ID code: '5NEF' 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' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' G A 6 alpha beta 171 194 177 174 210 C1' G A 7 alpha beta 205 228 211 208 244 C1' A A 8 alpha beta 239 261 245 242 277 C1' C A 9 alpha beta 272 292 278 275 308 C1' G A 10 alpha beta 303 326 309 306 342 C1' A A 11 alpha beta 337 359 343 340 375 C1' C A 12 alpha beta 370 390 376 373 406 C1' C A 13 alpha beta 401 421 407 404 437 C1' C A 14 alpha beta 432 452 438 435 468 C1' C A 15 alpha beta 463 483 469 466 499 C1' A A 16 alpha beta 494 516 500 497 533 C1' CBV A 17 alpha beta 528 550 534 531 565 C1' C A 18 alpha beta 560 581 566 563 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' G A 5 OK OK 142 138 158 141 174 C2' G A 6 OK OK 176 172 192 175 208 C2' G A 7 OK OK 210 206 226 209 242 C2' A A 8 OK OK 244 240 259 243 275 C2' C A 9 OK OK 277 273 290 276 306 C2' G A 10 OK OK 308 304 324 307 340 C2' A A 11 OK OK 342 338 357 341 373 C2' C A 12 OK OK 375 371 388 374 404 C2' C A 13 OK OK 406 402 419 405 435 C2' C A 14 OK OK 437 433 450 436 466 C2' C A 15 OK OK 468 464 481 467 497 C2' A A 16 OK OK 499 495 514 498 531 C2' CBV A 17 OK OK 533 529 548 532 563 C2' C A 18 OK OK 565 561 579 564 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' G A 5 OK OK 136 157 139 140 172 C3' G A 6 OK OK 170 191 173 174 206 C3' G A 7 OK OK 204 225 207 208 240 C3' A A 8 OK OK 238 258 241 242 273 C3' C A 9 OK OK 271 289 274 275 304 C3' G A 10 OK OK 302 323 305 306 338 C3' A A 11 OK OK 336 356 339 340 371 C3' C A 12 OK OK 369 387 372 373 402 C3' C A 13 OK OK 400 418 403 404 433 C3' C A 14 OK OK 431 449 434 435 464 C3' C A 15 OK OK 462 480 465 466 495 C3' A A 16 OK OK 493 513 496 497 529 C3' CBV A 17 OK OK 527 546 530 531 561 C3' C A 18 OK OK 559 577 562 563 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' G A 5 OK OK 138 156 135 137 170 C4' G A 6 OK OK 172 190 169 171 204 C4' G A 7 OK OK 206 224 203 205 238 C4' A A 8 OK OK 240 257 237 239 271 C4' C A 9 OK OK 273 288 270 272 302 C4' G A 10 OK OK 304 322 301 303 336 C4' A A 11 OK OK 338 355 335 337 369 C4' C A 12 OK OK 371 386 368 370 400 C4' C A 13 OK OK 402 417 399 401 431 C4' C A 14 OK OK 433 448 430 432 462 C4' C A 15 OK OK 464 479 461 463 493 C4' A A 16 OK OK 495 512 492 494 527 C4' CBV A 17 OK OK 529 545 526 528 559 C4' C A 18 OK OK 561 576 558 560 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' G A 5 OK OK 134 154 155 136 169 C5' G A 6 OK OK 168 188 189 170 203 C5' G A 7 OK OK 202 222 223 204 237 C5' A A 8 OK OK 236 255 256 238 270 C5' C A 9 OK OK 269 286 287 271 301 C5' G A 10 OK OK 300 320 321 302 335 C5' A A 11 OK OK 334 353 354 336 368 C5' C A 12 OK OK 367 384 385 369 399 C5' C A 13 OK OK 398 415 416 400 430 C5' C A 14 OK OK 429 446 447 431 461 C5' C A 15 OK OK 460 477 478 462 492 C5' A A 16 OK OK 491 510 511 493 526 C5' CBV A 17 distorted distorted 525 543 544 527 558 C5' C A 18 OK OK 557 574 575 559 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P G A 5 distorted distorted 105 132 133 134 165 P G A 6 distorted distorted 139 166 167 168 199 P G A 7 distorted distorted 173 200 201 202 233 P A A 8 distorted distorted 207 234 235 236 266 P C A 9 distorted distorted 241 267 268 269 297 P G A 10 distorted distorted 274 298 299 300 331 P A A 11 distorted distorted 305 332 333 334 364 P C A 12 distorted distorted 339 365 366 367 395 P C A 13 distorted distorted 372 396 397 398 426 P C A 14 distorted distorted 403 427 428 429 457 P C A 15 distorted distorted 434 458 459 460 488 P A A 16 distorted distorted 465 489 490 491 522 P CBV A 17 OK OK 496 523 524 525 554 P C A 18 distorted distorted 530 555 556 557 ---------------------------------------------------------------------------------