ID code: '1RME' 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' MCY A 1 alpha beta 13 21 1 10 42 C1' DC A 2 alpha beta 38 57 43 41 72 C1' DT A 3 alpha beta 68 88 73 71 104 C1' DC A 4 alpha beta 100 119 105 103 134 C1' DC A 5 alpha beta 130 150 135 133 164 C1' MCY B 1 alpha beta 168 176 156 165 197 C1' DC B 2 alpha beta 193 212 198 196 227 C1' DT B 3 alpha beta 223 243 228 226 259 C1' DC B 4 alpha beta 255 274 260 258 289 C1' DC B 5 alpha beta 285 305 290 288 319 C1' MCY C 1 alpha beta 323 331 311 320 352 C1' DC C 2 alpha beta 348 367 353 351 382 C1' DT C 3 alpha beta 378 398 383 381 414 C1' DC C 4 alpha beta 410 429 415 413 444 C1' DC C 5 alpha beta 440 460 445 443 474 C1' MCY D 1 alpha beta 478 486 466 475 507 C1' DC D 2 alpha beta 503 522 508 506 537 C1' DT D 3 alpha beta 533 553 538 536 569 C1' DC D 4 alpha beta 565 584 570 568 599 C1' DC D 5 alpha beta 595 615 600 598 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' MCY A 1 OK OK 9 11 22 23 41 C2' DC A 2 OK OK 42 39 55 56 71 C2' DT A 3 OK OK 72 69 86 87 103 C2' DC A 4 OK OK 104 101 117 118 133 C2' DC A 5 OK OK 134 131 148 149 165 C2' MCY B 1 OK OK 164 166 177 178 196 C2' DC B 2 OK OK 197 194 210 211 226 C2' DT B 3 OK OK 227 224 241 242 258 C2' DC B 4 OK OK 259 256 272 273 288 C2' DC B 5 OK OK 289 286 303 304 320 C2' MCY C 1 OK OK 319 321 332 333 351 C2' DC C 2 OK OK 352 349 365 366 381 C2' DT C 3 OK OK 382 379 396 397 413 C2' DC C 4 OK OK 414 411 427 428 443 C2' DC C 5 OK OK 444 441 458 459 475 C2' MCY D 1 OK OK 474 476 487 488 506 C2' DC D 2 OK OK 507 504 520 521 536 C2' DT D 3 OK OK 537 534 551 552 568 C2' DC D 4 OK OK 569 566 582 583 598 C2' DC D 5 OK OK 599 596 613 614 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 11 C3' MCY A 1 OK OK 12 24 14 10 39 C3' DC A 2 OK OK 37 54 40 41 69 C3' DT A 3 OK OK 67 85 70 71 101 C3' DC A 4 OK OK 99 116 102 103 131 C3' DC A 5 OK OK 129 146 132 133 166 C3' MCY B 1 OK OK 167 179 169 165 194 C3' DC B 2 OK OK 192 209 195 196 224 C3' DT B 3 OK OK 222 240 225 226 256 C3' DC B 4 OK OK 254 271 257 258 286 C3' DC B 5 OK OK 284 301 287 288 321 C3' MCY C 1 OK OK 322 334 324 320 349 C3' DC C 2 OK OK 347 364 350 351 379 C3' DT C 3 OK OK 377 395 380 381 411 C3' DC C 4 OK OK 409 426 412 413 441 C3' DC C 5 OK OK 439 456 442 443 476 C3' MCY D 1 OK OK 477 489 479 475 504 C3' DC D 2 OK OK 502 519 505 506 534 C3' DT D 3 OK OK 532 550 535 536 566 C3' DC D 4 OK OK 564 581 567 568 596 C3' DC D 5 OK OK 594 611 597 598 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 12 C4' MCY A 1 OK OK 11 25 15 13 37 C4' DC A 2 OK OK 39 53 36 38 67 C4' DT A 3 OK OK 69 84 66 68 99 C4' DC A 4 OK OK 101 115 98 100 129 C4' DC A 5 OK OK 131 145 128 130 167 C4' MCY B 1 OK OK 166 180 170 168 192 C4' DC B 2 OK OK 194 208 191 193 222 C4' DT B 3 OK OK 224 239 221 223 254 C4' DC B 4 OK OK 256 270 253 255 284 C4' DC B 5 OK OK 286 300 283 285 322 C4' MCY C 1 OK OK 321 335 325 323 347 C4' DC C 2 OK OK 349 363 346 348 377 C4' DT C 3 OK OK 379 394 376 378 409 C4' DC C 4 OK OK 411 425 408 410 439 C4' DC C 5 OK OK 441 455 438 440 477 C4' MCY D 1 OK OK 476 490 480 478 502 C4' DC D 2 OK OK 504 518 501 503 532 C4' DT D 3 OK OK 534 549 531 533 564 C4' DC D 4 OK OK 566 580 563 565 594 C4' DC D 5 OK OK 596 610 593 595 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 15 C5' MCY A 1 OK OK 16 26 27 12 36 C5' DC A 2 OK OK 35 51 52 37 66 C5' DT A 3 OK OK 65 82 83 67 98 C5' DC A 4 OK OK 97 113 114 99 128 C5' DC A 5 OK OK 127 143 144 129 170 C5' MCY B 1 OK OK 171 181 182 167 191 C5' DC B 2 OK OK 190 206 207 192 221 C5' DT B 3 OK OK 220 237 238 222 253 C5' DC B 4 OK OK 252 268 269 254 283 C5' DC B 5 OK OK 282 298 299 284 325 C5' MCY C 1 OK OK 326 336 337 322 346 C5' DC C 2 OK OK 345 361 362 347 376 C5' DT C 3 OK OK 375 392 393 377 408 C5' DC C 4 OK OK 407 423 424 409 438 C5' DC C 5 OK OK 437 453 454 439 480 C5' MCY D 1 OK OK 481 491 492 477 501 C5' DC D 2 OK OK 500 516 517 502 531 C5' DT D 3 OK OK 530 547 548 532 563 C5' DC D 4 OK OK 562 578 579 564 593 C5' DC D 5 OK OK 592 608 609 594 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P DC A 2 distorted distorted 14 33 34 35 62 P DT A 3 distorted distorted 40 63 64 65 94 P DC A 4 distorted distorted 70 95 96 97 124 P DC A 5 distorted distorted 102 125 126 127 187 P DC B 2 distorted distorted 169 188 189 190 217 P DT B 3 distorted distorted 195 218 219 220 249 P DC B 4 distorted distorted 225 250 251 252 279 P DC B 5 distorted distorted 257 280 281 282 342 P DC C 2 distorted distorted 324 343 344 345 372 P DT C 3 distorted distorted 350 373 374 375 404 P DC C 4 distorted distorted 380 405 406 407 434 P DC C 5 distorted distorted 412 435 436 437 497 P DC D 2 distorted distorted 479 498 499 500 527 P DT D 3 distorted distorted 505 528 529 530 559 P DC D 4 distorted distorted 535 560 561 562 589 P DC D 5 distorted distorted 567 590 591 592 ---------------------------------------------------------------------------------