ID code: '2ZY6' 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' G A 1 beta 7 13 10 35 C1' C A 2 beta 30 36 33 55 C1' C A 3 beta 50 56 53 75 C1' C A 4 beta 70 76 73 95 C1' G A 5 beta 90 96 93 118 C1' G A 6 beta 113 119 116 141 C1' A A 7 beta 136 142 139 163 C1' U A 8 beta 158 164 161 183 C1' A A 9 beta 178 184 181 205 C1' G A 10 beta 200 206 203 228 C1' U A 11 beta 223 229 226 248 C1' G A 12 beta 243 249 246 271 C1' U A 13 beta 266 272 269 291 C1' C A 14 beta 286 292 289 311 C1' C A 15 beta 306 312 309 331 C1' U A 16 beta 326 332 329 351 C1' U A 17 beta 346 352 349 371 C1' G A 18 beta 366 372 369 394 C1' G A 19 beta 389 395 392 417 C1' G A 20 beta 412 418 415 440 C1' A A 21 beta 435 441 438 462 C1' A A 22 beta 457 463 460 484 C1' A A 23 beta 479 485 482 506 C1' C A 24 beta 501 507 504 526 C1' C A 25 beta 521 527 524 546 C1' G A 26 beta 541 547 544 569 C1' A A 27 beta 564 570 567 591 C1' G A 28 beta 586 592 589 614 C1' U A 29 beta 609 615 612 634 C1' C A 30 beta 629 635 632 654 C1' C A 31 beta 649 655 652 674 C1' G A 32 beta 669 675 672 697 C1' G A 33 beta 692 698 695 720 C1' G A 34 beta 715 721 718 743 C1' C A 35 beta 738 744 741 763 C1' A A 36 beta 758 764 761 785 C1' C A 37 beta 780 786 783 805 C1' C A 38 beta 800 806 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK 12 8 11 33 C2' C A 2 OK 35 31 34 53 C2' C A 3 OK 55 51 54 73 C2' C A 4 OK 75 71 74 93 C2' G A 5 OK 95 91 94 116 C2' G A 6 OK 118 114 117 139 C2' A A 7 OK 141 137 140 161 C2' U A 8 OK 163 159 162 181 C2' A A 9 OK 183 179 182 203 C2' G A 10 OK 205 201 204 226 C2' U A 11 OK 228 224 227 246 C2' G A 12 OK 248 244 247 269 C2' U A 13 OK 271 267 270 289 C2' C A 14 OK 291 287 290 309 C2' C A 15 OK 311 307 310 329 C2' U A 16 OK 331 327 330 349 C2' U A 17 OK 351 347 350 369 C2' G A 18 OK 371 367 370 392 C2' G A 19 OK 394 390 393 415 C2' G A 20 OK 417 413 416 438 C2' A A 21 OK 440 436 439 460 C2' A A 22 OK 462 458 461 482 C2' A A 23 OK 484 480 483 504 C2' C A 24 OK 506 502 505 524 C2' C A 25 OK 526 522 525 544 C2' G A 26 OK 546 542 545 567 C2' A A 27 OK 569 565 568 589 C2' G A 28 OK 591 587 590 612 C2' U A 29 OK 614 610 613 632 C2' C A 30 OK 634 630 633 652 C2' C A 31 OK 654 650 653 672 C2' G A 32 OK 674 670 673 695 C2' G A 33 OK 697 693 696 718 C2' G A 34 OK 720 716 719 741 C2' C A 35 OK 743 739 742 761 C2' A A 36 OK 763 759 762 783 C2' C A 37 OK 785 781 784 803 C2' C A 38 OK 805 801 804 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK 6 9 10 31 C3' C A 2 OK 29 32 33 51 C3' C A 3 OK 49 52 53 71 C3' C A 4 OK 69 72 73 91 C3' G A 5 OK 89 92 93 114 C3' G A 6 OK 112 115 116 137 C3' A A 7 OK 135 138 139 159 C3' U A 8 OK 157 160 161 179 C3' A A 9 OK 177 180 181 201 C3' G A 10 OK 199 202 203 224 C3' U A 11 OK 222 225 226 244 C3' G A 12 OK 242 245 246 267 C3' U A 13 OK 265 268 269 287 C3' C A 14 OK 285 288 289 307 C3' C A 15 OK 305 308 309 327 C3' U A 16 OK 325 328 329 347 C3' U A 17 OK 345 348 349 367 C3' G A 18 OK 365 368 369 390 C3' G A 19 OK 388 391 392 413 C3' G A 20 OK 411 414 415 436 C3' A A 21 OK 434 437 438 458 C3' A A 22 OK 456 459 460 480 C3' A A 23 OK 478 481 482 502 C3' C A 24 OK 500 503 504 522 C3' C A 25 OK 520 523 524 542 C3' G A 26 OK 540 543 544 565 C3' A A 27 OK 563 566 567 587 C3' G A 28 OK 585 588 589 610 C3' U A 29 OK 608 611 612 630 C3' C A 30 OK 628 631 632 650 C3' C A 31 OK 648 651 652 670 C3' G A 32 OK 668 671 672 693 C3' G A 33 OK 691 694 695 716 C3' G A 34 OK 714 717 718 739 C3' C A 35 OK 737 740 741 759 C3' A A 36 OK 757 760 761 781 C3' C A 37 OK 779 782 783 801 C3' C A 38 OK 799 802 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK 8 5 7 29 C4' C A 2 OK 31 28 30 49 C4' C A 3 OK 51 48 50 69 C4' C A 4 OK 71 68 70 89 C4' G A 5 OK 91 88 90 112 C4' G A 6 OK 114 111 113 135 C4' A A 7 OK 137 134 136 157 C4' U A 8 OK 159 156 158 177 C4' A A 9 OK 179 176 178 199 C4' G A 10 OK 201 198 200 222 C4' U A 11 OK 224 221 223 242 C4' G A 12 OK 244 241 243 265 C4' U A 13 OK 267 264 266 285 C4' C A 14 OK 287 284 286 305 C4' C A 15 OK 307 304 306 325 C4' U A 16 OK 327 324 326 345 C4' U A 17 OK 347 344 346 365 C4' G A 18 OK 367 364 366 388 C4' G A 19 OK 390 387 389 411 C4' G A 20 OK 413 410 412 434 C4' A A 21 OK 436 433 435 456 C4' A A 22 OK 458 455 457 478 C4' A A 23 OK 480 477 479 500 C4' C A 24 OK 502 499 501 520 C4' C A 25 OK 522 519 521 540 C4' G A 26 OK 542 539 541 563 C4' A A 27 OK 565 562 564 585 C4' G A 28 OK 587 584 586 608 C4' U A 29 OK 610 607 609 628 C4' C A 30 OK 630 627 629 648 C4' C A 31 OK 650 647 649 668 C4' G A 32 OK 670 667 669 691 C4' G A 33 OK 693 690 692 714 C4' G A 34 OK 716 713 715 737 C4' C A 35 OK 739 736 738 757 C4' A A 36 OK 759 756 758 779 C4' C A 37 OK 781 778 780 799 C4' C A 38 OK 801 798 800 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 4 6 28 C5' C A 2 27 29 48 C5' C A 3 47 49 68 C5' C A 4 67 69 88 C5' G A 5 87 89 111 C5' G A 6 110 112 134 C5' A A 7 133 135 156 C5' U A 8 155 157 176 C5' A A 9 175 177 198 C5' G A 10 197 199 221 C5' U A 11 220 222 241 C5' G A 12 240 242 264 C5' U A 13 263 265 284 C5' C A 14 283 285 304 C5' C A 15 303 305 324 C5' U A 16 323 325 344 C5' U A 17 343 345 364 C5' G A 18 363 365 387 C5' G A 19 386 388 410 C5' G A 20 409 411 433 C5' A A 21 432 434 455 C5' A A 22 454 456 477 C5' A A 23 476 478 499 C5' C A 24 498 500 519 C5' C A 25 518 520 539 C5' G A 26 538 540 562 C5' A A 27 561 563 584 C5' G A 28 583 585 607 C5' U A 29 606 608 627 C5' C A 30 626 628 647 C5' C A 31 646 648 667 C5' G A 32 666 668 690 C5' G A 33 689 691 713 C5' G A 34 712 714 736 C5' C A 35 735 737 756 C5' A A 36 755 757 778 C5' C A 37 777 779 798 C5' C A 38 797 799 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 24 P C A 2 distorted distorted 9 25 26 27 44 P C A 3 distorted distorted 32 45 46 47 64 P C A 4 distorted distorted 52 65 66 67 84 P G A 5 distorted distorted 72 85 86 87 107 P G A 6 distorted distorted 92 108 109 110 130 P A A 7 distorted distorted 115 131 132 133 152 P U A 8 distorted distorted 138 153 154 155 172 P A A 9 distorted distorted 160 173 174 175 194 P G A 10 distorted distorted 180 195 196 197 217 P U A 11 distorted distorted 202 218 219 220 237 P G A 12 distorted distorted 225 238 239 240 260 P U A 13 distorted distorted 245 261 262 263 280 P C A 14 distorted distorted 268 281 282 283 300 P C A 15 distorted distorted 288 301 302 303 320 P U A 16 distorted distorted 308 321 322 323 340 P U A 17 distorted distorted 328 341 342 343 360 P G A 18 distorted distorted 348 361 362 363 383 P G A 19 distorted distorted 368 384 385 386 406 P G A 20 distorted distorted 391 407 408 409 429 P A A 21 distorted distorted 414 430 431 432 451 P A A 22 distorted distorted 437 452 453 454 473 P A A 23 distorted distorted 459 474 475 476 495 P C A 24 distorted distorted 481 496 497 498 515 P C A 25 distorted distorted 503 516 517 518 535 P G A 26 distorted distorted 523 536 537 538 558 P A A 27 distorted distorted 543 559 560 561 580 P G A 28 distorted distorted 566 581 582 583 603 P U A 29 distorted distorted 588 604 605 606 623 P C A 30 distorted distorted 611 624 625 626 643 P C A 31 distorted distorted 631 644 645 646 663 P G A 32 distorted distorted 651 664 665 666 686 P G A 33 distorted distorted 671 687 688 689 709 P G A 34 distorted distorted 694 710 711 712 732 P C A 35 distorted distorted 717 733 734 735 752 P A A 36 distorted distorted 740 753 754 755 774 P C A 37 distorted distorted 760 775 776 777 794 P C A 38 distorted distorted 782 795 796 797 ---------------------------------------------------------------------------------