ID code: '1KOD' 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' --------------------------------------------------------------------------------- 12 C1' A A 5 beta 7 13 10 34 C1' G A 6 beta 29 35 32 57 C1' A A 7 beta 52 58 55 79 C1' A A 8 beta 74 80 77 101 C1' G A 9 beta 96 102 99 124 C1' G A 10 beta 119 125 122 147 C1' A A 11 beta 142 148 145 169 C1' G A 12 beta 164 170 167 192 C1' U A 13 beta 187 193 190 212 C1' G A 14 beta 207 213 210 235 C1' U A 15 beta 230 236 233 256 C1' A B 27 beta 251 257 254 278 C1' C B 28 beta 273 279 276 298 C1' G B 29 beta 293 299 296 321 C1' G B 30 beta 316 322 319 344 C1' U B 31 beta 339 345 342 364 C1' U B 32 beta 359 365 362 384 C1' A B 33 beta 379 385 382 406 C1' G B 34 beta 401 407 404 429 C1' G B 35 beta 424 430 427 452 C1' U B 36 beta 447 453 450 472 C1' C B 37 beta 467 473 470 492 C1' G B 38 beta 487 493 490 515 C1' C B 39 beta 510 516 513 535 C1' U B 40 beta 530 536 533 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A A 5 OK 12 8 11 32 C2' G A 6 OK 34 30 33 55 C2' A A 7 OK 57 53 56 77 C2' A A 8 OK 79 75 78 99 C2' G A 9 OK 101 97 100 122 C2' G A 10 OK 124 120 123 145 C2' A A 11 OK 147 143 146 167 C2' G A 12 OK 169 165 168 190 C2' U A 13 OK 192 188 191 210 C2' G A 14 OK 212 208 211 233 C2' U A 15 OK 235 231 234 254 C2' A B 27 OK 256 252 255 276 C2' C B 28 OK 278 274 277 296 C2' G B 29 OK 298 294 297 319 C2' G B 30 OK 321 317 320 342 C2' U B 31 OK 344 340 343 362 C2' U B 32 OK 364 360 363 382 C2' A B 33 OK 384 380 383 404 C2' G B 34 OK 406 402 405 427 C2' G B 35 OK 429 425 428 450 C2' U B 36 OK 452 448 451 470 C2' C B 37 OK 472 468 471 490 C2' G B 38 OK 492 488 491 513 C2' C B 39 OK 515 511 514 533 C2' U B 40 OK 535 531 534 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A A 5 OK 6 9 10 30 C3' G A 6 OK 28 31 32 53 C3' A A 7 OK 51 54 55 75 C3' A A 8 OK 73 76 77 97 C3' G A 9 OK 95 98 99 120 C3' G A 10 OK 118 121 122 143 C3' A A 11 OK 141 144 145 165 C3' G A 12 OK 163 166 167 188 C3' U A 13 OK 186 189 190 208 C3' G A 14 OK 206 209 210 231 C3' U A 15 OK 229 232 233 252 C3' A B 27 OK 250 253 254 274 C3' C B 28 OK 272 275 276 294 C3' G B 29 OK 292 295 296 317 C3' G B 30 OK 315 318 319 340 C3' U B 31 OK 338 341 342 360 C3' U B 32 OK 358 361 362 380 C3' A B 33 OK 378 381 382 402 C3' G B 34 OK 400 403 404 425 C3' G B 35 OK 423 426 427 448 C3' U B 36 OK 446 449 450 468 C3' C B 37 OK 466 469 470 488 C3' G B 38 OK 486 489 490 511 C3' C B 39 OK 509 512 513 531 C3' U B 40 OK 529 532 533 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A A 5 OK 8 5 7 28 C4' G A 6 OK 30 27 29 51 C4' A A 7 OK 53 50 52 73 C4' A A 8 OK 75 72 74 95 C4' G A 9 OK 97 94 96 118 C4' G A 10 OK 120 117 119 141 C4' A A 11 OK 143 140 142 163 C4' G A 12 OK 165 162 164 186 C4' U A 13 OK 188 185 187 206 C4' G A 14 OK 208 205 207 229 C4' U A 15 OK 231 228 230 250 C4' A B 27 OK 252 249 251 272 C4' C B 28 OK 274 271 273 292 C4' G B 29 OK 294 291 293 315 C4' G B 30 OK 317 314 316 338 C4' U B 31 OK 340 337 339 358 C4' U B 32 OK 360 357 359 378 C4' A B 33 OK 380 377 379 400 C4' G B 34 OK 402 399 401 423 C4' G B 35 OK 425 422 424 446 C4' U B 36 OK 448 445 447 466 C4' C B 37 OK 468 465 467 486 C4' G B 38 OK 488 485 487 509 C4' C B 39 OK 511 508 510 529 C4' U B 40 OK 531 528 530 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A A 5 4 6 27 C5' G A 6 26 28 50 C5' A A 7 49 51 72 C5' A A 8 71 73 94 C5' G A 9 93 95 117 C5' G A 10 116 118 140 C5' A A 11 139 141 162 C5' G A 12 161 163 185 C5' U A 13 184 186 205 C5' G A 14 204 206 228 C5' U A 15 227 229 249 C5' A B 27 248 250 271 C5' C B 28 270 272 291 C5' G B 29 290 292 314 C5' G B 30 313 315 337 C5' U B 31 336 338 357 C5' U B 32 356 358 377 C5' A B 33 376 378 399 C5' G B 34 398 400 422 C5' G B 35 421 423 445 C5' U B 36 444 446 465 C5' C B 37 464 466 485 C5' G B 38 484 486 508 C5' C B 39 507 509 528 C5' U B 40 527 529 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A A 5 OK OK 2 3 4 23 P G A 6 distorted distorted 9 24 25 26 46 P A A 7 distorted distorted 31 47 48 49 68 P A A 8 distorted distorted 54 69 70 71 90 P G A 9 distorted distorted 76 91 92 93 113 P G A 10 distorted distorted 98 114 115 116 136 P A A 11 distorted distorted 121 137 138 139 158 P G A 12 distorted distorted 144 159 160 161 181 P U A 13 distorted distorted 166 182 183 184 201 P G A 14 distorted distorted 189 202 203 204 224 P U A 15 distorted distorted 209 225 226 227 245 P A B 27 OK OK 246 247 248 267 P C B 28 distorted distorted 253 268 269 270 287 P G B 29 distorted distorted 275 288 289 290 310 P G B 30 distorted distorted 295 311 312 313 333 P U B 31 distorted distorted 318 334 335 336 353 P U B 32 distorted distorted 341 354 355 356 373 P A B 33 distorted distorted 361 374 375 376 395 P G B 34 distorted distorted 381 396 397 398 418 P G B 35 distorted distorted 403 419 420 421 441 P U B 36 distorted distorted 426 442 443 444 461 P C B 37 distorted distorted 449 462 463 464 481 P G B 38 distorted distorted 469 482 483 484 504 P C B 39 distorted distorted 489 505 506 507 524 P U B 40 distorted distorted 512 525 526 527 ---------------------------------------------------------------------------------