ID code: '3ND4' 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' A A 1 alpha beta 4 26 10 7 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' A A 3 alpha beta 72 94 78 75 110 C1' G A 4 alpha beta 105 128 111 108 144 C1' A A 5 alpha beta 139 161 145 142 177 C1' A A 6 alpha beta 172 194 178 175 210 C1' G A 7 alpha beta 205 228 211 208 244 C1' A A 8 alpha beta 239 261 245 242 277 C1' U A 9 alpha beta 272 292 278 275 307 C1' C A 10 alpha beta 302 322 308 305 338 C1' U A 11 alpha beta 333 353 339 336 368 C1' U A 12 alpha beta 363 383 369 366 398 C1' C A 13 alpha beta 393 413 399 396 429 C1' U A 14 alpha beta 424 444 430 427 459 C1' C A 15 alpha beta 454 474 460 457 490 C1' U A 16 alpha beta 485 506 491 488 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A A 1 OK OK 9 5 24 8 41 C2' G A 2 OK OK 43 39 59 42 75 C2' A A 3 OK OK 77 73 92 76 108 C2' G A 4 OK OK 110 106 126 109 142 C2' A A 5 OK OK 144 140 159 143 175 C2' A A 6 OK OK 177 173 192 176 208 C2' G A 7 OK OK 210 206 226 209 242 C2' A A 8 OK OK 244 240 259 243 275 C2' U A 9 OK OK 277 273 290 276 305 C2' C A 10 OK OK 307 303 320 306 336 C2' U A 11 OK OK 338 334 351 337 366 C2' U A 12 OK OK 368 364 381 367 396 C2' C A 13 OK OK 398 394 411 397 427 C2' U A 14 OK OK 429 425 442 428 457 C2' C A 15 OK OK 459 455 472 458 488 C2' U A 16 OK OK 490 486 504 489 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A A 1 OK OK 3 23 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' A A 3 OK OK 71 91 74 75 106 C3' G A 4 OK OK 104 125 107 108 140 C3' A A 5 OK OK 138 158 141 142 173 C3' A A 6 OK OK 171 191 174 175 206 C3' G A 7 OK OK 204 225 207 208 240 C3' A A 8 OK OK 238 258 241 242 273 C3' U A 9 OK OK 271 289 274 275 303 C3' C A 10 OK OK 301 319 304 305 334 C3' U A 11 OK OK 332 350 335 336 364 C3' U A 12 OK OK 362 380 365 366 394 C3' C A 13 OK OK 392 410 395 396 425 C3' U A 14 OK OK 423 441 426 427 455 C3' C A 15 OK OK 453 471 456 457 486 C3' U A 16 OK OK 484 502 487 488 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A A 1 OK OK 5 22 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' A A 3 OK OK 73 90 70 72 104 C4' G A 4 OK OK 106 124 103 105 138 C4' A A 5 OK OK 140 157 137 139 171 C4' A A 6 OK OK 173 190 170 172 204 C4' G A 7 OK OK 206 224 203 205 238 C4' A A 8 OK OK 240 257 237 239 271 C4' U A 9 OK OK 273 288 270 272 301 C4' C A 10 OK OK 303 318 300 302 332 C4' U A 11 OK OK 334 349 331 333 362 C4' U A 12 OK OK 364 379 361 363 392 C4' C A 13 OK OK 394 409 391 393 423 C4' U A 14 OK OK 425 440 422 424 453 C4' C A 15 OK OK 455 470 452 454 484 C4' U A 16 OK OK 486 501 483 485 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A A 1 OK OK 1 20 21 3 36 C5' G A 2 OK OK 35 55 56 37 70 C5' A A 3 OK OK 69 88 89 71 103 C5' G A 4 OK OK 102 122 123 104 137 C5' A A 5 OK OK 136 155 156 138 170 C5' A A 6 OK OK 169 188 189 171 203 C5' G A 7 OK OK 202 222 223 204 237 C5' A A 8 OK OK 236 255 256 238 270 C5' U A 9 OK OK 269 286 287 271 300 C5' C A 10 OK OK 299 316 317 301 331 C5' U A 11 OK OK 330 347 348 332 361 C5' U A 12 OK OK 360 377 378 362 391 C5' C A 13 OK OK 390 407 408 392 422 C5' U A 14 OK OK 421 438 439 423 452 C5' C A 15 OK OK 451 468 469 453 483 C5' U A 16 OK OK 482 499 500 484 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P A A 3 distorted distorted 40 67 68 69 99 P G A 4 distorted distorted 74 100 101 102 133 P A A 5 distorted distorted 107 134 135 136 166 P A A 6 distorted distorted 141 167 168 169 199 P G A 7 distorted distorted 174 200 201 202 233 P A A 8 distorted distorted 207 234 235 236 266 P U A 9 distorted distorted 241 267 268 269 296 P C A 10 distorted distorted 274 297 298 299 327 P U A 11 distorted distorted 304 328 329 330 357 P U A 12 distorted distorted 335 358 359 360 387 P C A 13 distorted distorted 365 388 389 390 418 P U A 14 distorted distorted 395 419 420 421 448 P C A 15 distorted distorted 426 449 450 451 479 P U A 16 distorted distorted 456 480 481 482 ---------------------------------------------------------------------------------