ID code: '2JSE' 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' U A 5 alpha beta 140 160 146 143 175 C1' G A 6 alpha beta 170 193 176 173 209 C1' G A 7 alpha beta 204 227 210 207 243 C1' C A 8 alpha beta 238 258 244 241 274 C1' C A 9 alpha beta 269 289 275 272 305 C1' G A 10 alpha beta 300 323 306 303 339 C1' A A 11 alpha beta 334 356 340 337 372 C1' A A 12 alpha beta 367 389 373 370 405 C1' A A 13 alpha beta 400 422 406 403 438 C1' G A 14 alpha beta 433 456 439 436 472 C1' G A 15 alpha beta 467 490 473 470 506 C1' C A 16 alpha beta 501 521 507 504 537 C1' A A 17 alpha beta 532 554 538 535 570 C1' U A 18 alpha beta 565 585 571 568 600 C1' C A 19 alpha beta 595 615 601 598 631 C1' U A 20 alpha beta 626 646 632 629 661 C1' C A 21 alpha beta 656 676 662 659 692 C1' C A 22 alpha beta 687 708 693 690 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 5 OK OK 145 141 158 144 173 C2' G A 6 OK OK 175 171 191 174 207 C2' G A 7 OK OK 209 205 225 208 241 C2' C A 8 OK OK 243 239 256 242 272 C2' C A 9 OK OK 274 270 287 273 303 C2' G A 10 OK OK 305 301 321 304 337 C2' A A 11 OK OK 339 335 354 338 370 C2' A A 12 OK OK 372 368 387 371 403 C2' A A 13 OK OK 405 401 420 404 436 C2' G A 14 OK OK 438 434 454 437 470 C2' G A 15 OK OK 472 468 488 471 504 C2' C A 16 OK OK 506 502 519 505 535 C2' A A 17 OK OK 537 533 552 536 568 C2' U A 18 OK OK 570 566 583 569 598 C2' C A 19 OK OK 600 596 613 599 629 C2' U A 20 OK OK 631 627 644 630 659 C2' C A 21 OK OK 661 657 674 660 690 C2' C A 22 OK OK 692 688 706 691 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 5 OK OK 139 157 142 143 171 C3' G A 6 OK OK 169 190 172 173 205 C3' G A 7 OK OK 203 224 206 207 239 C3' C A 8 OK OK 237 255 240 241 270 C3' C A 9 OK OK 268 286 271 272 301 C3' G A 10 OK OK 299 320 302 303 335 C3' A A 11 OK OK 333 353 336 337 368 C3' A A 12 OK OK 366 386 369 370 401 C3' A A 13 OK OK 399 419 402 403 434 C3' G A 14 OK OK 432 453 435 436 468 C3' G A 15 OK OK 466 487 469 470 502 C3' C A 16 OK OK 500 518 503 504 533 C3' A A 17 OK OK 531 551 534 535 566 C3' U A 18 OK OK 564 582 567 568 596 C3' C A 19 OK OK 594 612 597 598 627 C3' U A 20 OK OK 625 643 628 629 657 C3' C A 21 OK OK 655 673 658 659 688 C3' C A 22 OK OK 686 704 689 690 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 5 OK OK 141 156 138 140 169 C4' G A 6 OK OK 171 189 168 170 203 C4' G A 7 OK OK 205 223 202 204 237 C4' C A 8 OK OK 239 254 236 238 268 C4' C A 9 OK OK 270 285 267 269 299 C4' G A 10 OK OK 301 319 298 300 333 C4' A A 11 OK OK 335 352 332 334 366 C4' A A 12 OK OK 368 385 365 367 399 C4' A A 13 OK OK 401 418 398 400 432 C4' G A 14 OK OK 434 452 431 433 466 C4' G A 15 OK OK 468 486 465 467 500 C4' C A 16 OK OK 502 517 499 501 531 C4' A A 17 OK OK 533 550 530 532 564 C4' U A 18 OK OK 566 581 563 565 594 C4' C A 19 OK OK 596 611 593 595 625 C4' U A 20 OK OK 627 642 624 626 655 C4' C A 21 OK OK 657 672 654 656 686 C4' C A 22 OK OK 688 703 685 687 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 5 OK OK 137 154 155 139 168 C5' G A 6 OK OK 167 187 188 169 202 C5' G A 7 OK OK 201 221 222 203 236 C5' C A 8 OK OK 235 252 253 237 267 C5' C A 9 OK OK 266 283 284 268 298 C5' G A 10 OK OK 297 317 318 299 332 C5' A A 11 OK OK 331 350 351 333 365 C5' A A 12 OK OK 364 383 384 366 398 C5' A A 13 OK OK 397 416 417 399 431 C5' G A 14 OK OK 430 450 451 432 465 C5' G A 15 OK OK 464 484 485 466 499 C5' C A 16 OK OK 498 515 516 500 530 C5' A A 17 OK OK 529 548 549 531 563 C5' U A 18 OK OK 562 579 580 564 593 C5' C A 19 OK OK 592 609 610 594 624 C5' U A 20 OK OK 623 640 641 625 654 C5' C A 21 OK OK 653 670 671 655 685 C5' C A 22 OK OK 684 701 702 686 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 5 distorted distorted 108 135 136 137 164 P G A 6 distorted distorted 142 165 166 167 198 P G A 7 distorted distorted 172 199 200 201 232 P C A 8 distorted distorted 206 233 234 235 263 P C A 9 distorted distorted 240 264 265 266 294 P G A 10 distorted distorted 271 295 296 297 328 P A A 11 distorted distorted 302 329 330 331 361 P A A 12 distorted distorted 336 362 363 364 394 P A A 13 distorted distorted 369 395 396 397 427 P G A 14 distorted distorted 402 428 429 430 461 P G A 15 distorted distorted 435 462 463 464 495 P C A 16 distorted distorted 469 496 497 498 526 P A A 17 distorted distorted 503 527 528 529 559 P U A 18 distorted distorted 534 560 561 562 589 P C A 19 distorted distorted 567 590 591 592 620 P U A 20 distorted distorted 597 621 622 623 650 P C A 21 distorted distorted 628 651 652 653 681 P C A 22 distorted distorted 658 682 683 684 ---------------------------------------------------------------------------------