ID code: '3CW1' 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' --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A V 1 2 P U V 2 3 P A V 3 4 P C V 4 5 P U V 5 6 P U V 6 7 P A V 7 8 P C V 8 9 P C V 9 10 P U V 10 11 P G V 11 12 P G V 12 13 P C V 13 14 P A V 14 15 P G V 15 16 P G V 16 17 P G V 17 18 P G V 18 19 P A V 19 20 P G V 20 21 P A V 21 22 P U V 22 23 P A V 23 24 P C V 24 25 P C V 25 26 P A V 26 27 P U V 27 28 P G V 28 29 P A V 29 30 P U V 30 31 P C V 31 32 P A V 32 33 P C V 33 34 P G V 34 35 P A V 35 36 P A V 36 37 P G V 37 38 P G V 38 39 P U V 39 40 P G V 40 41 P G V 41 42 P U V 42 43 P U V 43 44 P U V 44 45 P U V 45 46 P C V 46 47 P C V 47 48 P C V 48 49 P A V 49 50 P G V 50 51 P G V 51 52 P G V 52 53 P G V 53 54 P A V 54 55 P G V 55 56 P A V 56 57 P C V 83 58 P G V 84 59 P U V 85 60 P C V 86 61 P C V 87 62 P C V 88 63 P C V 89 64 P U V 90 65 P G V 91 66 P C V 92 67 P G V 93 68 P A V 94 69 P U V 95 70 P U V 96 71 P U V 97 72 P C V 98 73 P C V 99 74 P C V 100 75 P C V 101 76 P A V 102 77 P A V 103 78 P A V 104 79 P U V 105 80 P G V 106 81 P U V 107 82 P G V 108 83 P G V 109 84 P G V 110 85 P A V 111 86 P A V 112 87 P A V 113 88 P C V 114 89 P U V 115 90 P C V 116 91 P G V 117 92 P A V 118 93 P C V 119 94 P U V 120 95 P G V 121 96 P C V 122 97 P A V 123 98 P U V 124 99 P A V 125 100 P A V 126 101 P U V 127 102 P U V 128 103 P U V 129 104 P G V 130 105 P U V 131 106 P G V 132 107 P G V 133 108 P U V 134 109 P A V 135 110 P G V 136 111 P U V 137 112 P G V 138 113 P G V 139 114 P G V 140 115 P G V 141 116 P G V 142 117 P A V 143 118 P C V 144 119 P U V 145 120 P G V 146 121 P C V 147 122 P G V 148 123 P U V 149 124 P U V 150 125 P C V 151 126 P G V 152 127 P C V 153 128 P G V 154 129 P C V 155 130 P U V 156 131 P U V 157 132 P U V 158 133 P C V 159 134 P C V 160 135 P C V 161 136 P C V 162 137 P U V 163 138 P G V 164 140 P A v 201 141 P U v 202 142 P A v 203 143 P C v 204 144 P U v 205 145 P U v 206 146 P A v 207 147 P C v 208 148 P C v 209 149 P U v 210 150 P G v 211 151 P G v 212 152 P C v 213 153 P A v 214 154 P G v 215 155 P G v 216 156 P G v 217 157 P G v 218 158 P A v 219 159 P G v 220 160 P A v 221 161 P U v 222 162 P A v 223 163 P C v 224 164 P C v 225 165 P A v 226 166 P U v 227 167 P G v 228 168 P A v 229 169 P U v 230 170 P C v 231 171 P A v 232 172 P C v 233 173 P G v 234 174 P A v 235 175 P A v 236 176 P G v 237 177 P G v 238 178 P U v 239 179 P G v 240 180 P G v 241 181 P U v 242 182 P U v 243 183 P U v 244 184 P U v 245 185 P C v 246 186 P C v 247 187 P C v 248 188 P A v 249 189 P G v 250 190 P G v 251 191 P G v 252 192 P G v 253 193 P A v 254 194 P G v 255 195 P A v 256 196 P C v 283 197 P G v 284 198 P U v 285 199 P C v 286 200 P C v 287 201 P C v 288 202 P C v 289 203 P U v 290 204 P G v 291 205 P C v 292 206 P G v 293 207 P A v 294 208 P U v 295 209 P U v 296 210 P U v 297 211 P C v 298 212 P C v 299 213 P C v 300 214 P C v 301 215 P A v 302 216 P A v 303 217 P A v 304 218 P U v 305 219 P G v 306 220 P U v 307 221 P G v 308 222 P G v 309 223 P G v 310 224 P A v 311 225 P A v 312 226 P A v 313 227 P C v 314 228 P U v 315 229 P C v 316 230 P G v 317 231 P A v 318 232 P C v 319 233 P U v 320 234 P G v 321 235 P C v 322 236 P A v 323 237 P U v 324 238 P A v 325 239 P A v 326 240 P U v 327 241 P U v 328 242 P U v 329 243 P G v 330 244 P U v 331 245 P G v 332 246 P G v 333 247 P U v 334 248 P A v 335 249 P G v 336 250 P U v 337 251 P G v 338 252 P G v 339 253 P G v 340 254 P G v 341 255 P G v 342 256 P A v 343 257 P C v 344 258 P U v 345 259 P G v 346 260 P C v 347 261 P G v 348 262 P U v 349 263 P U v 350 264 P C v 351 265 P G v 352 266 P C v 353 267 P G v 354 268 P C v 355 269 P U v 356 270 P U v 357 271 P U v 358 272 P C v 359 273 P C v 360 274 P C v 361 275 P C v 362 276 P U v 363 277 P G v 364 279 P A w 401 280 P U w 402 281 P A w 403 282 P C w 404 283 P U w 405 284 P U w 406 285 P A w 407 286 P C w 408 287 P C w 409 288 P U w 410 289 P G w 411 290 P G w 412 291 P C w 413 292 P A w 414 293 P G w 415 294 P G w 416 295 P G w 417 296 P G w 418 297 P A w 419 298 P G w 420 299 P A w 421 300 P U w 422 301 P A w 423 302 P C w 424 303 P C w 425 304 P A w 426 305 P U w 427 306 P G w 428 307 P A w 429 308 P U w 430 309 P C w 431 310 P A w 432 311 P C w 433 312 P G w 434 313 P A w 435 314 P A w 436 315 P G w 437 316 P G w 438 317 P U w 439 318 P G w 440 319 P G w 441 320 P U w 442 321 P U w 443 322 P U w 444 323 P U w 445 324 P C w 446 325 P C w 447 326 P C w 448 327 P A w 449 328 P G w 450 329 P G w 451 330 P G w 452 331 P G w 453 332 P A w 454 333 P G w 455 334 P A w 456 335 P C w 483 336 P G w 484 337 P U w 485 338 P C w 486 339 P C w 487 340 P C w 488 341 P C w 489 342 P U w 490 343 P G w 491 344 P C w 492 345 P G w 493 346 P A w 494 347 P U w 495 348 P U w 496 349 P U w 497 350 P C w 498 351 P C w 499 352 P C w 500 353 P C w 501 354 P A w 502 355 P A w 503 356 P A w 504 357 P U w 505 358 P G w 506 359 P U w 507 360 P G w 508 361 P G w 509 362 P G w 510 363 P A w 511 364 P A w 512 365 P A w 513 366 P C w 514 367 P U w 515 368 P C w 516 369 P G w 517 370 P A w 518 371 P C w 519 372 P U w 520 373 P G w 521 374 P C w 522 375 P A w 523 376 P U w 524 377 P A w 525 378 P A w 526 379 P U w 527 380 P U w 528 381 P U w 529 382 P G w 530 383 P U w 531 384 P G w 532 385 P G w 533 386 P U w 534 387 P A w 535 388 P G w 536 389 P U w 537 390 P G w 538 391 P G w 539 392 P G w 540 393 P G w 541 394 P G w 542 395 P A w 543 396 P C w 544 397 P U w 545 398 P G w 546 399 P C w 547 400 P G w 548 401 P U w 549 402 P U w 550 403 P C w 551 404 P G w 552 405 P C w 553 406 P G w 554 407 P C w 555 408 P U w 556 409 P U w 557 410 P U w 558 411 P C w 559 412 P C w 560 413 P C w 561 414 P C w 562 415 P U w 563 416 P G w 564 418 P A x 601 419 P U x 602 420 P A x 603 421 P C x 604 422 P U x 605 423 P U x 606 424 P A x 607 425 P C x 608 426 P C x 609 427 P U x 610 428 P G x 611 429 P G x 612 430 P C x 613 431 P A x 614 432 P G x 615 433 P G x 616 434 P G x 617 435 P G x 618 436 P A x 619 437 P G x 620 438 P A x 621 439 P U x 622 440 P A x 623 441 P C x 624 442 P C x 625 443 P A x 626 444 P U x 627 445 P G x 628 446 P A x 629 447 P U x 630 448 P C x 631 449 P A x 632 450 P C x 633 451 P G x 634 452 P A x 635 453 P A x 636 454 P G x 637 455 P G x 638 456 P U x 639 457 P G x 640 458 P G x 641 459 P U x 642 460 P U x 643 461 P U x 644 462 P U x 645 463 P C x 646 464 P C x 647 465 P C x 648 466 P A x 649 467 P G x 650 468 P G x 651 469 P G x 652 470 P G x 653 471 P A x 654 472 P G x 655 473 P A x 656 474 P C x 683 475 P G x 684 476 P U x 685 477 P C x 686 478 P C x 687 479 P C x 688 480 P C x 689 481 P U x 690 482 P G x 691 483 P C x 692 484 P G x 693 485 P A x 694 486 P U x 695 487 P U x 696 488 P U x 697 489 P C x 698 490 P C x 699 491 P C x 700 492 P C x 701 493 P A x 702 494 P A x 703 495 P A x 704 496 P U x 705 497 P G x 706 498 P U x 707 499 P G x 708 500 P G x 709 501 P G x 710 502 P A x 711 503 P A x 712 504 P A x 713 505 P C x 714 506 P U x 715 507 P C x 716 508 P G x 717 509 P A x 718 510 P C x 719 511 P U x 720 512 P G x 721 513 P C x 722 514 P A x 723 515 P U x 724 516 P A x 725 517 P A x 726 518 P U x 727 519 P U x 728 520 P U x 729 521 P G x 730 522 P U x 731 523 P G x 732 524 P G x 733 525 P U x 734 526 P A x 735 527 P G x 736 528 P U x 737 529 P G x 738 530 P G x 739 531 P G x 740 532 P G x 741 533 P G x 742 534 P A x 743 535 P C x 744 536 P U x 745 537 P G x 746 538 P C x 747 539 P G x 748 540 P U x 749 541 P U x 750 542 P C x 751 543 P G x 752 544 P C x 753 545 P G x 754 546 P C x 755 547 P U x 756 548 P U x 757 549 P U x 758 550 P C x 759 551 P C x 760 552 P C x 761 553 P C x 762 554 P U x 763 555 P G x 764 ---------------------------------------------------------------------------------