ID code: '2L6I' 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 42 alpha beta 4 27 10 7 44 C1' A A 43 alpha beta 39 61 45 42 77 C1' U A 44 alpha beta 72 92 78 75 107 C1' C A 45 alpha beta 102 122 108 105 138 C1' U A 46 alpha beta 133 153 139 136 168 C1' C A 47 alpha beta 163 183 169 166 199 C1' U A 48 alpha beta 194 214 200 197 229 C1' U A 49 alpha beta 224 244 230 227 259 C1' G A 50 alpha beta 254 277 260 257 293 C1' U A 51 alpha beta 288 308 294 291 323 C1' A A 52 alpha beta 318 340 324 321 356 C1' G A 53 alpha beta 351 374 357 354 390 C1' A A 54 alpha beta 385 407 391 388 423 C1' U A 55 alpha beta 418 438 424 421 453 C1' C A 56 alpha beta 448 468 454 451 484 C1' A A 57 alpha beta 479 502 485 482 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 42 OK OK 9 5 25 8 42 C2' A A 43 OK OK 44 40 59 43 75 C2' U A 44 OK OK 77 73 90 76 105 C2' C A 45 OK OK 107 103 120 106 136 C2' U A 46 OK OK 138 134 151 137 166 C2' C A 47 OK OK 168 164 181 167 197 C2' U A 48 OK OK 199 195 212 198 227 C2' U A 49 OK OK 229 225 242 228 257 C2' G A 50 OK OK 259 255 275 258 291 C2' U A 51 OK OK 293 289 306 292 321 C2' A A 52 OK OK 323 319 338 322 354 C2' G A 53 OK OK 356 352 372 355 388 C2' A A 54 OK OK 390 386 405 389 421 C2' U A 55 OK OK 423 419 436 422 451 C2' C A 56 OK OK 453 449 466 452 482 C2' A A 57 OK OK 484 480 500 483 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 42 OK OK 3 24 6 7 40 C3' A A 43 OK OK 38 58 41 42 73 C3' U A 44 OK OK 71 89 74 75 103 C3' C A 45 OK OK 101 119 104 105 134 C3' U A 46 OK OK 132 150 135 136 164 C3' C A 47 OK OK 162 180 165 166 195 C3' U A 48 OK OK 193 211 196 197 225 C3' U A 49 OK OK 223 241 226 227 255 C3' G A 50 OK OK 253 274 256 257 289 C3' U A 51 OK OK 287 305 290 291 319 C3' A A 52 OK OK 317 337 320 321 352 C3' G A 53 OK OK 350 371 353 354 386 C3' A A 54 OK OK 384 404 387 388 419 C3' U A 55 OK OK 417 435 420 421 449 C3' C A 56 OK OK 447 465 450 451 480 C3' A A 57 OK OK 478 498 481 482 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 42 OK OK 5 23 2 4 38 C4' A A 43 OK OK 40 57 37 39 71 C4' U A 44 OK OK 73 88 70 72 101 C4' C A 45 OK OK 103 118 100 102 132 C4' U A 46 OK OK 134 149 131 133 162 C4' C A 47 OK OK 164 179 161 163 193 C4' U A 48 OK OK 195 210 192 194 223 C4' U A 49 OK OK 225 240 222 224 253 C4' G A 50 OK OK 255 273 252 254 287 C4' U A 51 OK OK 289 304 286 288 317 C4' A A 52 OK OK 319 336 316 318 350 C4' G A 53 OK OK 352 370 349 351 384 C4' A A 54 OK OK 386 403 383 385 417 C4' U A 55 OK OK 419 434 416 418 447 C4' C A 56 OK OK 449 464 446 448 478 C4' A A 57 OK OK 480 497 477 479 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 42 OK OK 1 21 22 3 37 C5' A A 43 OK OK 36 55 56 38 70 C5' U A 44 OK OK 69 86 87 71 100 C5' C A 45 OK OK 99 116 117 101 131 C5' U A 46 OK OK 130 147 148 132 161 C5' C A 47 OK OK 160 177 178 162 192 C5' U A 48 OK OK 191 208 209 193 222 C5' U A 49 OK OK 221 238 239 223 252 C5' G A 50 OK OK 251 271 272 253 286 C5' U A 51 OK OK 285 302 303 287 316 C5' A A 52 OK OK 315 334 335 317 349 C5' G A 53 OK OK 348 368 369 350 383 C5' A A 54 OK OK 382 401 402 384 416 C5' U A 55 OK OK 415 432 433 417 446 C5' C A 56 OK OK 445 462 463 447 477 C5' A A 57 OK OK 476 495 496 478 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 43 distorted distorted 6 34 35 36 66 P U A 44 distorted distorted 41 67 68 69 96 P C A 45 distorted distorted 74 97 98 99 127 P U A 46 distorted distorted 104 128 129 130 157 P C A 47 distorted distorted 135 158 159 160 188 P U A 48 distorted distorted 165 189 190 191 218 P U A 49 distorted distorted 196 219 220 221 248 P G A 50 distorted distorted 226 249 250 251 282 P U A 51 distorted distorted 256 283 284 285 312 P A A 52 distorted distorted 290 313 314 315 345 P G A 53 distorted distorted 320 346 347 348 379 P A A 54 distorted distorted 353 380 381 382 412 P U A 55 distorted distorted 387 413 414 415 442 P C A 56 distorted distorted 420 443 444 445 473 P A A 57 distorted distorted 450 474 475 476 ---------------------------------------------------------------------------------