ID code: '1YN1' 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 690 alpha beta 4 27 10 7 44 C1' C A 691 alpha beta 39 59 45 42 75 C1' G A 692 alpha beta 70 93 76 73 109 C1' A A 693 alpha beta 104 126 110 107 142 C1' G A 694 alpha beta 137 160 143 140 176 C1' U A 695 alpha beta 171 191 177 174 206 C1' U A 696 alpha beta 201 221 207 204 236 C1' G A 697 alpha beta 231 254 237 234 270 C1' A A 698 alpha beta 265 287 271 268 303 C1' C A 699 alpha beta 298 318 304 301 334 C1' U A 700 alpha beta 329 349 335 332 364 C1' A A 701 alpha beta 359 381 365 362 397 C1' C A 702 alpha beta 392 412 398 395 428 C1' U A 703 alpha beta 423 443 429 426 458 C1' C A 704 alpha beta 453 473 459 456 489 C1' G A 705 alpha beta 484 507 490 487 523 C1' C A 706 alpha beta 518 539 524 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 690 OK OK 9 5 25 8 42 C2' C A 691 OK OK 44 40 57 43 73 C2' G A 692 OK OK 75 71 91 74 107 C2' A A 693 OK OK 109 105 124 108 140 C2' G A 694 OK OK 142 138 158 141 174 C2' U A 695 OK OK 176 172 189 175 204 C2' U A 696 OK OK 206 202 219 205 234 C2' G A 697 OK OK 236 232 252 235 268 C2' A A 698 OK OK 270 266 285 269 301 C2' C A 699 OK OK 303 299 316 302 332 C2' U A 700 OK OK 334 330 347 333 362 C2' A A 701 OK OK 364 360 379 363 395 C2' C A 702 OK OK 397 393 410 396 426 C2' U A 703 OK OK 428 424 441 427 456 C2' C A 704 OK OK 458 454 471 457 487 C2' G A 705 OK OK 489 485 505 488 521 C2' C A 706 OK OK 523 519 537 522 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 690 OK OK 3 24 6 7 40 C3' C A 691 OK OK 38 56 41 42 71 C3' G A 692 OK OK 69 90 72 73 105 C3' A A 693 OK OK 103 123 106 107 138 C3' G A 694 OK OK 136 157 139 140 172 C3' U A 695 OK OK 170 188 173 174 202 C3' U A 696 OK OK 200 218 203 204 232 C3' G A 697 OK OK 230 251 233 234 266 C3' A A 698 OK OK 264 284 267 268 299 C3' C A 699 OK OK 297 315 300 301 330 C3' U A 700 OK OK 328 346 331 332 360 C3' A A 701 OK OK 358 378 361 362 393 C3' C A 702 OK OK 391 409 394 395 424 C3' U A 703 OK OK 422 440 425 426 454 C3' C A 704 OK OK 452 470 455 456 485 C3' G A 705 OK OK 483 504 486 487 519 C3' C A 706 OK OK 517 535 520 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 690 OK OK 5 23 2 4 38 C4' C A 691 OK OK 40 55 37 39 69 C4' G A 692 OK OK 71 89 68 70 103 C4' A A 693 OK OK 105 122 102 104 136 C4' G A 694 OK OK 138 156 135 137 170 C4' U A 695 OK OK 172 187 169 171 200 C4' U A 696 OK OK 202 217 199 201 230 C4' G A 697 OK OK 232 250 229 231 264 C4' A A 698 OK OK 266 283 263 265 297 C4' C A 699 OK OK 299 314 296 298 328 C4' U A 700 OK OK 330 345 327 329 358 C4' A A 701 OK OK 360 377 357 359 391 C4' C A 702 OK OK 393 408 390 392 422 C4' U A 703 OK OK 424 439 421 423 452 C4' C A 704 OK OK 454 469 451 453 483 C4' G A 705 OK OK 485 503 482 484 517 C4' C A 706 OK OK 519 534 516 518 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 690 OK OK 1 21 22 3 37 C5' C A 691 OK OK 36 53 54 38 68 C5' G A 692 OK OK 67 87 88 69 102 C5' A A 693 OK OK 101 120 121 103 135 C5' G A 694 OK OK 134 154 155 136 169 C5' U A 695 OK OK 168 185 186 170 199 C5' U A 696 OK OK 198 215 216 200 229 C5' G A 697 OK OK 228 248 249 230 263 C5' A A 698 OK OK 262 281 282 264 296 C5' C A 699 OK OK 295 312 313 297 327 C5' U A 700 OK OK 326 343 344 328 357 C5' A A 701 OK OK 356 375 376 358 390 C5' C A 702 OK OK 389 406 407 391 421 C5' U A 703 OK OK 420 437 438 422 451 C5' C A 704 OK OK 450 467 468 452 482 C5' G A 705 OK OK 481 501 502 483 516 C5' C A 706 OK OK 515 532 533 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 691 distorted distorted 6 34 35 36 64 P G A 692 distorted distorted 41 65 66 67 98 P A A 693 distorted distorted 72 99 100 101 131 P G A 694 distorted distorted 106 132 133 134 165 P U A 695 distorted distorted 139 166 167 168 195 P U A 696 distorted distorted 173 196 197 198 225 P G A 697 distorted distorted 203 226 227 228 259 P A A 698 distorted distorted 233 260 261 262 292 P C A 699 distorted distorted 267 293 294 295 323 P U A 700 distorted distorted 300 324 325 326 353 P A A 701 distorted distorted 331 354 355 356 386 P C A 702 distorted distorted 361 387 388 389 417 P U A 703 distorted distorted 394 418 419 420 447 P C A 704 distorted distorted 425 448 449 450 478 P G A 705 distorted distorted 455 479 480 481 512 P C A 706 distorted distorted 486 513 514 515 ---------------------------------------------------------------------------------