ID code: '1I3Y' 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' U A 4 alpha beta 104 124 110 107 139 C1' G A 5 alpha beta 134 157 140 137 173 C1' G A 6 alpha beta 168 191 174 171 207 C1' C A 7 alpha beta 202 222 208 205 235 C1' OMU A 8 alpha beta 242 251 227 236 271 C1' G A 9 alpha beta 266 289 272 269 305 C1' U A 10 alpha beta 300 320 306 303 335 C1' U A 11 alpha beta 330 350 336 333 365 C1' C A 12 alpha beta 360 380 366 363 396 C1' G A 13 alpha beta 391 414 397 394 430 C1' C A 14 alpha beta 425 445 431 428 461 C1' C A 15 alpha beta 456 476 462 459 492 C1' A A 16 alpha beta 487 509 493 490 525 C1' G A 17 alpha beta 520 543 526 523 559 C1' C A 18 alpha beta 554 574 560 557 590 C1' C A 19 alpha beta 585 606 591 588 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 4 OK OK 109 105 122 108 137 C2' G A 5 OK OK 139 135 155 138 171 C2' G A 6 OK OK 173 169 189 172 205 C2' C A 7 OK OK 207 203 220 206 236 C2' OMU A 8 OK OK 235 239 252 237 269 C2' G A 9 OK OK 271 267 287 270 303 C2' U A 10 OK OK 305 301 318 304 333 C2' U A 11 OK OK 335 331 348 334 363 C2' C A 12 OK OK 365 361 378 364 394 C2' G A 13 OK OK 396 392 412 395 428 C2' C A 14 OK OK 430 426 443 429 459 C2' C A 15 OK OK 461 457 474 460 490 C2' A A 16 OK OK 492 488 507 491 523 C2' G A 17 OK OK 525 521 541 524 557 C2' C A 18 OK OK 559 555 572 558 588 C2' C A 19 OK OK 590 586 604 589 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 103 121 106 107 135 C3' G A 5 OK OK 133 154 136 137 169 C3' G A 6 OK OK 167 188 170 171 203 C3' C A 7 OK OK 201 219 204 205 239 C3' OMU A 8 OK OK 240 256 241 236 267 C3' G A 9 OK OK 265 286 268 269 301 C3' U A 10 OK OK 299 317 302 303 331 C3' U A 11 OK OK 329 347 332 333 361 C3' C A 12 OK OK 359 377 362 363 392 C3' G A 13 OK OK 390 411 393 394 426 C3' C A 14 OK OK 424 442 427 428 457 C3' C A 15 OK OK 455 473 458 459 488 C3' A A 16 OK OK 486 506 489 490 521 C3' G A 17 OK OK 519 540 522 523 555 C3' C A 18 OK OK 553 571 556 557 586 C3' C A 19 OK OK 584 602 587 588 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 105 120 102 104 133 C4' G A 5 OK OK 135 153 132 134 167 C4' G A 6 OK OK 169 187 166 168 201 C4' C A 7 OK OK 203 218 200 202 240 C4' OMU A 8 OK OK 239 257 243 242 265 C4' G A 9 OK OK 267 285 264 266 299 C4' U A 10 OK OK 301 316 298 300 329 C4' U A 11 OK OK 331 346 328 330 359 C4' C A 12 OK OK 361 376 358 360 390 C4' G A 13 OK OK 392 410 389 391 424 C4' C A 14 OK OK 426 441 423 425 455 C4' C A 15 OK OK 457 472 454 456 486 C4' A A 16 OK OK 488 505 485 487 519 C4' G A 17 OK OK 521 539 518 520 553 C4' C A 18 OK OK 555 570 552 554 584 C4' C A 19 OK OK 586 601 583 585 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 101 118 119 103 132 C5' G A 5 OK OK 131 151 152 133 166 C5' G A 6 OK OK 165 185 186 167 200 C5' C A 7 OK OK 199 216 217 201 243 C5' OMU A 8 OK OK 244 258 259 240 264 C5' G A 9 OK OK 263 283 284 265 298 C5' U A 10 OK OK 297 314 315 299 328 C5' U A 11 OK OK 327 344 345 329 358 C5' C A 12 OK OK 357 374 375 359 389 C5' G A 13 OK OK 388 408 409 390 423 C5' C A 14 OK OK 422 439 440 424 454 C5' C A 15 OK OK 453 470 471 455 485 C5' A A 16 OK OK 484 503 504 486 518 C5' G A 17 OK OK 517 537 538 519 552 C5' C A 18 OK OK 551 568 569 553 583 C5' C A 19 OK OK 582 599 600 584 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 4 distorted distorted 75 99 100 101 128 P G A 5 distorted distorted 106 129 130 131 162 P G A 6 distorted distorted 136 163 164 165 196 P C A 7 distorted distorted 170 197 198 199 245 P OMU A 8 distorted distorted 204 246 247 244 260 P G A 9 distorted distorted 241 261 262 263 294 P U A 10 distorted distorted 268 295 296 297 324 P U A 11 distorted distorted 302 325 326 327 354 P C A 12 distorted distorted 332 355 356 357 385 P G A 13 distorted distorted 362 386 387 388 419 P C A 14 distorted distorted 393 420 421 422 450 P C A 15 distorted distorted 427 451 452 453 481 P A A 16 distorted distorted 458 482 483 484 514 P G A 17 distorted distorted 489 515 516 517 548 P C A 18 distorted distorted 522 549 550 551 579 P C A 19 distorted distorted 556 580 581 582 ---------------------------------------------------------------------------------