ID code: '2M21' 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' C A 3 alpha beta 73 93 79 76 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' A A 5 alpha beta 138 160 144 141 176 C1' U A 6 alpha beta 171 191 177 174 206 C1' A A 7 alpha beta 201 223 207 204 239 C1' C A 8 alpha beta 234 254 240 237 270 C1' A A 9 alpha beta 265 287 271 268 303 C1' C A 10 alpha beta 298 318 304 301 334 C1' U A 11 alpha beta 329 349 335 332 364 C1' A A 12 alpha beta 359 381 365 362 397 C1' U A 13 alpha beta 392 412 398 395 427 C1' U A 14 alpha beta 422 442 428 425 457 C1' U A 15 alpha beta 452 472 458 455 487 C1' A A 16 alpha beta 482 504 488 485 520 C1' U A 17 alpha beta 515 535 521 518 550 C1' C A 18 alpha beta 545 565 551 548 581 C1' G A 19 alpha beta 576 599 582 579 615 C1' C A 20 alpha beta 610 630 616 613 646 C1' C A 21 alpha beta 641 662 647 644 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' G A 4 OK OK 109 105 125 108 141 C2' A A 5 OK OK 143 139 158 142 174 C2' U A 6 OK OK 176 172 189 175 204 C2' A A 7 OK OK 206 202 221 205 237 C2' C A 8 OK OK 239 235 252 238 268 C2' A A 9 OK OK 270 266 285 269 301 C2' C A 10 OK OK 303 299 316 302 332 C2' U A 11 OK OK 334 330 347 333 362 C2' A A 12 OK OK 364 360 379 363 395 C2' U A 13 OK OK 397 393 410 396 425 C2' U A 14 OK OK 427 423 440 426 455 C2' U A 15 OK OK 457 453 470 456 485 C2' A A 16 OK OK 487 483 502 486 518 C2' U A 17 OK OK 520 516 533 519 548 C2' C A 18 OK OK 550 546 563 549 579 C2' G A 19 OK OK 581 577 597 580 613 C2' C A 20 OK OK 615 611 628 614 644 C2' C A 21 OK OK 646 642 660 645 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' G A 4 OK OK 103 124 106 107 139 C3' A A 5 OK OK 137 157 140 141 172 C3' U A 6 OK OK 170 188 173 174 202 C3' A A 7 OK OK 200 220 203 204 235 C3' C A 8 OK OK 233 251 236 237 266 C3' A A 9 OK OK 264 284 267 268 299 C3' C A 10 OK OK 297 315 300 301 330 C3' U A 11 OK OK 328 346 331 332 360 C3' A A 12 OK OK 358 378 361 362 393 C3' U A 13 OK OK 391 409 394 395 423 C3' U A 14 OK OK 421 439 424 425 453 C3' U A 15 OK OK 451 469 454 455 483 C3' A A 16 OK OK 481 501 484 485 516 C3' U A 17 OK OK 514 532 517 518 546 C3' C A 18 OK OK 544 562 547 548 577 C3' G A 19 OK OK 575 596 578 579 611 C3' C A 20 OK OK 609 627 612 613 642 C3' C A 21 OK OK 640 658 643 644 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' G A 4 OK OK 105 123 102 104 137 C4' A A 5 OK OK 139 156 136 138 170 C4' U A 6 OK OK 172 187 169 171 200 C4' A A 7 OK OK 202 219 199 201 233 C4' C A 8 OK OK 235 250 232 234 264 C4' A A 9 OK OK 266 283 263 265 297 C4' C A 10 OK OK 299 314 296 298 328 C4' U A 11 OK OK 330 345 327 329 358 C4' A A 12 OK OK 360 377 357 359 391 C4' U A 13 OK OK 393 408 390 392 421 C4' U A 14 OK OK 423 438 420 422 451 C4' U A 15 OK OK 453 468 450 452 481 C4' A A 16 OK OK 483 500 480 482 514 C4' U A 17 OK OK 516 531 513 515 544 C4' C A 18 OK OK 546 561 543 545 575 C4' G A 19 OK OK 577 595 574 576 609 C4' C A 20 OK OK 611 626 608 610 640 C4' C A 21 OK OK 642 657 639 641 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' G A 4 OK OK 101 121 122 103 136 C5' A A 5 OK OK 135 154 155 137 169 C5' U A 6 OK OK 168 185 186 170 199 C5' A A 7 OK OK 198 217 218 200 232 C5' C A 8 OK OK 231 248 249 233 263 C5' A A 9 OK OK 262 281 282 264 296 C5' C A 10 OK OK 295 312 313 297 327 C5' U A 11 OK OK 326 343 344 328 357 C5' A A 12 OK OK 356 375 376 358 390 C5' U A 13 OK OK 389 406 407 391 420 C5' U A 14 OK OK 419 436 437 421 450 C5' U A 15 OK OK 449 466 467 451 480 C5' A A 16 OK OK 479 498 499 481 513 C5' U A 17 OK OK 512 529 530 514 543 C5' C A 18 OK OK 542 559 560 544 574 C5' G A 19 OK OK 573 593 594 575 608 C5' C A 20 OK OK 607 624 625 609 639 C5' C A 21 OK OK 638 655 656 640 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P G A 4 distorted distorted 75 99 100 101 132 P A A 5 distorted distorted 106 133 134 135 165 P U A 6 distorted distorted 140 166 167 168 195 P A A 7 distorted distorted 173 196 197 198 228 P C A 8 distorted distorted 203 229 230 231 259 P A A 9 distorted distorted 236 260 261 262 292 P C A 10 distorted distorted 267 293 294 295 323 P U A 11 distorted distorted 300 324 325 326 353 P A A 12 distorted distorted 331 354 355 356 386 P U A 13 distorted distorted 361 387 388 389 416 P U A 14 distorted distorted 394 417 418 419 446 P U A 15 distorted distorted 424 447 448 449 476 P A A 16 distorted distorted 454 477 478 479 509 P U A 17 distorted distorted 484 510 511 512 539 P C A 18 distorted distorted 517 540 541 542 570 P G A 19 distorted distorted 547 571 572 573 604 P C A 20 distorted distorted 578 605 606 607 635 P C A 21 distorted distorted 612 636 637 638 ---------------------------------------------------------------------------------