ID code: '2K41' 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 44 C1' U A 2 alpha beta 39 59 45 42 74 C1' C A 3 alpha beta 69 89 75 72 105 C1' G A 4 alpha beta 100 123 106 103 139 C1' U A 5 alpha beta 134 154 140 137 169 C1' G A 6 alpha beta 164 187 170 167 203 C1' C A 7 alpha beta 198 218 204 201 234 C1' U A 8 alpha beta 229 249 235 232 264 C1' G A 9 alpha beta 259 283 265 262 297 C1' C B 10 alpha beta 292 312 298 295 329 C1' A B 11 alpha beta 324 346 330 327 362 C1' G B 12 alpha beta 357 380 363 360 396 C1' C B 13 alpha beta 391 411 397 394 427 C1' C B 14 alpha beta 422 442 428 425 458 C1' G B 15 alpha beta 453 476 459 456 492 C1' A B 16 alpha beta 487 509 493 490 525 C1' C B 17 alpha beta 520 541 526 523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 42 C2' U A 2 OK OK 44 40 57 43 72 C2' C A 3 OK OK 74 70 87 73 103 C2' G A 4 OK OK 105 101 121 104 137 C2' U A 5 OK OK 139 135 152 138 167 C2' G A 6 OK OK 169 165 185 168 201 C2' C A 7 OK OK 203 199 216 202 232 C2' U A 8 OK OK 234 230 247 233 262 C2' G A 9 OK OK 264 260 281 263 295 C2' C B 10 OK OK 297 293 310 296 327 C2' A B 11 OK OK 329 325 344 328 360 C2' G B 12 OK OK 362 358 378 361 394 C2' C B 13 OK OK 396 392 409 395 425 C2' C B 14 OK OK 427 423 440 426 456 C2' G B 15 OK OK 458 454 474 457 490 C2' A B 16 OK OK 492 488 507 491 523 C2' C B 17 OK OK 525 521 539 524 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' U A 2 OK OK 38 56 41 42 70 C3' C A 3 OK OK 68 86 71 72 101 C3' G A 4 OK OK 99 120 102 103 135 C3' U A 5 OK OK 133 151 136 137 165 C3' G A 6 OK OK 163 184 166 167 199 C3' C A 7 OK OK 197 215 200 201 230 C3' U A 8 OK OK 228 246 231 232 260 C3' G A 9 OK OK 258 279 261 262 293 C3' C B 10 OK OK 291 309 294 295 325 C3' A B 11 OK OK 323 343 326 327 358 C3' G B 12 OK OK 356 377 359 360 392 C3' C B 13 OK OK 390 408 393 394 423 C3' C B 14 OK OK 421 439 424 425 454 C3' G B 15 OK OK 452 473 455 456 488 C3' A B 16 OK OK 486 506 489 490 521 C3' C B 17 OK OK 519 537 522 523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' U A 2 OK OK 40 55 37 39 68 C4' C A 3 OK OK 70 85 67 69 99 C4' G A 4 OK OK 101 119 98 100 133 C4' U A 5 OK OK 135 150 132 134 163 C4' G A 6 OK OK 165 183 162 164 197 C4' C A 7 OK OK 199 214 196 198 228 C4' U A 8 OK OK 230 245 227 229 258 C4' G A 9 OK OK 260 278 257 259 291 C4' C B 10 OK OK 293 308 290 292 323 C4' A B 11 OK OK 325 342 322 324 356 C4' G B 12 OK OK 358 376 355 357 390 C4' C B 13 OK OK 392 407 389 391 421 C4' C B 14 OK OK 423 438 420 422 452 C4' G B 15 OK OK 454 472 451 453 486 C4' A B 16 OK OK 488 505 485 487 519 C4' C B 17 OK OK 521 536 518 520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 37 C5' U A 2 OK OK 36 53 54 38 67 C5' C A 3 OK OK 66 83 84 68 98 C5' G A 4 OK OK 97 117 118 99 132 C5' U A 5 OK OK 131 148 149 133 162 C5' G A 6 OK OK 161 181 182 163 196 C5' C A 7 OK OK 195 212 213 197 227 C5' U A 8 OK OK 226 243 244 228 257 C5' G A 9 OK OK 256 276 277 258 290 C5' C B 10 OK OK 289 306 307 291 322 C5' A B 11 OK OK 321 340 341 323 355 C5' G B 12 OK OK 354 374 375 356 389 C5' C B 13 OK OK 388 405 406 390 420 C5' C B 14 OK OK 419 436 437 421 451 C5' G B 15 OK OK 450 470 471 452 485 C5' A B 16 OK OK 484 503 504 486 518 C5' C B 17 OK OK 517 534 535 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P U A 2 distorted distorted 6 34 35 36 63 P C A 3 distorted distorted 41 64 65 66 94 P G A 4 distorted distorted 71 95 96 97 128 P U A 5 distorted distorted 102 129 130 131 158 P G A 6 distorted distorted 136 159 160 161 192 P C A 7 distorted distorted 166 193 194 195 223 P U A 8 distorted distorted 200 224 225 226 253 P G A 9 distorted distorted 231 254 255 256 318 P A B 11 distorted distorted 294 319 320 321 351 P G B 12 distorted distorted 326 352 353 354 385 P C B 13 distorted distorted 359 386 387 388 416 P C B 14 distorted distorted 393 417 418 419 447 P G B 15 distorted distorted 424 448 449 450 481 P A B 16 distorted distorted 455 482 483 484 514 P C B 17 distorted distorted 489 515 516 517 ---------------------------------------------------------------------------------