ID code: '3KS8' 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' A E 1 beta 4 10 7 31 C1' G E 2 beta 26 32 29 54 C1' A E 3 beta 49 55 52 76 C1' A E 4 beta 71 77 74 98 C1' G E 5 beta 93 99 96 121 C1' G E 6 beta 116 122 119 144 C1' A E 7 beta 139 145 142 166 C1' G E 8 beta 161 167 164 189 C1' G E 9 beta 184 190 187 212 C1' G E 10 beta 207 213 210 235 C1' A E 11 beta 230 236 233 257 C1' G E 12 beta 252 258 255 280 C1' G E 13 beta 275 281 278 303 C1' G E 14 beta 298 304 301 326 C1' A E 15 beta 321 327 324 348 C1' G E 16 beta 343 349 346 371 C1' G E 17 beta 366 372 369 394 C1' A E 18 beta 389 395 392 414 C1' U F 1 beta 409 415 412 434 C1' C F 2 beta 429 435 432 454 C1' C F 3 beta 449 455 452 474 C1' U F 4 beta 469 475 472 494 C1' C F 5 beta 489 495 492 514 C1' C F 6 beta 509 515 512 534 C1' C F 7 beta 529 535 532 554 C1' U F 8 beta 549 555 552 574 C1' C F 9 beta 569 575 572 594 C1' C F 10 beta 589 595 592 614 C1' C F 11 beta 609 615 612 634 C1' U F 12 beta 629 635 632 654 C1' C F 13 beta 649 655 652 674 C1' C F 14 beta 669 675 672 694 C1' U F 15 beta 689 695 692 714 C1' U F 16 beta 709 715 712 734 C1' C F 17 beta 729 735 732 754 C1' U F 18 beta 749 755 752 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A E 1 OK 9 5 8 29 C2' G E 2 OK 31 27 30 52 C2' A E 3 OK 54 50 53 74 C2' A E 4 OK 76 72 75 96 C2' G E 5 OK 98 94 97 119 C2' G E 6 OK 121 117 120 142 C2' A E 7 OK 144 140 143 164 C2' G E 8 OK 166 162 165 187 C2' G E 9 OK 189 185 188 210 C2' G E 10 OK 212 208 211 233 C2' A E 11 OK 235 231 234 255 C2' G E 12 OK 257 253 256 278 C2' G E 13 OK 280 276 279 301 C2' G E 14 OK 303 299 302 324 C2' A E 15 OK 326 322 325 346 C2' G E 16 OK 348 344 347 369 C2' G E 17 OK 371 367 370 392 C2' A E 18 OK 394 390 393 412 C2' U F 1 OK 414 410 413 432 C2' C F 2 OK 434 430 433 452 C2' C F 3 OK 454 450 453 472 C2' U F 4 OK 474 470 473 492 C2' C F 5 OK 494 490 493 512 C2' C F 6 OK 514 510 513 532 C2' C F 7 OK 534 530 533 552 C2' U F 8 OK 554 550 553 572 C2' C F 9 OK 574 570 573 592 C2' C F 10 OK 594 590 593 612 C2' C F 11 OK 614 610 613 632 C2' U F 12 OK 634 630 633 652 C2' C F 13 OK 654 650 653 672 C2' C F 14 OK 674 670 673 692 C2' U F 15 OK 694 690 693 712 C2' U F 16 OK 714 710 713 732 C2' C F 17 OK 734 730 733 752 C2' U F 18 OK 754 750 753 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A E 1 OK 3 6 7 27 C3' G E 2 OK 25 28 29 50 C3' A E 3 OK 48 51 52 72 C3' A E 4 OK 70 73 74 94 C3' G E 5 OK 92 95 96 117 C3' G E 6 OK 115 118 119 140 C3' A E 7 OK 138 141 142 162 C3' G E 8 OK 160 163 164 185 C3' G E 9 OK 183 186 187 208 C3' G E 10 OK 206 209 210 231 C3' A E 11 OK 229 232 233 253 C3' G E 12 OK 251 254 255 276 C3' G E 13 OK 274 277 278 299 C3' G E 14 OK 297 300 301 322 C3' A E 15 OK 320 323 324 344 C3' G E 16 OK 342 345 346 367 C3' G E 17 OK 365 368 369 390 C3' A E 18 OK 388 391 392 410 C3' U F 1 OK 408 411 412 430 C3' C F 2 OK 428 431 432 450 C3' C F 3 OK 448 451 452 470 C3' U F 4 OK 468 471 472 490 C3' C F 5 OK 488 491 492 510 C3' C F 6 OK 508 511 512 530 C3' C F 7 OK 528 531 532 550 C3' U F 8 OK 548 551 552 570 C3' C F 9 OK 568 571 572 590 C3' C F 10 OK 588 591 592 610 C3' C F 11 OK 608 611 612 630 C3' U F 12 OK 628 631 632 650 C3' C F 13 OK 648 651 652 670 C3' C F 14 OK 668 671 672 690 C3' U F 15 OK 688 691 692 710 C3' U F 16 OK 708 711 712 730 C3' C F 17 OK 728 731 732 750 C3' U F 18 OK 748 751 752 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A E 1 OK 5 2 4 25 C4' G E 2 OK 27 24 26 48 C4' A E 3 OK 50 47 49 70 C4' A E 4 OK 72 69 71 92 C4' G E 5 OK 94 91 93 115 C4' G E 6 OK 117 114 116 138 C4' A E 7 OK 140 137 139 160 C4' G E 8 OK 162 159 161 183 C4' G E 9 OK 185 182 184 206 C4' G E 10 OK 208 205 207 229 C4' A E 11 OK 231 228 230 251 C4' G E 12 OK 253 250 252 274 C4' G E 13 OK 276 273 275 297 C4' G E 14 OK 299 296 298 320 C4' A E 15 OK 322 319 321 342 C4' G E 16 OK 344 341 343 365 C4' G E 17 OK 367 364 366 388 C4' A E 18 OK 390 387 389 408 C4' U F 1 OK 410 407 409 428 C4' C F 2 OK 430 427 429 448 C4' C F 3 OK 450 447 449 468 C4' U F 4 OK 470 467 469 488 C4' C F 5 OK 490 487 489 508 C4' C F 6 OK 510 507 509 528 C4' C F 7 OK 530 527 529 548 C4' U F 8 OK 550 547 549 568 C4' C F 9 OK 570 567 569 588 C4' C F 10 OK 590 587 589 608 C4' C F 11 OK 610 607 609 628 C4' U F 12 OK 630 627 629 648 C4' C F 13 OK 650 647 649 668 C4' C F 14 OK 670 667 669 688 C4' U F 15 OK 690 687 689 708 C4' U F 16 OK 710 707 709 728 C4' C F 17 OK 730 727 729 748 C4' U F 18 OK 750 747 749 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A E 1 1 3 24 C5' G E 2 23 25 47 C5' A E 3 46 48 69 C5' A E 4 68 70 91 C5' G E 5 90 92 114 C5' G E 6 113 115 137 C5' A E 7 136 138 159 C5' G E 8 158 160 182 C5' G E 9 181 183 205 C5' G E 10 204 206 228 C5' A E 11 227 229 250 C5' G E 12 249 251 273 C5' G E 13 272 274 296 C5' G E 14 295 297 319 C5' A E 15 318 320 341 C5' G E 16 340 342 364 C5' G E 17 363 365 387 C5' A E 18 386 388 407 C5' U F 1 406 408 427 C5' C F 2 426 428 447 C5' C F 3 446 448 467 C5' U F 4 466 468 487 C5' C F 5 486 488 507 C5' C F 6 506 508 527 C5' C F 7 526 528 547 C5' U F 8 546 548 567 C5' C F 9 566 568 587 C5' C F 10 586 588 607 C5' C F 11 606 608 627 C5' U F 12 626 628 647 C5' C F 13 646 648 667 C5' C F 14 666 668 687 C5' U F 15 686 688 707 C5' U F 16 706 708 727 C5' C F 17 726 728 747 C5' U F 18 746 748 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P G E 2 distorted distorted 6 21 22 23 43 P A E 3 distorted distorted 28 44 45 46 65 P A E 4 distorted distorted 51 66 67 68 87 P G E 5 distorted distorted 73 88 89 90 110 P G E 6 distorted distorted 95 111 112 113 133 P A E 7 distorted distorted 118 134 135 136 155 P G E 8 distorted distorted 141 156 157 158 178 P G E 9 distorted distorted 163 179 180 181 201 P G E 10 distorted distorted 186 202 203 204 224 P A E 11 distorted distorted 209 225 226 227 246 P G E 12 distorted distorted 232 247 248 249 269 P G E 13 distorted distorted 254 270 271 272 292 P G E 14 distorted distorted 277 293 294 295 315 P A E 15 distorted distorted 300 316 317 318 337 P G E 16 distorted distorted 323 338 339 340 360 P G E 17 distorted distorted 345 361 362 363 383 P A E 18 distorted distorted 368 384 385 386 423 P C F 2 distorted distorted 411 424 425 426 443 P C F 3 distorted distorted 431 444 445 446 463 P U F 4 distorted distorted 451 464 465 466 483 P C F 5 distorted distorted 471 484 485 486 503 P C F 6 distorted distorted 491 504 505 506 523 P C F 7 distorted distorted 511 524 525 526 543 P U F 8 distorted distorted 531 544 545 546 563 P C F 9 distorted distorted 551 564 565 566 583 P C F 10 distorted distorted 571 584 585 586 603 P C F 11 distorted distorted 591 604 605 606 623 P U F 12 distorted distorted 611 624 625 626 643 P C F 13 distorted distorted 631 644 645 646 663 P C F 14 distorted distorted 651 664 665 666 683 P U F 15 distorted distorted 671 684 685 686 703 P U F 16 distorted distorted 691 704 705 706 723 P C F 17 distorted distorted 711 724 725 726 743 P U F 18 distorted distorted 731 744 745 746 ---------------------------------------------------------------------------------