ID code: '1AUD' 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 B 19 beta 4 10 7 32 C1' G B 20 beta 27 33 30 55 C1' C B 21 beta 50 56 53 75 C1' A B 22 beta 70 76 73 97 C1' G B 23 beta 92 98 95 120 C1' A B 24 beta 115 121 118 142 C1' G B 25 beta 137 143 140 165 C1' U B 26 beta 160 166 163 185 C1' C B 27 beta 180 186 183 205 C1' C B 28 beta 200 206 203 225 C1' U B 29 beta 220 226 223 245 C1' U B 30 beta 240 246 243 265 C1' C B 33 beta 260 266 263 285 C1' G B 34 beta 280 286 283 308 C1' G B 35 beta 303 309 306 331 C1' G B 36 beta 326 332 329 354 C1' A B 37 beta 349 355 352 376 C1' C B 38 beta 371 377 374 396 C1' A B 39 beta 391 397 394 418 C1' U B 40 beta 413 419 416 438 C1' U B 41 beta 433 439 436 458 C1' G B 42 beta 453 459 456 481 C1' C B 43 beta 476 482 479 501 C1' A B 44 beta 496 502 499 523 C1' C B 45 beta 518 524 521 543 C1' C B 46 beta 538 544 541 563 C1' U B 47 beta 558 564 561 583 C1' G B 48 beta 578 584 581 606 C1' C B 49 beta 601 607 604 626 C1' C B 50 beta 621 627 624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 19 OK 9 5 8 30 C2' G B 20 OK 32 28 31 53 C2' C B 21 OK 55 51 54 73 C2' A B 22 OK 75 71 74 95 C2' G B 23 OK 97 93 96 118 C2' A B 24 OK 120 116 119 140 C2' G B 25 OK 142 138 141 163 C2' U B 26 OK 165 161 164 183 C2' C B 27 OK 185 181 184 203 C2' C B 28 OK 205 201 204 223 C2' U B 29 OK 225 221 224 243 C2' U B 30 OK 245 241 244 263 C2' C B 33 OK 265 261 264 283 C2' G B 34 OK 285 281 284 306 C2' G B 35 OK 308 304 307 329 C2' G B 36 OK 331 327 330 352 C2' A B 37 OK 354 350 353 374 C2' C B 38 OK 376 372 375 394 C2' A B 39 OK 396 392 395 416 C2' U B 40 OK 418 414 417 436 C2' U B 41 OK 438 434 437 456 C2' G B 42 OK 458 454 457 479 C2' C B 43 OK 481 477 480 499 C2' A B 44 OK 501 497 500 521 C2' C B 45 OK 523 519 522 541 C2' C B 46 OK 543 539 542 561 C2' U B 47 OK 563 559 562 581 C2' G B 48 OK 583 579 582 604 C2' C B 49 OK 606 602 605 624 C2' C B 50 OK 626 622 625 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 19 OK 3 6 7 28 C3' G B 20 OK 26 29 30 51 C3' C B 21 OK 49 52 53 71 C3' A B 22 OK 69 72 73 93 C3' G B 23 OK 91 94 95 116 C3' A B 24 OK 114 117 118 138 C3' G B 25 OK 136 139 140 161 C3' U B 26 OK 159 162 163 181 C3' C B 27 OK 179 182 183 201 C3' C B 28 OK 199 202 203 221 C3' U B 29 OK 219 222 223 241 C3' U B 30 OK 239 242 243 261 C3' C B 33 OK 259 262 263 281 C3' G B 34 OK 279 282 283 304 C3' G B 35 OK 302 305 306 327 C3' G B 36 OK 325 328 329 350 C3' A B 37 OK 348 351 352 372 C3' C B 38 OK 370 373 374 392 C3' A B 39 OK 390 393 394 414 C3' U B 40 OK 412 415 416 434 C3' U B 41 OK 432 435 436 454 C3' G B 42 OK 452 455 456 477 C3' C B 43 OK 475 478 479 497 C3' A B 44 OK 495 498 499 519 C3' C B 45 OK 517 520 521 539 C3' C B 46 OK 537 540 541 559 C3' U B 47 OK 557 560 561 579 C3' G B 48 OK 577 580 581 602 C3' C B 49 OK 600 603 604 622 C3' C B 50 OK 620 623 624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 19 OK 5 2 4 26 C4' G B 20 OK 28 25 27 49 C4' C B 21 OK 51 48 50 69 C4' A B 22 OK 71 68 70 91 C4' G B 23 OK 93 90 92 114 C4' A B 24 OK 116 113 115 136 C4' G B 25 OK 138 135 137 159 C4' U B 26 OK 161 158 160 179 C4' C B 27 OK 181 178 180 199 C4' C B 28 OK 201 198 200 219 C4' U B 29 OK 221 218 220 239 C4' U B 30 OK 241 238 240 259 C4' C B 33 OK 261 258 260 279 C4' G B 34 OK 281 278 280 302 C4' G B 35 OK 304 301 303 325 C4' G B 36 OK 327 324 326 348 C4' A B 37 OK 350 347 349 370 C4' C B 38 OK 372 369 371 390 C4' A B 39 OK 392 389 391 412 C4' U B 40 OK 414 411 413 432 C4' U B 41 OK 434 431 433 452 C4' G B 42 OK 454 451 453 475 C4' C B 43 OK 477 474 476 495 C4' A B 44 OK 497 494 496 517 C4' C B 45 OK 519 516 518 537 C4' C B 46 OK 539 536 538 557 C4' U B 47 OK 559 556 558 577 C4' G B 48 OK 579 576 578 600 C4' C B 49 OK 602 599 601 620 C4' C B 50 OK 622 619 621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 19 1 3 25 C5' G B 20 24 26 48 C5' C B 21 47 49 68 C5' A B 22 67 69 90 C5' G B 23 89 91 113 C5' A B 24 112 114 135 C5' G B 25 134 136 158 C5' U B 26 157 159 178 C5' C B 27 177 179 198 C5' C B 28 197 199 218 C5' U B 29 217 219 238 C5' U B 30 237 239 258 C5' C B 33 257 259 278 C5' G B 34 277 279 301 C5' G B 35 300 302 324 C5' G B 36 323 325 347 C5' A B 37 346 348 369 C5' C B 38 368 370 389 C5' A B 39 388 390 411 C5' U B 40 410 412 431 C5' U B 41 430 432 451 C5' G B 42 450 452 474 C5' C B 43 473 475 494 C5' A B 44 493 495 516 C5' C B 45 515 517 536 C5' C B 46 535 537 556 C5' U B 47 555 557 576 C5' G B 48 575 577 599 C5' C B 49 598 600 619 C5' C B 50 618 620 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G B 20 distorted distorted 6 22 23 24 44 P C B 21 distorted distorted 29 45 46 47 64 P A B 22 distorted distorted 52 65 66 67 86 P G B 23 distorted distorted 72 87 88 89 109 P A B 24 distorted distorted 94 110 111 112 131 P G B 25 distorted distorted 117 132 133 134 154 P U B 26 distorted distorted 139 155 156 157 174 P C B 27 distorted distorted 162 175 176 177 194 P C B 28 distorted distorted 182 195 196 197 214 P U B 29 distorted distorted 202 215 216 217 234 P U B 30 distorted distorted 222 235 236 237 254 P C B 33 distorted distorted 242 255 256 257 274 P G B 34 distorted distorted 262 275 276 277 297 P G B 35 distorted distorted 282 298 299 300 320 P G B 36 distorted distorted 305 321 322 323 343 P A B 37 distorted distorted 328 344 345 346 365 P C B 38 distorted distorted 351 366 367 368 385 P A B 39 distorted distorted 373 386 387 388 407 P U B 40 distorted distorted 393 408 409 410 427 P U B 41 distorted distorted 415 428 429 430 447 P G B 42 distorted distorted 435 448 449 450 470 P C B 43 distorted distorted 455 471 472 473 490 P A B 44 distorted distorted 478 491 492 493 512 P C B 45 distorted distorted 498 513 514 515 532 P C B 46 distorted distorted 520 533 534 535 552 P U B 47 distorted distorted 540 553 554 555 572 P G B 48 distorted distorted 560 573 574 575 595 P C B 49 distorted distorted 580 596 597 598 615 P C B 50 distorted distorted 603 616 617 618 ---------------------------------------------------------------------------------