ID code: '1A1T' 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' --------------------------------------------------------------------------------- 12 C1' G B 201 alpha beta 7 30 13 10 46 C1' G B 202 alpha beta 41 64 47 44 80 C1' A B 203 alpha beta 75 97 81 78 113 C1' C B 204 alpha beta 108 128 114 111 144 C1' U B 205 alpha beta 139 159 145 142 174 C1' A B 206 alpha beta 169 191 175 172 207 C1' G B 207 alpha beta 202 225 208 205 241 C1' C B 208 alpha beta 236 256 242 239 272 C1' G B 209 alpha beta 267 290 273 270 306 C1' G B 210 alpha beta 301 324 307 304 340 C1' A B 211 alpha beta 335 357 341 338 373 C1' G B 212 alpha beta 368 391 374 371 407 C1' G B 213 alpha beta 402 425 408 405 441 C1' C B 214 alpha beta 436 456 442 439 472 C1' U B 215 alpha beta 467 487 473 470 502 C1' A B 216 alpha beta 497 519 503 500 535 C1' G B 217 alpha beta 530 553 536 533 569 C1' U B 218 alpha beta 564 584 570 567 599 C1' C B 219 alpha beta 594 614 600 597 630 C1' C B 220 alpha beta 625 645 631 628 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G B 201 OK OK 12 8 28 11 44 C2' G B 202 OK OK 46 42 62 45 78 C2' A B 203 OK OK 80 76 95 79 111 C2' C B 204 OK OK 113 109 126 112 142 C2' U B 205 OK OK 144 140 157 143 172 C2' A B 206 OK OK 174 170 189 173 205 C2' G B 207 OK OK 207 203 223 206 239 C2' C B 208 OK OK 241 237 254 240 270 C2' G B 209 OK OK 272 268 288 271 304 C2' G B 210 OK OK 306 302 322 305 338 C2' A B 211 OK OK 340 336 355 339 371 C2' G B 212 OK OK 373 369 389 372 405 C2' G B 213 OK OK 407 403 423 406 439 C2' C B 214 OK OK 441 437 454 440 470 C2' U B 215 OK OK 472 468 485 471 500 C2' A B 216 OK OK 502 498 517 501 533 C2' G B 217 OK OK 535 531 551 534 567 C2' U B 218 OK OK 569 565 582 568 597 C2' C B 219 OK OK 599 595 612 598 628 C2' C B 220 OK OK 630 626 643 629 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G B 201 OK OK 6 27 9 10 42 C3' G B 202 OK OK 40 61 43 44 76 C3' A B 203 OK OK 74 94 77 78 109 C3' C B 204 OK OK 107 125 110 111 140 C3' U B 205 OK OK 138 156 141 142 170 C3' A B 206 OK OK 168 188 171 172 203 C3' G B 207 OK OK 201 222 204 205 237 C3' C B 208 OK OK 235 253 238 239 268 C3' G B 209 OK OK 266 287 269 270 302 C3' G B 210 OK OK 300 321 303 304 336 C3' A B 211 OK OK 334 354 337 338 369 C3' G B 212 OK OK 367 388 370 371 403 C3' G B 213 OK OK 401 422 404 405 437 C3' C B 214 OK OK 435 453 438 439 468 C3' U B 215 OK OK 466 484 469 470 498 C3' A B 216 OK OK 496 516 499 500 531 C3' G B 217 OK OK 529 550 532 533 565 C3' U B 218 OK OK 563 581 566 567 595 C3' C B 219 OK OK 593 611 596 597 626 C3' C B 220 OK OK 624 642 627 628 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G B 201 OK OK 8 26 5 7 40 C4' G B 202 OK OK 42 60 39 41 74 C4' A B 203 OK OK 76 93 73 75 107 C4' C B 204 OK OK 109 124 106 108 138 C4' U B 205 OK OK 140 155 137 139 168 C4' A B 206 OK OK 170 187 167 169 201 C4' G B 207 OK OK 203 221 200 202 235 C4' C B 208 OK OK 237 252 234 236 266 C4' G B 209 OK OK 268 286 265 267 300 C4' G B 210 OK OK 302 320 299 301 334 C4' A B 211 OK OK 336 353 333 335 367 C4' G B 212 OK OK 369 387 366 368 401 C4' G B 213 OK OK 403 421 400 402 435 C4' C B 214 OK OK 437 452 434 436 466 C4' U B 215 OK OK 468 483 465 467 496 C4' A B 216 OK OK 498 515 495 497 529 C4' G B 217 OK OK 531 549 528 530 563 C4' U B 218 OK OK 565 580 562 564 593 C4' C B 219 OK OK 595 610 592 594 624 C4' C B 220 OK OK 626 641 623 625 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G B 201 OK OK 4 24 25 6 39 C5' G B 202 OK OK 38 58 59 40 73 C5' A B 203 OK OK 72 91 92 74 106 C5' C B 204 OK OK 105 122 123 107 137 C5' U B 205 OK OK 136 153 154 138 167 C5' A B 206 OK OK 166 185 186 168 200 C5' G B 207 OK OK 199 219 220 201 234 C5' C B 208 OK OK 233 250 251 235 265 C5' G B 209 OK OK 264 284 285 266 299 C5' G B 210 OK OK 298 318 319 300 333 C5' A B 211 OK OK 332 351 352 334 366 C5' G B 212 OK OK 365 385 386 367 400 C5' G B 213 OK OK 399 419 420 401 434 C5' C B 214 OK OK 433 450 451 435 465 C5' U B 215 OK OK 464 481 482 466 495 C5' A B 216 OK OK 494 513 514 496 528 C5' G B 217 OK OK 527 547 548 529 562 C5' U B 218 OK OK 561 578 579 563 592 C5' C B 219 OK OK 591 608 609 593 623 C5' C B 220 OK OK 622 639 640 624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G B 201 distorted distorted 2 3 4 35 P G B 202 distorted distorted 9 36 37 38 69 P A B 203 distorted distorted 43 70 71 72 102 P C B 204 distorted distorted 77 103 104 105 133 P U B 205 distorted distorted 110 134 135 136 163 P A B 206 distorted distorted 141 164 165 166 196 P G B 207 distorted distorted 171 197 198 199 230 P C B 208 distorted distorted 204 231 232 233 261 P G B 209 distorted distorted 238 262 263 264 295 P G B 210 distorted distorted 269 296 297 298 329 P A B 211 distorted distorted 303 330 331 332 362 P G B 212 distorted distorted 337 363 364 365 396 P G B 213 distorted distorted 370 397 398 399 430 P C B 214 distorted distorted 404 431 432 433 461 P U B 215 distorted distorted 438 462 463 464 491 P A B 216 distorted distorted 469 492 493 494 524 P G B 217 distorted distorted 499 525 526 527 558 P U B 218 distorted distorted 532 559 560 561 588 P C B 219 distorted distorted 566 589 590 591 619 P C B 220 distorted distorted 596 620 621 622 ---------------------------------------------------------------------------------