ID code: '1BAE' 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' DT A 4 alpha beta 100 120 105 103 136 C1' DT A 5 alpha beta 132 152 137 135 168 C1' DA A 6 alpha beta 164 185 169 167 200 C1' DC A 7 alpha beta 196 215 201 199 230 C1' DC A 8 alpha beta 226 246 231 229 260 C1' MCY B 1 alpha beta 264 272 252 261 293 C1' DC B 2 alpha beta 289 308 294 292 323 C1' DT B 3 alpha beta 319 339 324 322 355 C1' DT B 4 alpha beta 351 371 356 354 387 C1' DT B 5 alpha beta 383 403 388 386 419 C1' DA B 6 alpha beta 415 436 420 418 451 C1' DC B 7 alpha beta 447 466 452 450 481 C1' DC B 8 alpha beta 477 497 482 480 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' DT A 4 OK OK 104 101 118 119 135 C2' DT A 5 OK OK 136 133 150 151 167 C2' DA A 6 OK OK 168 165 183 184 199 C2' DC A 7 OK OK 200 197 213 214 229 C2' DC A 8 OK OK 230 227 244 245 261 C2' MCY B 1 OK OK 260 262 273 274 292 C2' DC B 2 OK OK 293 290 306 307 322 C2' DT B 3 OK OK 323 320 337 338 354 C2' DT B 4 OK OK 355 352 369 370 386 C2' DT B 5 OK OK 387 384 401 402 418 C2' DA B 6 OK OK 419 416 434 435 450 C2' DC B 7 OK OK 451 448 464 465 480 C2' DC B 8 OK OK 481 478 495 496 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DT A 4 OK OK 99 117 102 103 133 C3' DT A 5 OK OK 131 149 134 135 165 C3' DA A 6 OK OK 163 182 166 167 197 C3' DC A 7 OK OK 195 212 198 199 227 C3' DC A 8 OK OK 225 242 228 229 262 C3' MCY B 1 OK OK 263 275 265 261 290 C3' DC B 2 OK OK 288 305 291 292 320 C3' DT B 3 OK OK 318 336 321 322 352 C3' DT B 4 OK OK 350 368 353 354 384 C3' DT B 5 OK OK 382 400 385 386 416 C3' DA B 6 OK OK 414 433 417 418 448 C3' DC B 7 OK OK 446 463 449 450 478 C3' DC B 8 OK OK 476 493 479 480 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DT A 4 OK OK 101 116 98 100 131 C4' DT A 5 OK OK 133 148 130 132 163 C4' DA A 6 OK OK 165 181 162 164 195 C4' DC A 7 OK OK 197 211 194 196 225 C4' DC A 8 OK OK 227 241 224 226 263 C4' MCY B 1 OK OK 262 276 266 264 288 C4' DC B 2 OK OK 290 304 287 289 318 C4' DT B 3 OK OK 320 335 317 319 350 C4' DT B 4 OK OK 352 367 349 351 382 C4' DT B 5 OK OK 384 399 381 383 414 C4' DA B 6 OK OK 416 432 413 415 446 C4' DC B 7 OK OK 448 462 445 447 476 C4' DC B 8 OK OK 478 492 475 477 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DT A 4 OK OK 97 114 115 99 130 C5' DT A 5 OK OK 129 146 147 131 162 C5' DA A 6 OK OK 161 179 180 163 194 C5' DC A 7 OK OK 193 209 210 195 224 C5' DC A 8 OK OK 223 239 240 225 266 C5' MCY B 1 OK OK 267 277 278 263 287 C5' DC B 2 OK OK 286 302 303 288 317 C5' DT B 3 OK OK 316 333 334 318 349 C5' DT B 4 OK OK 348 365 366 350 381 C5' DT B 5 OK OK 380 397 398 382 413 C5' DA B 6 OK OK 412 430 431 414 445 C5' DC B 7 OK OK 444 460 461 446 475 C5' DC B 8 OK OK 474 490 491 476 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 DT A 4 distorted distorted 70 95 96 97 126 P DT A 5 distorted distorted 102 127 128 129 158 P DA A 6 distorted distorted 134 159 160 161 190 P DC A 7 distorted distorted 166 191 192 193 220 P DC A 8 distorted distorted 198 221 222 223 283 P DC B 2 distorted distorted 265 284 285 286 313 P DT B 3 distorted distorted 291 314 315 316 345 P DT B 4 distorted distorted 321 346 347 348 377 P DT B 5 distorted distorted 353 378 379 380 409 P DA B 6 distorted distorted 385 410 411 412 441 P DC B 7 distorted distorted 417 442 443 444 471 P DC B 8 distorted distorted 449 472 473 474 ---------------------------------------------------------------------------------