ID code: '1JU7' 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 1 alpha beta 4 27 10 7 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' C A 3 alpha beta 72 92 78 75 108 C1' C A 4 alpha beta 103 123 109 106 139 C1' C A 5 alpha beta 134 154 140 137 170 C1' U A 6 alpha beta 165 185 171 168 200 C1' U A 7 alpha beta 195 215 201 198 230 C1' U A 8 alpha beta 225 245 231 228 260 C1' U A 9 alpha beta 255 275 261 258 290 C1' C A 10 alpha beta 285 305 291 288 321 C1' A A 11 alpha beta 316 338 322 319 354 C1' G A 12 alpha beta 349 372 355 352 388 C1' G A 13 alpha beta 383 406 389 386 422 C1' G A 14 alpha beta 417 440 423 420 456 C1' C A 15 alpha beta 451 471 457 454 487 C1' C A 16 alpha beta 482 502 488 485 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 41 C2' G A 2 OK OK 43 39 59 42 75 C2' C A 3 OK OK 77 73 90 76 106 C2' C A 4 OK OK 108 104 121 107 137 C2' C A 5 OK OK 139 135 152 138 168 C2' U A 6 OK OK 170 166 183 169 198 C2' U A 7 OK OK 200 196 213 199 228 C2' U A 8 OK OK 230 226 243 229 258 C2' U A 9 OK OK 260 256 273 259 288 C2' C A 10 OK OK 290 286 303 289 319 C2' A A 11 OK OK 321 317 336 320 352 C2' G A 12 OK OK 354 350 370 353 386 C2' G A 13 OK OK 388 384 404 387 420 C2' G A 14 OK OK 422 418 438 421 454 C2' C A 15 OK OK 456 452 469 455 485 C2' C A 16 OK OK 487 483 500 486 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' C A 3 OK OK 71 89 74 75 104 C3' C A 4 OK OK 102 120 105 106 135 C3' C A 5 OK OK 133 151 136 137 166 C3' U A 6 OK OK 164 182 167 168 196 C3' U A 7 OK OK 194 212 197 198 226 C3' U A 8 OK OK 224 242 227 228 256 C3' U A 9 OK OK 254 272 257 258 286 C3' C A 10 OK OK 284 302 287 288 317 C3' A A 11 OK OK 315 335 318 319 350 C3' G A 12 OK OK 348 369 351 352 384 C3' G A 13 OK OK 382 403 385 386 418 C3' G A 14 OK OK 416 437 419 420 452 C3' C A 15 OK OK 450 468 453 454 483 C3' C A 16 OK OK 481 499 484 485 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' C A 3 OK OK 73 88 70 72 102 C4' C A 4 OK OK 104 119 101 103 133 C4' C A 5 OK OK 135 150 132 134 164 C4' U A 6 OK OK 166 181 163 165 194 C4' U A 7 OK OK 196 211 193 195 224 C4' U A 8 OK OK 226 241 223 225 254 C4' U A 9 OK OK 256 271 253 255 284 C4' C A 10 OK OK 286 301 283 285 315 C4' A A 11 OK OK 317 334 314 316 348 C4' G A 12 OK OK 350 368 347 349 382 C4' G A 13 OK OK 384 402 381 383 416 C4' G A 14 OK OK 418 436 415 417 450 C4' C A 15 OK OK 452 467 449 451 481 C4' C A 16 OK OK 483 498 480 482 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 36 C5' G A 2 OK OK 35 55 56 37 70 C5' C A 3 OK OK 69 86 87 71 101 C5' C A 4 OK OK 100 117 118 102 132 C5' C A 5 OK OK 131 148 149 133 163 C5' U A 6 OK OK 162 179 180 164 193 C5' U A 7 OK OK 192 209 210 194 223 C5' U A 8 OK OK 222 239 240 224 253 C5' U A 9 OK OK 252 269 270 254 283 C5' C A 10 OK OK 282 299 300 284 314 C5' A A 11 OK OK 313 332 333 315 347 C5' G A 12 OK OK 346 366 367 348 381 C5' G A 13 OK OK 380 400 401 382 415 C5' G A 14 OK OK 414 434 435 416 449 C5' C A 15 OK OK 448 465 466 450 480 C5' C A 16 OK OK 479 496 497 481 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P C A 3 distorted distorted 40 67 68 69 97 P C A 4 distorted distorted 74 98 99 100 128 P C A 5 distorted distorted 105 129 130 131 159 P U A 6 distorted distorted 136 160 161 162 189 P U A 7 distorted distorted 167 190 191 192 219 P U A 8 distorted distorted 197 220 221 222 249 P U A 9 distorted distorted 227 250 251 252 279 P C A 10 distorted distorted 257 280 281 282 310 P A A 11 distorted distorted 287 311 312 313 343 P G A 12 distorted distorted 318 344 345 346 377 P G A 13 distorted distorted 351 378 379 380 411 P G A 14 distorted distorted 385 412 413 414 445 P C A 15 distorted distorted 419 446 447 448 476 P C A 16 distorted distorted 453 477 478 479 ---------------------------------------------------------------------------------