ID code: '1DN7' 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' --------------------------------------------------------------------------------- 8 C1' G A 1 beta 4 9 7 30 C1' G A 2 beta 26 31 29 52 C1' G A 3 beta 48 53 51 74 C1' G A 4 beta 70 75 73 93 C1' G A 5 beta 89 94 92 115 C1' G A 6 beta 111 116 114 137 C1' G A 7 beta 133 138 136 159 C1' G A 8 beta 155 160 158 178 C1' G A 9 beta 174 179 177 200 C1' G A 10 beta 196 201 199 222 C1' G A 11 beta 218 223 221 244 C1' G A 12 beta 240 245 243 263 C1' G A 13 beta 259 264 262 285 C1' G A 14 beta 281 286 284 307 C1' G A 15 beta 303 308 306 329 C1' G A 16 beta 325 330 328 349 C1' C B 1 beta 345 350 348 368 C1' C B 2 beta 364 369 367 387 C1' C B 3 beta 383 388 386 406 C1' C B 4 beta 402 407 405 422 C1' C B 5 beta 418 423 421 441 C1' C B 6 beta 437 442 440 460 C1' C B 7 beta 456 461 459 479 C1' C B 8 beta 475 480 478 495 C1' C B 9 beta 491 496 494 514 C1' C B 10 beta 510 515 513 533 C1' C B 11 beta 529 534 532 552 C1' C B 12 beta 548 553 551 568 C1' C B 13 beta 564 569 567 587 C1' C B 14 beta 583 588 586 606 C1' C B 15 beta 602 607 605 625 C1' C B 16 beta 621 626 624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 8 5 29 C2' G A 2 30 27 51 C2' G A 3 52 49 73 C2' G A 4 74 71 92 C2' G A 5 93 90 114 C2' G A 6 115 112 136 C2' G A 7 137 134 158 C2' G A 8 159 156 177 C2' G A 9 178 175 199 C2' G A 10 200 197 221 C2' G A 11 222 219 243 C2' G A 12 244 241 262 C2' G A 13 263 260 284 C2' G A 14 285 282 306 C2' G A 15 307 304 328 C2' G A 16 329 326 348 C2' C B 1 349 346 367 C2' C B 2 368 365 386 C2' C B 3 387 384 405 C2' C B 4 406 403 421 C2' C B 5 422 419 440 C2' C B 6 441 438 459 C2' C B 7 460 457 478 C2' C B 8 479 476 494 C2' C B 9 495 492 513 C2' C B 10 514 511 532 C2' C B 11 533 530 551 C2' C B 12 552 549 567 C2' C B 13 568 565 586 C2' C B 14 587 584 605 C2' C B 15 606 603 624 C2' C B 16 625 622 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 27 C3' G A 2 OK 25 28 29 49 C3' G A 3 OK 47 50 51 71 C3' G A 4 OK 69 72 73 90 C3' G A 5 OK 88 91 92 112 C3' G A 6 OK 110 113 114 134 C3' G A 7 OK 132 135 136 156 C3' G A 8 OK 154 157 158 175 C3' G A 9 OK 173 176 177 197 C3' G A 10 OK 195 198 199 219 C3' G A 11 OK 217 220 221 241 C3' G A 12 OK 239 242 243 260 C3' G A 13 OK 258 261 262 282 C3' G A 14 OK 280 283 284 304 C3' G A 15 OK 302 305 306 326 C3' G A 16 OK 324 327 328 346 C3' C B 1 OK 344 347 348 365 C3' C B 2 OK 363 366 367 384 C3' C B 3 OK 382 385 386 403 C3' C B 4 OK 401 404 405 419 C3' C B 5 OK 417 420 421 438 C3' C B 6 OK 436 439 440 457 C3' C B 7 OK 455 458 459 476 C3' C B 8 OK 474 477 478 492 C3' C B 9 OK 490 493 494 511 C3' C B 10 OK 509 512 513 530 C3' C B 11 OK 528 531 532 549 C3' C B 12 OK 547 550 551 565 C3' C B 13 OK 563 566 567 584 C3' C B 14 OK 582 585 586 603 C3' C B 15 OK 601 604 605 622 C3' C B 16 OK 620 623 624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 25 C4' G A 2 OK 27 24 26 47 C4' G A 3 OK 49 46 48 69 C4' G A 4 OK 71 68 70 88 C4' G A 5 OK 90 87 89 110 C4' G A 6 OK 112 109 111 132 C4' G A 7 OK 134 131 133 154 C4' G A 8 OK 156 153 155 173 C4' G A 9 OK 175 172 174 195 C4' G A 10 OK 197 194 196 217 C4' G A 11 OK 219 216 218 239 C4' G A 12 OK 241 238 240 258 C4' G A 13 OK 260 257 259 280 C4' G A 14 OK 282 279 281 302 C4' G A 15 OK 304 301 303 324 C4' G A 16 OK 326 323 325 344 C4' C B 1 OK 346 343 345 363 C4' C B 2 OK 365 362 364 382 C4' C B 3 OK 384 381 383 401 C4' C B 4 OK 403 400 402 417 C4' C B 5 OK 419 416 418 436 C4' C B 6 OK 438 435 437 455 C4' C B 7 OK 457 454 456 474 C4' C B 8 OK 476 473 475 490 C4' C B 9 OK 492 489 491 509 C4' C B 10 OK 511 508 510 528 C4' C B 11 OK 530 527 529 547 C4' C B 12 OK 549 546 548 563 C4' C B 13 OK 565 562 564 582 C4' C B 14 OK 584 581 583 601 C4' C B 15 OK 603 600 602 620 C4' C B 16 OK 622 619 621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 24 C5' G A 2 23 25 46 C5' G A 3 45 47 68 C5' G A 4 67 69 87 C5' G A 5 86 88 109 C5' G A 6 108 110 131 C5' G A 7 130 132 153 C5' G A 8 152 154 172 C5' G A 9 171 173 194 C5' G A 10 193 195 216 C5' G A 11 215 217 238 C5' G A 12 237 239 257 C5' G A 13 256 258 279 C5' G A 14 278 280 301 C5' G A 15 300 302 323 C5' G A 16 322 324 343 C5' C B 1 342 344 362 C5' C B 2 361 363 381 C5' C B 3 380 382 400 C5' C B 4 399 401 416 C5' C B 5 415 417 435 C5' C B 6 434 436 454 C5' C B 7 453 455 473 C5' C B 8 472 474 489 C5' C B 9 488 490 508 C5' C B 10 507 509 527 C5' C B 11 526 528 546 C5' C B 12 545 547 562 C5' C B 13 561 563 581 C5' C B 14 580 582 600 C5' C B 15 599 601 619 C5' C B 16 618 620 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P G A 2 distorted distorted 6 21 22 23 42 P G A 3 distorted distorted 28 43 44 45 64 P G A 4 distorted distorted 50 65 66 67 105 P G A 6 distorted distorted 91 106 107 108 127 P G A 7 distorted distorted 113 128 129 130 149 P G A 8 distorted distorted 135 150 151 152 190 P G A 10 distorted distorted 176 191 192 193 212 P G A 11 distorted distorted 198 213 214 215 234 P G A 12 distorted distorted 220 235 236 237 275 P G A 14 distorted distorted 261 276 277 278 297 P G A 15 distorted distorted 283 298 299 300 319 P G A 16 distorted distorted 305 320 321 322 358 P C B 2 distorted distorted 347 359 360 361 377 P C B 3 distorted distorted 366 378 379 380 396 P C B 4 distorted distorted 385 397 398 399 431 P C B 6 distorted distorted 420 432 433 434 450 P C B 7 distorted distorted 439 451 452 453 469 P C B 8 distorted distorted 458 470 471 472 504 P C B 10 distorted distorted 493 505 506 507 523 P C B 11 distorted distorted 512 524 525 526 542 P C B 12 distorted distorted 531 543 544 545 577 P C B 14 distorted distorted 566 578 579 580 596 P C B 15 distorted distorted 585 597 598 599 615 P C B 16 distorted distorted 604 616 617 618 ---------------------------------------------------------------------------------