ID code: '2MS5' 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' --------------------------------------------------------------------------------- 13 C1' C S 1 alpha beta 8 29 14 11 45 C1' C S 2 alpha beta 40 60 46 43 76 C1' G S 3 alpha beta 71 94 77 74 110 C1' C S 4 alpha beta 105 125 111 108 141 C1' A S 5 alpha beta 136 158 142 139 174 C1' G S 6 alpha beta 169 192 175 172 208 C1' C S 7 alpha beta 203 223 209 206 239 C1' G S 8 alpha beta 234 257 240 237 273 C1' G S 9 alpha beta 268 291 274 271 309 C1' C A 1 alpha beta 304 325 310 307 341 C1' C A 2 alpha beta 336 356 342 339 372 C1' G A 3 alpha beta 367 390 373 370 406 C1' C A 4 alpha beta 401 421 407 404 437 C1' A A 5 alpha beta 432 454 438 435 470 C1' G A 6 alpha beta 465 488 471 468 504 C1' C A 7 alpha beta 499 519 505 502 535 C1' G A 8 alpha beta 530 553 536 533 569 C1' G A 9 alpha beta 564 587 570 567 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' C S 1 OK OK 13 9 27 12 43 C2' C S 2 OK OK 45 41 58 44 74 C2' G S 3 OK OK 76 72 92 75 108 C2' C S 4 OK OK 110 106 123 109 139 C2' A S 5 OK OK 141 137 156 140 172 C2' G S 6 OK OK 174 170 190 173 206 C2' C S 7 OK OK 208 204 221 207 237 C2' G S 8 OK OK 239 235 255 238 271 C2' G S 9 OK OK 273 269 289 272 307 C2' C A 1 OK OK 309 305 323 308 339 C2' C A 2 OK OK 341 337 354 340 370 C2' G A 3 OK OK 372 368 388 371 404 C2' C A 4 OK OK 406 402 419 405 435 C2' A A 5 OK OK 437 433 452 436 468 C2' G A 6 OK OK 470 466 486 469 502 C2' C A 7 OK OK 504 500 517 503 533 C2' G A 8 OK OK 535 531 551 534 567 C2' G A 9 OK OK 569 565 585 568 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' C S 1 OK OK 7 26 10 11 41 C3' C S 2 OK OK 39 57 42 43 72 C3' G S 3 OK OK 70 91 73 74 106 C3' C S 4 OK OK 104 122 107 108 137 C3' A S 5 OK OK 135 155 138 139 170 C3' G S 6 OK OK 168 189 171 172 204 C3' C S 7 OK OK 202 220 205 206 235 C3' G S 8 OK OK 233 254 236 237 269 C3' G S 9 OK OK 267 288 270 271 305 C3' C A 1 OK OK 303 322 306 307 337 C3' C A 2 OK OK 335 353 338 339 368 C3' G A 3 OK OK 366 387 369 370 402 C3' C A 4 OK OK 400 418 403 404 433 C3' A A 5 OK OK 431 451 434 435 466 C3' G A 6 OK OK 464 485 467 468 500 C3' C A 7 OK OK 498 516 501 502 531 C3' G A 8 OK OK 529 550 532 533 565 C3' G A 9 OK OK 563 584 566 567 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' C S 1 OK OK 9 25 6 8 39 C4' C S 2 OK OK 41 56 38 40 70 C4' G S 3 OK OK 72 90 69 71 104 C4' C S 4 OK OK 106 121 103 105 135 C4' A S 5 OK OK 137 154 134 136 168 C4' G S 6 OK OK 170 188 167 169 202 C4' C S 7 OK OK 204 219 201 203 233 C4' G S 8 OK OK 235 253 232 234 267 C4' G S 9 OK OK 269 287 266 268 303 C4' C A 1 OK OK 305 321 302 304 335 C4' C A 2 OK OK 337 352 334 336 366 C4' G A 3 OK OK 368 386 365 367 400 C4' C A 4 OK OK 402 417 399 401 431 C4' A A 5 OK OK 433 450 430 432 464 C4' G A 6 OK OK 466 484 463 465 498 C4' C A 7 OK OK 500 515 497 499 529 C4' G A 8 OK OK 531 549 528 530 563 C4' G A 9 OK OK 565 583 562 564 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' C S 1 OK OK 5 23 24 7 38 C5' C S 2 OK OK 37 54 55 39 69 C5' G S 3 OK OK 68 88 89 70 103 C5' C S 4 OK OK 102 119 120 104 134 C5' A S 5 OK OK 133 152 153 135 167 C5' G S 6 OK OK 166 186 187 168 201 C5' C S 7 OK OK 200 217 218 202 232 C5' G S 8 OK OK 231 251 252 233 266 C5' G S 9 OK OK 265 285 286 267 302 C5' C A 1 OK OK 301 319 320 303 334 C5' C A 2 OK OK 333 350 351 335 365 C5' G A 3 OK OK 364 384 385 366 399 C5' C A 4 OK OK 398 415 416 400 430 C5' A A 5 OK OK 429 448 449 431 463 C5' G A 6 OK OK 462 482 483 464 497 C5' C A 7 OK OK 496 513 514 498 528 C5' G A 8 OK OK 527 547 548 529 562 C5' G A 9 OK OK 561 581 582 563 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P C S 1 distorted distorted 3 4 5 34 P C S 2 distorted distorted 10 35 36 37 65 P G S 3 distorted distorted 42 66 67 68 99 P C S 4 distorted distorted 73 100 101 102 130 P A S 5 distorted distorted 107 131 132 133 163 P G S 6 distorted distorted 138 164 165 166 197 P C S 7 distorted distorted 171 198 199 200 228 P G S 8 distorted distorted 205 229 230 231 262 P G S 9 distorted distorted 236 263 264 265 298 P C A 1 distorted distorted 299 300 301 330 P C A 2 distorted distorted 306 331 332 333 361 P G A 3 distorted distorted 338 362 363 364 395 P C A 4 distorted distorted 369 396 397 398 426 P A A 5 distorted distorted 403 427 428 429 459 P G A 6 distorted distorted 434 460 461 462 493 P C A 7 distorted distorted 467 494 495 496 524 P G A 8 distorted distorted 501 525 526 527 558 P G A 9 distorted distorted 532 559 560 561 ---------------------------------------------------------------------------------