ID code: '4YN6' 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' --------------------------------------------------------------------------------- 12 C1' U A 1 beta 7 13 10 32 C1' U A 2 beta 27 33 30 52 C1' G A 3 beta 47 53 50 75 C1' G A 4 beta 70 76 73 98 C1' G A 5 beta 93 99 96 121 C1' C A 6 beta 116 122 119 141 C1' C A 7 beta 136 142 139 161 C1' A A 8 beta 156 162 159 183 C1' G A 9 beta 178 184 181 206 C1' C A 10 beta 201 207 204 226 C1' A A 11 beta 221 227 224 248 C1' G A 12 beta 243 249 246 271 C1' C A 13 beta 266 272 269 291 C1' A A 14 beta 286 292 289 313 C1' G A 15 beta 308 314 311 336 C1' G A 16 beta 331 337 334 359 C1' U A 17 beta 354 360 357 379 C1' C A 18 beta 374 380 377 399 C1' C A 19 beta 394 400 397 420 C1' U B 1 beta 415 421 418 440 C1' U B 2 beta 435 441 438 460 C1' G B 3 beta 455 461 458 483 C1' G B 4 beta 478 484 481 506 C1' G B 5 beta 501 507 504 529 C1' C B 6 beta 524 530 527 549 C1' C B 7 beta 544 550 547 569 C1' A B 8 beta 564 570 567 591 C1' G B 9 beta 586 592 589 614 C1' C B 10 beta 609 615 612 634 C1' A B 11 beta 629 635 632 656 C1' G B 12 beta 651 657 654 679 C1' C B 13 beta 674 680 677 699 C1' A B 14 beta 694 700 697 721 C1' G B 15 beta 716 722 719 744 C1' G B 16 beta 739 745 742 767 C1' U B 17 beta 762 768 765 787 C1' C B 18 beta 782 788 785 807 C1' C B 19 beta 802 808 805 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' U A 1 OK 12 8 11 30 C2' U A 2 OK 32 28 31 50 C2' G A 3 OK 52 48 51 73 C2' G A 4 OK 75 71 74 96 C2' G A 5 OK 98 94 97 119 C2' C A 6 OK 121 117 120 139 C2' C A 7 OK 141 137 140 159 C2' A A 8 OK 161 157 160 181 C2' G A 9 OK 183 179 182 204 C2' C A 10 OK 206 202 205 224 C2' A A 11 OK 226 222 225 246 C2' G A 12 OK 248 244 247 269 C2' C A 13 OK 271 267 270 289 C2' A A 14 OK 291 287 290 311 C2' G A 15 OK 313 309 312 334 C2' G A 16 OK 336 332 335 357 C2' U A 17 OK 359 355 358 377 C2' C A 18 OK 379 375 378 397 C2' C A 19 OK 399 395 398 418 C2' U B 1 OK 420 416 419 438 C2' U B 2 OK 440 436 439 458 C2' G B 3 OK 460 456 459 481 C2' G B 4 OK 483 479 482 504 C2' G B 5 OK 506 502 505 527 C2' C B 6 OK 529 525 528 547 C2' C B 7 OK 549 545 548 567 C2' A B 8 OK 569 565 568 589 C2' G B 9 OK 591 587 590 612 C2' C B 10 OK 614 610 613 632 C2' A B 11 OK 634 630 633 654 C2' G B 12 OK 656 652 655 677 C2' C B 13 OK 679 675 678 697 C2' A B 14 OK 699 695 698 719 C2' G B 15 OK 721 717 720 742 C2' G B 16 OK 744 740 743 765 C2' U B 17 OK 767 763 766 785 C2' C B 18 OK 787 783 786 805 C2' C B 19 OK 807 803 806 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' U A 1 OK 6 9 10 28 C3' U A 2 OK 26 29 30 48 C3' G A 3 OK 46 49 50 71 C3' G A 4 OK 69 72 73 94 C3' G A 5 OK 92 95 96 117 C3' C A 6 OK 115 118 119 137 C3' C A 7 OK 135 138 139 157 C3' A A 8 OK 155 158 159 179 C3' G A 9 OK 177 180 181 202 C3' C A 10 OK 200 203 204 222 C3' A A 11 OK 220 223 224 244 C3' G A 12 OK 242 245 246 267 C3' C A 13 OK 265 268 269 287 C3' A A 14 OK 285 288 289 309 C3' G A 15 OK 307 310 311 332 C3' G A 16 OK 330 333 334 355 C3' U A 17 OK 353 356 357 375 C3' C A 18 OK 373 376 377 395 C3' C A 19 OK 393 396 397 416 C3' U B 1 OK 414 417 418 436 C3' U B 2 OK 434 437 438 456 C3' G B 3 OK 454 457 458 479 C3' G B 4 OK 477 480 481 502 C3' G B 5 OK 500 503 504 525 C3' C B 6 OK 523 526 527 545 C3' C B 7 OK 543 546 547 565 C3' A B 8 OK 563 566 567 587 C3' G B 9 OK 585 588 589 610 C3' C B 10 OK 608 611 612 630 C3' A B 11 OK 628 631 632 652 C3' G B 12 OK 650 653 654 675 C3' C B 13 OK 673 676 677 695 C3' A B 14 OK 693 696 697 717 C3' G B 15 OK 715 718 719 740 C3' G B 16 OK 738 741 742 763 C3' U B 17 OK 761 764 765 783 C3' C B 18 OK 781 784 785 803 C3' C B 19 OK 801 804 805 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' U A 1 OK 8 5 7 26 C4' U A 2 OK 28 25 27 46 C4' G A 3 OK 48 45 47 69 C4' G A 4 OK 71 68 70 92 C4' G A 5 OK 94 91 93 115 C4' C A 6 OK 117 114 116 135 C4' C A 7 OK 137 134 136 155 C4' A A 8 OK 157 154 156 177 C4' G A 9 OK 179 176 178 200 C4' C A 10 OK 202 199 201 220 C4' A A 11 OK 222 219 221 242 C4' G A 12 OK 244 241 243 265 C4' C A 13 OK 267 264 266 285 C4' A A 14 OK 287 284 286 307 C4' G A 15 OK 309 306 308 330 C4' G A 16 OK 332 329 331 353 C4' U A 17 OK 355 352 354 373 C4' C A 18 OK 375 372 374 393 C4' C A 19 OK 395 392 394 414 C4' U B 1 OK 416 413 415 434 C4' U B 2 OK 436 433 435 454 C4' G B 3 OK 456 453 455 477 C4' G B 4 OK 479 476 478 500 C4' G B 5 OK 502 499 501 523 C4' C B 6 OK 525 522 524 543 C4' C B 7 OK 545 542 544 563 C4' A B 8 OK 565 562 564 585 C4' G B 9 OK 587 584 586 608 C4' C B 10 OK 610 607 609 628 C4' A B 11 OK 630 627 629 650 C4' G B 12 OK 652 649 651 673 C4' C B 13 OK 675 672 674 693 C4' A B 14 OK 695 692 694 715 C4' G B 15 OK 717 714 716 738 C4' G B 16 OK 740 737 739 761 C4' U B 17 OK 763 760 762 781 C4' C B 18 OK 783 780 782 801 C4' C B 19 OK 803 800 802 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' U A 1 4 6 25 C5' U A 2 24 26 45 C5' G A 3 44 46 68 C5' G A 4 67 69 91 C5' G A 5 90 92 114 C5' C A 6 113 115 134 C5' C A 7 133 135 154 C5' A A 8 153 155 176 C5' G A 9 175 177 199 C5' C A 10 198 200 219 C5' A A 11 218 220 241 C5' G A 12 240 242 264 C5' C A 13 263 265 284 C5' A A 14 283 285 306 C5' G A 15 305 307 329 C5' G A 16 328 330 352 C5' U A 17 351 353 372 C5' C A 18 371 373 392 C5' C A 19 391 393 413 C5' U B 1 412 414 433 C5' U B 2 432 434 453 C5' G B 3 452 454 476 C5' G B 4 475 477 499 C5' G B 5 498 500 522 C5' C B 6 521 523 542 C5' C B 7 541 543 562 C5' A B 8 561 563 584 C5' G B 9 583 585 607 C5' C B 10 606 608 627 C5' A B 11 626 628 649 C5' G B 12 648 650 672 C5' C B 13 671 673 692 C5' A B 14 691 693 714 C5' G B 15 713 715 737 C5' G B 16 736 738 760 C5' U B 17 759 761 780 C5' C B 18 779 781 800 C5' C B 19 799 801 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P U A 1 distorted distorted 2 3 4 21 P U A 2 distorted distorted 9 22 23 24 41 P G A 3 distorted distorted 29 42 43 44 64 P G A 4 distorted distorted 49 65 66 67 87 P G A 5 distorted distorted 72 88 89 90 110 P C A 6 distorted distorted 95 111 112 113 130 P C A 7 distorted distorted 118 131 132 133 150 P A A 8 distorted distorted 138 151 152 153 172 P G A 9 distorted distorted 158 173 174 175 195 P C A 10 distorted distorted 180 196 197 198 215 P A A 11 distorted distorted 203 216 217 218 237 P G A 12 distorted distorted 223 238 239 240 260 P C A 13 distorted distorted 245 261 262 263 280 P A A 14 distorted distorted 268 281 282 283 302 P G A 15 distorted distorted 288 303 304 305 325 P G A 16 distorted distorted 310 326 327 328 348 P U A 17 distorted distorted 333 349 350 351 368 P C A 18 distorted distorted 356 369 370 371 388 P C A 19 distorted distorted 376 389 390 391 409 P U B 1 distorted distorted 410 411 412 429 P U B 2 OK OK 417 430 431 432 449 P G B 3 distorted distorted 437 450 451 452 472 P G B 4 distorted distorted 457 473 474 475 495 P G B 5 distorted distorted 480 496 497 498 518 P C B 6 distorted distorted 503 519 520 521 538 P C B 7 distorted distorted 526 539 540 541 558 P A B 8 distorted distorted 546 559 560 561 580 P G B 9 distorted distorted 566 581 582 583 603 P C B 10 distorted distorted 588 604 605 606 623 P A B 11 distorted distorted 611 624 625 626 645 P G B 12 distorted distorted 631 646 647 648 668 P C B 13 distorted distorted 653 669 670 671 688 P A B 14 distorted distorted 676 689 690 691 710 P G B 15 distorted distorted 696 711 712 713 733 P G B 16 distorted distorted 718 734 735 736 756 P U B 17 distorted distorted 741 757 758 759 776 P C B 18 distorted distorted 764 777 778 779 796 P C B 19 distorted distorted 784 797 798 799 817 P PO4 A 101 821 P PO4 B 101 ---------------------------------------------------------------------------------