ID code: '2QK9' 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 B 1 beta 4 10 7 31 C1' G B 2 beta 26 32 29 54 C1' U B 3 beta 49 55 52 74 C1' G B 4 beta 69 75 72 97 C1' C B 5 beta 92 98 95 117 C1' G B 6 beta 112 118 115 140 C1' A B 7 beta 135 141 138 162 C1' C B 8 beta 157 163 160 182 C1' A B 9 beta 177 183 180 204 C1' C B 10 beta 199 205 202 224 C1' C B 11 beta 219 225 222 244 C1' U B 12 beta 239 245 242 264 C1' G B 13 beta 259 265 262 287 C1' A B 14 beta 282 288 285 309 C1' U B 15 beta 304 310 307 329 C1' U B 16 beta 324 330 327 349 C1' C B 17 beta 344 350 347 369 C1' C B 18 beta 364 370 367 386 C1' DG C 19 beta 382 387 385 408 C1' DG C 20 beta 404 409 407 430 C1' DA C 21 beta 426 431 429 451 C1' DA C 22 beta 447 452 450 472 C1' DT C 23 beta 468 473 471 492 C1' DC C 24 beta 488 493 491 511 C1' DA C 25 beta 507 512 510 532 C1' DG C 26 beta 528 533 531 554 C1' DG C 27 beta 550 555 553 576 C1' DT C 28 beta 572 577 575 596 C1' DG C 29 beta 592 597 595 618 C1' DT C 30 beta 614 619 617 638 C1' DC C 31 beta 634 639 637 657 C1' DG C 32 beta 653 658 656 679 C1' DC C 33 beta 675 680 678 698 C1' DA C 34 beta 694 699 697 719 C1' DC C 35 beta 715 720 718 738 C1' DT C 36 beta 734 739 737 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A B 1 OK 9 5 8 29 C2' G B 2 OK 31 27 30 52 C2' U B 3 OK 54 50 53 72 C2' G B 4 OK 74 70 73 95 C2' C B 5 OK 97 93 96 115 C2' G B 6 OK 117 113 116 138 C2' A B 7 OK 140 136 139 160 C2' C B 8 OK 162 158 161 180 C2' A B 9 OK 182 178 181 202 C2' C B 10 OK 204 200 203 222 C2' C B 11 OK 224 220 223 242 C2' U B 12 OK 244 240 243 262 C2' G B 13 OK 264 260 263 285 C2' A B 14 OK 287 283 286 307 C2' U B 15 OK 309 305 308 327 C2' U B 16 OK 329 325 328 347 C2' C B 17 OK 349 345 348 367 C2' C B 18 OK 369 365 368 385 C2' DG C 19 386 383 407 C2' DG C 20 408 405 429 C2' DA C 21 430 427 450 C2' DA C 22 451 448 471 C2' DT C 23 472 469 491 C2' DC C 24 492 489 510 C2' DA C 25 511 508 531 C2' DG C 26 532 529 553 C2' DG C 27 554 551 575 C2' DT C 28 576 573 595 C2' DG C 29 596 593 617 C2' DT C 30 618 615 637 C2' DC C 31 638 635 656 C2' DG C 32 657 654 678 C2' DC C 33 679 676 697 C2' DA C 34 698 695 718 C2' DC C 35 719 716 737 C2' DT C 36 738 735 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A B 1 OK 3 6 7 27 C3' G B 2 OK 25 28 29 50 C3' U B 3 OK 48 51 52 70 C3' G B 4 OK 68 71 72 93 C3' C B 5 OK 91 94 95 113 C3' G B 6 OK 111 114 115 136 C3' A B 7 OK 134 137 138 158 C3' C B 8 OK 156 159 160 178 C3' A B 9 OK 176 179 180 200 C3' C B 10 OK 198 201 202 220 C3' C B 11 OK 218 221 222 240 C3' U B 12 OK 238 241 242 260 C3' G B 13 OK 258 261 262 283 C3' A B 14 OK 281 284 285 305 C3' U B 15 OK 303 306 307 325 C3' U B 16 OK 323 326 327 345 C3' C B 17 OK 343 346 347 365 C3' C B 18 OK 363 366 367 383 C3' DG C 19 OK 381 384 385 405 C3' DG C 20 OK 403 406 407 427 C3' DA C 21 OK 425 428 429 448 C3' DA C 22 OK 446 449 450 469 C3' DT C 23 OK 467 470 471 489 C3' DC C 24 OK 487 490 491 508 C3' DA C 25 OK 506 509 510 529 C3' DG C 26 OK 527 530 531 551 C3' DG C 27 OK 549 552 553 573 C3' DT C 28 OK 571 574 575 593 C3' DG C 29 OK 591 594 595 615 C3' DT C 30 OK 613 616 617 635 C3' DC C 31 OK 633 636 637 654 C3' DG C 32 OK 652 655 656 676 C3' DC C 33 OK 674 677 678 695 C3' DA C 34 OK 693 696 697 716 C3' DC C 35 OK 714 717 718 735 C3' DT C 36 OK 733 736 737 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A B 1 OK 5 2 4 25 C4' G B 2 OK 27 24 26 48 C4' U B 3 OK 50 47 49 68 C4' G B 4 OK 70 67 69 91 C4' C B 5 OK 93 90 92 111 C4' G B 6 OK 113 110 112 134 C4' A B 7 OK 136 133 135 156 C4' C B 8 OK 158 155 157 176 C4' A B 9 OK 178 175 177 198 C4' C B 10 OK 200 197 199 218 C4' C B 11 OK 220 217 219 238 C4' U B 12 OK 240 237 239 258 C4' G B 13 OK 260 257 259 281 C4' A B 14 OK 283 280 282 303 C4' U B 15 OK 305 302 304 323 C4' U B 16 OK 325 322 324 343 C4' C B 17 OK 345 342 344 363 C4' C B 18 OK 365 362 364 381 C4' DG C 19 OK 383 380 382 403 C4' DG C 20 OK 405 402 404 425 C4' DA C 21 OK 427 424 426 446 C4' DA C 22 OK 448 445 447 467 C4' DT C 23 OK 469 466 468 487 C4' DC C 24 OK 489 486 488 506 C4' DA C 25 OK 508 505 507 527 C4' DG C 26 OK 529 526 528 549 C4' DG C 27 OK 551 548 550 571 C4' DT C 28 OK 573 570 572 591 C4' DG C 29 OK 593 590 592 613 C4' DT C 30 OK 615 612 614 633 C4' DC C 31 OK 635 632 634 652 C4' DG C 32 OK 654 651 653 674 C4' DC C 33 OK 676 673 675 693 C4' DA C 34 OK 695 692 694 714 C4' DC C 35 OK 716 713 715 733 C4' DT C 36 OK 735 732 734 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A B 1 1 3 24 C5' G B 2 23 25 47 C5' U B 3 46 48 67 C5' G B 4 66 68 90 C5' C B 5 89 91 110 C5' G B 6 109 111 133 C5' A B 7 132 134 155 C5' C B 8 154 156 175 C5' A B 9 174 176 197 C5' C B 10 196 198 217 C5' C B 11 216 218 237 C5' U B 12 236 238 257 C5' G B 13 256 258 280 C5' A B 14 279 281 302 C5' U B 15 301 303 322 C5' U B 16 321 323 342 C5' C B 17 341 343 362 C5' C B 18 361 363 380 C5' DG C 19 379 381 402 C5' DG C 20 401 403 424 C5' DA C 21 423 425 445 C5' DA C 22 444 446 466 C5' DT C 23 465 467 486 C5' DC C 24 485 487 505 C5' DA C 25 504 506 526 C5' DG C 26 525 527 548 C5' DG C 27 547 549 570 C5' DT C 28 569 571 590 C5' DG C 29 589 591 612 C5' DT C 30 611 613 632 C5' DC C 31 631 633 651 C5' DG C 32 650 652 673 C5' DC C 33 672 674 692 C5' DA C 34 691 693 713 C5' DC C 35 712 714 732 C5' DT C 36 731 733 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P G B 2 distorted distorted 6 21 22 23 43 P U B 3 distorted distorted 28 44 45 46 63 P G B 4 distorted distorted 51 64 65 66 86 P C B 5 distorted distorted 71 87 88 89 106 P G B 6 distorted distorted 94 107 108 109 129 P A B 7 distorted distorted 114 130 131 132 151 P C B 8 distorted distorted 137 152 153 154 171 P A B 9 distorted distorted 159 172 173 174 193 P C B 10 distorted distorted 179 194 195 196 213 P C B 11 distorted distorted 201 214 215 216 233 P U B 12 distorted distorted 221 234 235 236 253 P G B 13 distorted distorted 241 254 255 256 276 P A B 14 distorted distorted 261 277 278 279 298 P U B 15 distorted distorted 284 299 300 301 318 P U B 16 distorted distorted 306 319 320 321 338 P C B 17 distorted distorted 326 339 340 341 358 P C B 18 distorted distorted 346 359 360 361 398 P DG C 20 distorted distorted 384 399 400 401 420 P DA C 21 distorted distorted 406 421 422 423 441 P DA C 22 distorted distorted 428 442 443 444 462 P DT C 23 distorted distorted 449 463 464 465 482 P DC C 24 distorted distorted 470 483 484 485 501 P DA C 25 distorted distorted 490 502 503 504 522 P DG C 26 distorted distorted 509 523 524 525 544 P DG C 27 distorted distorted 530 545 546 547 566 P DT C 28 distorted distorted 552 567 568 569 586 P DG C 29 distorted distorted 574 587 588 589 608 P DT C 30 distorted distorted 594 609 610 611 628 P DC C 31 distorted distorted 616 629 630 631 647 P DG C 32 distorted distorted 636 648 649 650 669 P DC C 33 distorted distorted 655 670 671 672 688 P DA C 34 distorted distorted 677 689 690 691 709 P DC C 35 distorted distorted 696 710 711 712 728 P DT C 36 distorted distorted 717 729 730 731 ---------------------------------------------------------------------------------