ID code: '1I3X' 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 202 222 208 205 238 C1' U A 8 alpha beta 233 253 239 236 268 C1' G A 9 alpha beta 263 286 269 266 302 C1' U A 10 alpha beta 297 317 303 300 332 C1' U A 11 alpha beta 327 347 333 330 362 C1' C A 12 alpha beta 357 377 363 360 393 C1' G A 13 alpha beta 388 411 394 391 427 C1' C A 14 alpha beta 422 442 428 425 458 C1' C A 15 alpha beta 453 473 459 456 489 C1' A A 16 alpha beta 484 506 490 487 522 C1' G A 17 alpha beta 517 540 523 520 556 C1' C A 18 alpha beta 551 571 557 554 587 C1' C A 19 alpha beta 582 603 588 585 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 8 OK OK 238 234 251 237 266 C2' G A 9 OK OK 268 264 284 267 300 C2' U A 10 OK OK 302 298 315 301 330 C2' U A 11 OK OK 332 328 345 331 360 C2' C A 12 OK OK 362 358 375 361 391 C2' G A 13 OK OK 393 389 409 392 425 C2' C A 14 OK OK 427 423 440 426 456 C2' C A 15 OK OK 458 454 471 457 487 C2' A A 16 OK OK 489 485 504 488 520 C2' G A 17 OK OK 522 518 538 521 554 C2' C A 18 OK OK 556 552 569 555 585 C2' C A 19 OK OK 587 583 601 586 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 201 219 204 205 234 C3' U A 8 OK OK 232 250 235 236 264 C3' G A 9 OK OK 262 283 265 266 298 C3' U A 10 OK OK 296 314 299 300 328 C3' U A 11 OK OK 326 344 329 330 358 C3' C A 12 OK OK 356 374 359 360 389 C3' G A 13 OK OK 387 408 390 391 423 C3' C A 14 OK OK 421 439 424 425 454 C3' C A 15 OK OK 452 470 455 456 485 C3' A A 16 OK OK 483 503 486 487 518 C3' G A 17 OK OK 516 537 519 520 552 C3' C A 18 OK OK 550 568 553 554 583 C3' C A 19 OK OK 581 599 584 585 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 203 218 200 202 232 C4' U A 8 OK OK 234 249 231 233 262 C4' G A 9 OK OK 264 282 261 263 296 C4' U A 10 OK OK 298 313 295 297 326 C4' U A 11 OK OK 328 343 325 327 356 C4' C A 12 OK OK 358 373 355 357 387 C4' G A 13 OK OK 389 407 386 388 421 C4' C A 14 OK OK 423 438 420 422 452 C4' C A 15 OK OK 454 469 451 453 483 C4' A A 16 OK OK 485 502 482 484 516 C4' G A 17 OK OK 518 536 515 517 550 C4' C A 18 OK OK 552 567 549 551 581 C4' C A 19 OK OK 583 598 580 582 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 199 216 217 201 231 C5' U A 8 OK OK 230 247 248 232 261 C5' G A 9 OK OK 260 280 281 262 295 C5' U A 10 OK OK 294 311 312 296 325 C5' U A 11 OK OK 324 341 342 326 355 C5' C A 12 OK OK 354 371 372 356 386 C5' G A 13 OK OK 385 405 406 387 420 C5' C A 14 OK OK 419 436 437 421 451 C5' C A 15 OK OK 450 467 468 452 482 C5' A A 16 OK OK 481 500 501 483 515 C5' G A 17 OK OK 514 534 535 516 549 C5' C A 18 OK OK 548 565 566 550 580 C5' C A 19 OK OK 579 596 597 581 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 170 197 198 199 227 P U A 8 distorted distorted 204 228 229 230 257 P G A 9 distorted distorted 235 258 259 260 291 P U A 10 distorted distorted 265 292 293 294 321 P U A 11 distorted distorted 299 322 323 324 351 P C A 12 distorted distorted 329 352 353 354 382 P G A 13 distorted distorted 359 383 384 385 416 P C A 14 distorted distorted 390 417 418 419 447 P C A 15 distorted distorted 424 448 449 450 478 P A A 16 distorted distorted 455 479 480 481 511 P G A 17 distorted distorted 486 512 513 514 545 P C A 18 distorted distorted 519 546 547 548 576 P C A 19 distorted distorted 553 577 578 579 ---------------------------------------------------------------------------------