 749 781 C3' A B 24 OK OK 779 799 782 783 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 C4' G A 4 OK OK 107 125 104 106 139 C4' G A 5 OK OK 141 159 138 140 173 C4' A A 6 OK OK 175 192 172 174 206 C4' G A 7 OK OK 208 226 205 207 240 C4' G A 8 OK OK 242 260 239 241 274 C4' A A 9 OK OK 276 293 273 275 307 C4' G A 10 OK OK 309 327 306 308 341 C4' G A 11 OK OK 343 361 340 342 375 C4' A A 12 OK OK 377 394 374 376 407 C4' G B 13 OK OK 409 427 406 408 442 C4' G B 14 OK OK 444 462 441 443 476 C4' A B 15 OK OK 478 495 475 477 509 C4' G B 16 OK OK 511 529 508 510 543 C4' G B 17 OK OK 545 563 542 544 577 C4' A B 18 OK OK 579 596 576 578 610 C4' G B 19 OK OK 612 630 609 611 644 C4' G B 20 OK OK 646 664 643 645 678 C4' A B 21 OK OK 680 697 677 679 711 C4' G B 22 OK OK 713 731 710 712 745 C4' G B 23 OK OK 747 765 744 746 779 C4' A B 24 OK OK 781 798 778 780 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 C5' G A 4 OK OK 103 123 124 105 138 C5' G A 5 OK OK 137 157 158 139 172 C5' A A 6 OK OK 171 190 191 173 205 C5' G A 7 OK OK 204 224 225 206 239 C5' G A 8 OK OK 238 258 259 240 273 C5' A A 9 OK OK 272 291 292 274 306 C5' G A 10 OK OK 305 325 326 307 340 C5' G A 11 OK OK 339 359 360 341 374 C5' A A 12 OK OK 373 392 393 375 406 C5' G B 13 OK OK 405 425 426 407 441 C5' G B 14 OK OK 440 460 461 442 475 C5' A B 15 OK OK 474 493 494 476 508 C5' G B 16 OK OK 507 527 528 509 542 C5' G B 17 OK OK 541 561 562 543 576 C5' A B 18 OK OK 575 594 595 577 609 C5' G B 19 OK OK 608 628 629 610 643 C5' G B 20 OK OK 642 662 663 644 677 C5' A B 21 OK OK 676 695 696 678 710 C5' G B 22 OK OK 709 729 730 711 744 C5' G B 23 OK OK 743 763 764 745 778 C5' A B 24 OK OK 777 796 797 779 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P G A 4 distorted distorted 75 101 102 103 134 P G A 5 distorted distorted 108 135 136 137 168 P A A 6 distorted distorted 142 169 170 171 201 P G A 7 distorted distorted 176 202 203 204 235 P G A 8 distorted distorted 209 236 237 238 269 P A A 9 distorted distorted 243 270 271 272 302 P G A 10 distorted distorted 277 303 304 305 336 P G A 11 distorted distorted 310 337 338 339 370 P A A 12 distorted distorted 344 371 372 373 437 P G B 14 distorted distorted 410 438 439 440 471 P A B 15 distorted distorted 445 472 473 474 504 P G B 16 distorted distorted 479 505 506 507 538 P G B 17 distorted distorted 512 539 540 541 572 P A B 18 distorted distorted 546 573 574 575 605 P G B 19 distorted distorted 580 606 607 608 639 P G B 20 distorted distorted 613 640 641 642 673 P A B 21 distorted distorted 647 674 675 676 706 P G B 22 distorted distorted 681 707 708 709 740 P G B 23 distorted distorted 714 741 742 743 774 P A B 24 distorted distorted 748 775 776 777 ---------------------------------------------------------------------------------