ID code: '2AWV' 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' DA A 5 alpha beta 130 151 135 133 166 C1' DC A 6 alpha beta 162 181 167 165 196 C1' DT A 7 alpha beta 192 212 197 195 228 C1' DC A 8 alpha beta 224 243 229 227 258 C1' DC A 9 alpha beta 254 274 259 257 288 C1' MCY B 1 alpha beta 292 300 280 289 321 C1' DC B 2 alpha beta 317 336 322 320 351 C1' DT B 3 alpha beta 347 367 352 350 383 C1' DC B 4 alpha beta 379 398 384 382 413 C1' DA B 5 alpha beta 409 430 414 412 445 C1' DC B 6 alpha beta 441 460 446 444 475 C1' DT B 7 alpha beta 471 491 476 474 507 C1' DC B 8 alpha beta 503 522 508 506 537 C1' DC B 9 alpha beta 533 552 538 536 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' DA A 5 OK OK 134 131 149 150 165 C2' DC A 6 OK OK 166 163 179 180 195 C2' DT A 7 OK OK 196 193 210 211 227 C2' DC A 8 OK OK 228 225 241 242 257 C2' DC A 9 OK OK 258 255 272 273 289 C2' MCY B 1 OK OK 288 290 301 302 320 C2' DC B 2 OK OK 321 318 334 335 350 C2' DT B 3 OK OK 351 348 365 366 382 C2' DC B 4 OK OK 383 380 396 397 412 C2' DA B 5 OK OK 413 410 428 429 444 C2' DC B 6 OK OK 445 442 458 459 474 C2' DT B 7 OK OK 475 472 489 490 506 C2' DC B 8 OK OK 507 504 520 521 536 C2' DC B 9 OK OK 537 534 550 551 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DA A 5 OK OK 129 148 132 133 163 C3' DC A 6 OK OK 161 178 164 165 193 C3' DT A 7 OK OK 191 209 194 195 225 C3' DC A 8 OK OK 223 240 226 227 255 C3' DC A 9 OK OK 253 270 256 257 290 C3' MCY B 1 OK OK 291 303 293 289 318 C3' DC B 2 OK OK 316 333 319 320 348 C3' DT B 3 OK OK 346 364 349 350 380 C3' DC B 4 OK OK 378 395 381 382 410 C3' DA B 5 OK OK 408 427 411 412 442 C3' DC B 6 OK OK 440 457 443 444 472 C3' DT B 7 OK OK 470 488 473 474 504 C3' DC B 8 OK OK 502 519 505 506 534 C3' DC B 9 OK OK 532 549 535 536 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DA A 5 OK OK 131 147 128 130 161 C4' DC A 6 OK OK 163 177 160 162 191 C4' DT A 7 OK OK 193 208 190 192 223 C4' DC A 8 OK OK 225 239 222 224 253 C4' DC A 9 OK OK 255 269 252 254 291 C4' MCY B 1 OK OK 290 304 294 292 316 C4' DC B 2 OK OK 318 332 315 317 346 C4' DT B 3 OK OK 348 363 345 347 378 C4' DC B 4 OK OK 380 394 377 379 408 C4' DA B 5 OK OK 410 426 407 409 440 C4' DC B 6 OK OK 442 456 439 441 470 C4' DT B 7 OK OK 472 487 469 471 502 C4' DC B 8 OK OK 504 518 501 503 532 C4' DC B 9 OK OK 534 548 531 533 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DA A 5 OK OK 127 145 146 129 160 C5' DC A 6 OK OK 159 175 176 161 190 C5' DT A 7 OK OK 189 206 207 191 222 C5' DC A 8 OK OK 221 237 238 223 252 C5' DC A 9 OK OK 251 267 268 253 294 C5' MCY B 1 OK OK 295 305 306 291 315 C5' DC B 2 OK OK 314 330 331 316 345 C5' DT B 3 OK OK 344 361 362 346 377 C5' DC B 4 OK OK 376 392 393 378 407 C5' DA B 5 OK OK 406 424 425 408 439 C5' DC B 6 OK OK 438 454 455 440 469 C5' DT B 7 OK OK 468 485 486 470 501 C5' DC B 8 OK OK 500 516 517 502 531 C5' DC B 9 OK OK 530 546 547 532 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 DA A 5 distorted distorted 102 125 126 127 156 P DC A 6 distorted distorted 132 157 158 159 186 P DT A 7 distorted distorted 164 187 188 189 218 P DC A 8 distorted distorted 194 219 220 221 248 P DC A 9 distorted distorted 226 249 250 251 311 P DC B 2 distorted distorted 293 312 313 314 341 P DT B 3 distorted distorted 319 342 343 344 373 P DC B 4 distorted distorted 349 374 375 376 403 P DA B 5 distorted distorted 381 404 405 406 435 P DC B 6 distorted distorted 411 436 437 438 465 P DT B 7 distorted distorted 443 466 467 468 497 P DC B 8 distorted distorted 473 498 499 500 527 P DC B 9 distorted distorted 505 528 529 530 ---------------------------------------------------------------------------------