ID code: '2O33' 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' U A 3 alpha beta 73 93 79 76 108 C1' U A 4 alpha beta 103 123 109 106 138 C1' U A 5 alpha beta 133 153 139 136 168 C1' G A 6 alpha beta 163 186 169 166 202 C1' C A 7 alpha beta 197 217 203 200 233 C1' C A 8 alpha beta 228 248 234 231 264 C1' U A 9 alpha beta 259 279 265 262 294 C1' U A 10 alpha beta 289 309 295 292 324 C1' U A 11 alpha beta 319 339 325 322 354 C1' U A 12 alpha beta 349 369 355 352 384 C1' G A 13 alpha beta 379 402 385 382 418 C1' G A 14 alpha beta 413 436 419 416 452 C1' C A 15 alpha beta 447 467 453 450 483 C1' U A 16 alpha beta 478 498 484 481 513 C1' U A 17 alpha beta 508 528 514 511 543 C1' A A 18 alpha beta 538 560 544 541 576 C1' C A 19 alpha beta 571 591 577 574 607 C1' C A 20 alpha beta 602 623 608 605 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 3 OK OK 78 74 91 77 106 C2' U A 4 OK OK 108 104 121 107 136 C2' U A 5 OK OK 138 134 151 137 166 C2' G A 6 OK OK 168 164 184 167 200 C2' C A 7 OK OK 202 198 215 201 231 C2' C A 8 OK OK 233 229 246 232 262 C2' U A 9 OK OK 264 260 277 263 292 C2' U A 10 OK OK 294 290 307 293 322 C2' U A 11 OK OK 324 320 337 323 352 C2' U A 12 OK OK 354 350 367 353 382 C2' G A 13 OK OK 384 380 400 383 416 C2' G A 14 OK OK 418 414 434 417 450 C2' C A 15 OK OK 452 448 465 451 481 C2' U A 16 OK OK 483 479 496 482 511 C2' U A 17 OK OK 513 509 526 512 541 C2' A A 18 OK OK 543 539 558 542 574 C2' C A 19 OK OK 576 572 589 575 605 C2' C A 20 OK OK 607 603 621 606 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 72 90 75 76 104 C3' U A 4 OK OK 102 120 105 106 134 C3' U A 5 OK OK 132 150 135 136 164 C3' G A 6 OK OK 162 183 165 166 198 C3' C A 7 OK OK 196 214 199 200 229 C3' C A 8 OK OK 227 245 230 231 260 C3' U A 9 OK OK 258 276 261 262 290 C3' U A 10 OK OK 288 306 291 292 320 C3' U A 11 OK OK 318 336 321 322 350 C3' U A 12 OK OK 348 366 351 352 380 C3' G A 13 OK OK 378 399 381 382 414 C3' G A 14 OK OK 412 433 415 416 448 C3' C A 15 OK OK 446 464 449 450 479 C3' U A 16 OK OK 477 495 480 481 509 C3' U A 17 OK OK 507 525 510 511 539 C3' A A 18 OK OK 537 557 540 541 572 C3' C A 19 OK OK 570 588 573 574 603 C3' C A 20 OK OK 601 619 604 605 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 74 89 71 73 102 C4' U A 4 OK OK 104 119 101 103 132 C4' U A 5 OK OK 134 149 131 133 162 C4' G A 6 OK OK 164 182 161 163 196 C4' C A 7 OK OK 198 213 195 197 227 C4' C A 8 OK OK 229 244 226 228 258 C4' U A 9 OK OK 260 275 257 259 288 C4' U A 10 OK OK 290 305 287 289 318 C4' U A 11 OK OK 320 335 317 319 348 C4' U A 12 OK OK 350 365 347 349 378 C4' G A 13 OK OK 380 398 377 379 412 C4' G A 14 OK OK 414 432 411 413 446 C4' C A 15 OK OK 448 463 445 447 477 C4' U A 16 OK OK 479 494 476 478 507 C4' U A 17 OK OK 509 524 506 508 537 C4' A A 18 OK OK 539 556 536 538 570 C4' C A 19 OK OK 572 587 569 571 601 C4' C A 20 OK OK 603 618 600 602 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 70 87 88 72 101 C5' U A 4 OK OK 100 117 118 102 131 C5' U A 5 OK OK 130 147 148 132 161 C5' G A 6 OK OK 160 180 181 162 195 C5' C A 7 OK OK 194 211 212 196 226 C5' C A 8 OK OK 225 242 243 227 257 C5' U A 9 OK OK 256 273 274 258 287 C5' U A 10 OK OK 286 303 304 288 317 C5' U A 11 OK OK 316 333 334 318 347 C5' U A 12 OK OK 346 363 364 348 377 C5' G A 13 OK OK 376 396 397 378 411 C5' G A 14 OK OK 410 430 431 412 445 C5' C A 15 OK OK 444 461 462 446 476 C5' U A 16 OK OK 475 492 493 477 506 C5' U A 17 OK OK 505 522 523 507 536 C5' A A 18 OK OK 535 554 555 537 569 C5' C A 19 OK OK 568 585 586 570 600 C5' C A 20 OK OK 599 616 617 601 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P U A 4 distorted distorted 75 98 99 100 127 P U A 5 distorted distorted 105 128 129 130 157 P G A 6 distorted distorted 135 158 159 160 191 P C A 7 distorted distorted 165 192 193 194 222 P C A 8 distorted distorted 199 223 224 225 253 P U A 9 distorted distorted 230 254 255 256 283 P U A 10 distorted distorted 261 284 285 286 313 P U A 11 distorted distorted 291 314 315 316 343 P U A 12 distorted distorted 321 344 345 346 373 P G A 13 distorted distorted 351 374 375 376 407 P G A 14 distorted distorted 381 408 409 410 441 P C A 15 distorted distorted 415 442 443 444 472 P U A 16 distorted distorted 449 473 474 475 502 P U A 17 distorted distorted 480 503 504 505 532 P A A 18 distorted distorted 510 533 534 535 565 P C A 19 distorted distorted 540 566 567 568 596 P C A 20 distorted distorted 573 597 598 599 ---------------------------------------------------------------------------------