ID code: '3Q50' 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' C A 1 beta 4 10 7 29 C1' U A 2 beta 24 30 27 49 C1' G A 3 beta 44 50 47 72 C1' G A 4 beta 67 73 70 95 C1' G A 5 beta 90 96 93 118 C1' U A 6 beta 113 119 116 138 C1' C A 7 beta 133 139 136 158 C1' G A 8 beta 153 159 156 181 C1' C A 9 beta 176 182 179 201 C1' A A 10 beta 196 202 199 223 C1' G A 11 beta 218 224 221 246 C1' U A 12 beta 241 247 244 266 C1' A A 13 beta 261 267 264 288 C1' A A 14 beta 283 289 286 310 C1' C A 15 beta 305 311 308 330 C1' C A 16 beta 325 331 328 350 C1' C A 17 beta 345 351 348 370 C1' C A 18 beta 365 371 368 390 C1' A A 19 beta 385 391 388 412 C1' G A 20 beta 407 413 410 435 C1' U A 21 beta 430 436 433 455 C1' U A 22 beta 450 456 453 475 C1' A A 23 beta 470 476 473 497 C1' A A 24 beta 492 498 495 519 C1' C A 25 beta 514 520 517 539 C1' A A 26 beta 534 540 537 561 C1' A A 27 beta 556 562 559 583 C1' A A 28 beta 578 584 581 605 C1' A A 29 beta 600 606 603 627 C1' C A 30 beta 622 628 625 647 C1' A A 31 beta 642 648 645 669 C1' A A 32 beta 664 670 667 691 C1' G A 33 beta 686 692 689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' U A 2 OK 29 25 28 47 C2' G A 3 OK 49 45 48 70 C2' G A 4 OK 72 68 71 93 C2' G A 5 OK 95 91 94 116 C2' U A 6 OK 118 114 117 136 C2' C A 7 OK 138 134 137 156 C2' G A 8 OK 158 154 157 179 C2' C A 9 OK 181 177 180 199 C2' A A 10 OK 201 197 200 221 C2' G A 11 OK 223 219 222 244 C2' U A 12 OK 246 242 245 264 C2' A A 13 OK 266 262 265 286 C2' A A 14 OK 288 284 287 308 C2' C A 15 OK 310 306 309 328 C2' C A 16 OK 330 326 329 348 C2' C A 17 OK 350 346 349 368 C2' C A 18 OK 370 366 369 388 C2' A A 19 OK 390 386 389 410 C2' G A 20 OK 412 408 411 433 C2' U A 21 OK 435 431 434 453 C2' U A 22 OK 455 451 454 473 C2' A A 23 OK 475 471 474 495 C2' A A 24 OK 497 493 496 517 C2' C A 25 OK 519 515 518 537 C2' A A 26 OK 539 535 538 559 C2' A A 27 OK 561 557 560 581 C2' A A 28 OK 583 579 582 603 C2' A A 29 OK 605 601 604 625 C2' C A 30 OK 627 623 626 645 C2' A A 31 OK 647 643 646 667 C2' A A 32 OK 669 665 668 689 C2' G A 33 OK 691 687 690 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' U A 2 OK 23 26 27 45 C3' G A 3 OK 43 46 47 68 C3' G A 4 OK 66 69 70 91 C3' G A 5 OK 89 92 93 114 C3' U A 6 OK 112 115 116 134 C3' C A 7 OK 132 135 136 154 C3' G A 8 OK 152 155 156 177 C3' C A 9 OK 175 178 179 197 C3' A A 10 OK 195 198 199 219 C3' G A 11 OK 217 220 221 242 C3' U A 12 OK 240 243 244 262 C3' A A 13 OK 260 263 264 284 C3' A A 14 OK 282 285 286 306 C3' C A 15 OK 304 307 308 326 C3' C A 16 OK 324 327 328 346 C3' C A 17 OK 344 347 348 366 C3' C A 18 OK 364 367 368 386 C3' A A 19 OK 384 387 388 408 C3' G A 20 OK 406 409 410 431 C3' U A 21 OK 429 432 433 451 C3' U A 22 OK 449 452 453 471 C3' A A 23 OK 469 472 473 493 C3' A A 24 OK 491 494 495 515 C3' C A 25 OK 513 516 517 535 C3' A A 26 OK 533 536 537 557 C3' A A 27 OK 555 558 559 579 C3' A A 28 OK 577 580 581 601 C3' A A 29 OK 599 602 603 623 C3' C A 30 OK 621 624 625 643 C3' A A 31 OK 641 644 645 665 C3' A A 32 OK 663 666 667 687 C3' G A 33 OK 685 688 689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' U A 2 OK 25 22 24 43 C4' G A 3 OK 45 42 44 66 C4' G A 4 OK 68 65 67 89 C4' G A 5 OK 91 88 90 112 C4' U A 6 OK 114 111 113 132 C4' C A 7 OK 134 131 133 152 C4' G A 8 OK 154 151 153 175 C4' C A 9 OK 177 174 176 195 C4' A A 10 OK 197 194 196 217 C4' G A 11 OK 219 216 218 240 C4' U A 12 OK 242 239 241 260 C4' A A 13 OK 262 259 261 282 C4' A A 14 OK 284 281 283 304 C4' C A 15 OK 306 303 305 324 C4' C A 16 OK 326 323 325 344 C4' C A 17 OK 346 343 345 364 C4' C A 18 OK 366 363 365 384 C4' A A 19 OK 386 383 385 406 C4' G A 20 OK 408 405 407 429 C4' U A 21 OK 431 428 430 449 C4' U A 22 OK 451 448 450 469 C4' A A 23 OK 471 468 470 491 C4' A A 24 OK 493 490 492 513 C4' C A 25 OK 515 512 514 533 C4' A A 26 OK 535 532 534 555 C4' A A 27 OK 557 554 556 577 C4' A A 28 OK 579 576 578 599 C4' A A 29 OK 601 598 600 621 C4' C A 30 OK 623 620 622 641 C4' A A 31 OK 643 640 642 663 C4' A A 32 OK 665 662 664 685 C4' G A 33 OK 687 684 686 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' U A 2 21 23 42 C5' G A 3 41 43 65 C5' G A 4 64 66 88 C5' G A 5 87 89 111 C5' U A 6 110 112 131 C5' C A 7 130 132 151 C5' G A 8 150 152 174 C5' C A 9 173 175 194 C5' A A 10 193 195 216 C5' G A 11 215 217 239 C5' U A 12 238 240 259 C5' A A 13 258 260 281 C5' A A 14 280 282 303 C5' C A 15 302 304 323 C5' C A 16 322 324 343 C5' C A 17 342 344 363 C5' C A 18 362 364 383 C5' A A 19 382 384 405 C5' G A 20 404 406 428 C5' U A 21 427 429 448 C5' U A 22 447 449 468 C5' A A 23 467 469 490 C5' A A 24 489 491 512 C5' C A 25 511 513 532 C5' A A 26 531 533 554 C5' A A 27 553 555 576 C5' A A 28 575 577 598 C5' A A 29 597 599 620 C5' C A 30 619 621 640 C5' A A 31 639 641 662 C5' A A 32 661 663 684 C5' G A 33 683 685 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U A 2 distorted distorted 6 19 20 21 38 P G A 3 distorted distorted 26 39 40 41 61 P G A 4 distorted distorted 46 62 63 64 84 P G A 5 distorted distorted 69 85 86 87 107 P U A 6 distorted distorted 92 108 109 110 127 P C A 7 distorted distorted 115 128 129 130 147 P G A 8 distorted distorted 135 148 149 150 170 P C A 9 distorted distorted 155 171 172 173 190 P A A 10 distorted distorted 178 191 192 193 212 P G A 11 distorted distorted 198 213 214 215 235 P U A 12 distorted distorted 220 236 237 238 255 P A A 13 distorted distorted 243 256 257 258 277 P A A 14 distorted distorted 263 278 279 280 299 P C A 15 distorted distorted 285 300 301 302 319 P C A 16 distorted distorted 307 320 321 322 339 P C A 17 distorted distorted 327 340 341 342 359 P C A 18 distorted distorted 347 360 361 362 379 P A A 19 distorted distorted 367 380 381 382 401 P G A 20 distorted distorted 387 402 403 404 424 P U A 21 distorted distorted 409 425 426 427 444 P U A 22 distorted distorted 432 445 446 447 464 P A A 23 distorted distorted 452 465 466 467 486 P A A 24 distorted distorted 472 487 488 489 508 P C A 25 distorted distorted 494 509 510 511 528 P A A 26 distorted distorted 516 529 530 531 550 P A A 27 distorted distorted 536 551 552 553 572 P A A 28 distorted distorted 558 573 574 575 594 P A A 29 distorted distorted 580 595 596 597 616 P C A 30 distorted distorted 602 617 618 619 636 P A A 31 distorted distorted 624 637 638 639 658 P A A 32 distorted distorted 644 659 660 661 680 P G A 33 distorted distorted 666 681 682 683 ---------------------------------------------------------------------------------