ID code: '1G22' 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' DA A 3 alpha beta 68 89 73 71 104 C1' DT A 4 alpha beta 100 120 105 103 136 C1' DT A 5 alpha beta 132 152 137 135 168 C1' DC A 6 alpha beta 164 183 169 167 198 C1' DC A 7 alpha beta 194 213 199 197 228 C1' DA A 8 alpha beta 224 245 229 227 260 C1' DU A 9 alpha beta 256 275 261 259 289 C1' DT A 10 alpha beta 285 305 290 288 321 C1' DC A 11 alpha beta 317 336 322 320 351 C1' DC A 12 alpha beta 347 366 352 350 381 C1' DU A 13 alpha beta 377 396 382 380 410 C1' DT A 14 alpha beta 406 426 411 409 442 C1' DT A 15 alpha beta 438 458 443 441 474 C1' DC A 16 alpha beta 470 489 475 473 504 C1' DC A 17 alpha beta 500 520 505 503 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' DA A 3 OK OK 72 69 87 88 103 C2' DT A 4 OK OK 104 101 118 119 135 C2' DT A 5 OK OK 136 133 150 151 167 C2' DC A 6 OK OK 168 165 181 182 197 C2' DC A 7 OK OK 198 195 211 212 227 C2' DA A 8 OK OK 228 225 243 244 259 C2' DU A 9 OK OK 260 257 273 274 288 C2' DT A 10 OK OK 289 286 303 304 320 C2' DC A 11 OK OK 321 318 334 335 350 C2' DC A 12 OK OK 351 348 364 365 380 C2' DU A 13 OK OK 381 378 394 395 409 C2' DT A 14 OK OK 410 407 424 425 441 C2' DT A 15 OK OK 442 439 456 457 473 C2' DC A 16 OK OK 474 471 487 488 503 C2' DC A 17 OK OK 504 501 518 519 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DA A 3 OK OK 67 86 70 71 101 C3' DT A 4 OK OK 99 117 102 103 133 C3' DT A 5 OK OK 131 149 134 135 165 C3' DC A 6 OK OK 163 180 166 167 195 C3' DC A 7 OK OK 193 210 196 197 225 C3' DA A 8 OK OK 223 242 226 227 257 C3' DU A 9 OK OK 255 272 258 259 286 C3' DT A 10 OK OK 284 302 287 288 318 C3' DC A 11 OK OK 316 333 319 320 348 C3' DC A 12 OK OK 346 363 349 350 378 C3' DU A 13 OK OK 376 393 379 380 407 C3' DT A 14 OK OK 405 423 408 409 439 C3' DT A 15 OK OK 437 455 440 441 471 C3' DC A 16 OK OK 469 486 472 473 501 C3' DC A 17 OK OK 499 516 502 503 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DA A 3 OK OK 69 85 66 68 99 C4' DT A 4 OK OK 101 116 98 100 131 C4' DT A 5 OK OK 133 148 130 132 163 C4' DC A 6 OK OK 165 179 162 164 193 C4' DC A 7 OK OK 195 209 192 194 223 C4' DA A 8 OK OK 225 241 222 224 255 C4' DU A 9 OK OK 257 271 254 256 284 C4' DT A 10 OK OK 286 301 283 285 316 C4' DC A 11 OK OK 318 332 315 317 346 C4' DC A 12 OK OK 348 362 345 347 376 C4' DU A 13 OK OK 378 392 375 377 405 C4' DT A 14 OK OK 407 422 404 406 437 C4' DT A 15 OK OK 439 454 436 438 469 C4' DC A 16 OK OK 471 485 468 470 499 C4' DC A 17 OK OK 501 515 498 500 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DA A 3 OK OK 65 83 84 67 98 C5' DT A 4 OK OK 97 114 115 99 130 C5' DT A 5 OK OK 129 146 147 131 162 C5' DC A 6 OK OK 161 177 178 163 192 C5' DC A 7 OK OK 191 207 208 193 222 C5' DA A 8 OK OK 221 239 240 223 254 C5' DU A 9 OK OK 253 269 270 255 283 C5' DT A 10 OK OK 282 299 300 284 315 C5' DC A 11 OK OK 314 330 331 316 345 C5' DC A 12 OK OK 344 360 361 346 375 C5' DU A 13 OK OK 374 390 391 376 404 C5' DT A 14 OK OK 403 420 421 405 436 C5' DT A 15 OK OK 435 452 453 437 468 C5' DC A 16 OK OK 467 483 484 469 498 C5' DC A 17 OK OK 497 513 514 499 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P DC A 2 distorted distorted 14 33 34 35 62 P DA A 3 distorted distorted 40 63 64 65 94 P DT A 4 distorted distorted 70 95 96 97 126 P DT A 5 distorted distorted 102 127 128 129 158 P DC A 6 distorted distorted 134 159 160 161 188 P DC A 7 distorted distorted 166 189 190 191 218 P DA A 8 distorted distorted 196 219 220 221 250 P DU A 9 distorted distorted 226 251 252 253 279 P DT A 10 distorted distorted 258 280 281 282 311 P DC A 11 distorted distorted 287 312 313 314 341 P DC A 12 distorted distorted 319 342 343 344 371 P DU A 13 distorted distorted 349 372 373 374 400 P DT A 14 distorted distorted 379 401 402 403 432 P DT A 15 distorted distorted 408 433 434 435 464 P DC A 16 distorted distorted 440 465 466 467 494 P DC A 17 distorted distorted 472 495 496 497 ---------------------------------------------------------------------------------