ID code: '3SSF' 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' --------------------------------------------------------------------------------- 10 C1' U A 1 beta 4 11 8 35 C1' A A 2 beta 30 36 33 57 C1' A A 3 beta 52 58 55 79 C1' A A 4 beta 74 80 77 101 C1' A A 5 beta 96 102 99 127 C1' G A 6 118 128 200 C1' A A 8 beta 195 201 198 222 C1' A A 9 beta 217 223 220 244 C1' A A 10 beta 239 245 242 266 C1' G A 11 beta 261 267 264 289 C1' G A 12 beta 284 290 287 309 C1' DC B 13 beta 305 310 308 328 C1' DC B 14 beta 324 329 327 347 C1' DT B 15 beta 343 348 346 367 C1' DT B 16 beta 363 368 366 387 C1' DT B 17 beta 383 388 386 407 C1' DT B 18 beta 403 408 406 427 C1' DC B 19 beta 423 428 426 446 C1' DT B 20 beta 442 447 445 466 C1' DT B 21 beta 462 467 465 486 C1' DT B 22 beta 482 487 485 506 C1' DT B 23 beta 502 507 505 526 C1' DA B 24 beta 522 527 525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8 C2' U A 1 OK 10 5 9 33 C2' A A 2 OK 35 31 34 55 C2' A A 3 OK 57 53 56 77 C2' A A 4 OK 79 75 78 99 C2' A A 5 OK 101 97 100 198 C2' A A 8 OK 200 196 199 220 C2' A A 9 OK 222 218 221 242 C2' A A 10 OK 244 240 243 264 C2' G A 11 OK 266 262 265 287 C2' G A 12 OK 289 285 288 308 C2' DC B 13 309 306 327 C2' DC B 14 328 325 346 C2' DT B 15 347 344 366 C2' DT B 16 367 364 386 C2' DT B 17 387 384 406 C2' DT B 18 407 404 426 C2' DC B 19 427 424 445 C2' DT B 20 446 443 465 C2' DT B 21 466 463 485 C2' DT B 22 486 483 505 C2' DT B 23 506 503 525 C2' DA B 24 526 523 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 3 8 31 C3' A A 2 OK 29 32 33 53 C3' A A 3 OK 51 54 55 75 C3' A A 4 OK 73 76 77 97 C3' A A 5 OK 95 98 99 196 C3' A A 8 197 198 218 C3' A A 9 OK 216 219 220 240 C3' A A 10 OK 238 241 242 262 C3' G A 11 OK 260 263 264 285 C3' G A 12 OK 283 286 287 306 C3' DC B 13 OK 304 307 308 325 C3' DC B 14 OK 323 326 327 344 C3' DT B 15 OK 342 345 346 364 C3' DT B 16 OK 362 365 366 384 C3' DT B 17 OK 382 385 386 404 C3' DT B 18 OK 402 405 406 424 C3' DC B 19 OK 422 425 426 443 C3' DT B 20 OK 441 444 445 463 C3' DT B 21 OK 461 464 465 483 C3' DT B 22 OK 481 484 485 503 C3' DT B 23 OK 501 504 505 523 C3' DA B 24 OK 521 524 525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK 5 2 4 29 C4' A A 2 31 30 51 C4' A A 3 OK 53 50 52 73 C4' A A 4 OK 75 72 74 95 C4' A A 5 OK 97 94 96 117 C4' G A 6 116 118 216 C4' A A 9 OK 218 215 217 238 C4' A A 10 OK 240 237 239 260 C4' G A 11 OK 262 259 261 283 C4' G A 12 OK 285 282 284 304 C4' DC B 13 OK 306 303 305 323 C4' DC B 14 OK 325 322 324 342 C4' DT B 15 OK 344 341 343 362 C4' DT B 16 OK 364 361 363 382 C4' DT B 17 OK 384 381 383 402 C4' DT B 18 OK 404 401 403 422 C4' DC B 19 OK 424 421 423 441 C4' DT B 20 OK 443 440 442 461 C4' DT B 21 OK 463 460 462 481 C4' DT B 22 OK 483 480 482 501 C4' DT B 23 OK 503 500 502 521 C4' DA B 24 OK 523 520 522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 1 3 50 C5' A A 3 49 51 72 C5' A A 4 71 73 94 C5' A A 5 93 95 116 C5' G A 6 115 117 215 C5' A A 9 214 216 237 C5' A A 10 236 238 259 C5' G A 11 258 260 282 C5' G A 12 281 283 303 C5' DC B 13 302 304 322 C5' DC B 14 321 323 341 C5' DT B 15 340 342 361 C5' DT B 16 360 362 381 C5' DT B 17 380 382 401 C5' DT B 18 400 402 421 C5' DC B 19 420 422 440 C5' DT B 20 439 441 460 C5' DT B 21 459 461 480 C5' DT B 22 479 481 500 C5' DT B 23 499 501 520 C5' DA B 24 519 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P A A 2 20 P A A 2 46 P A A 3 distorted distorted 32 47 48 49 68 P A A 4 distorted distorted 54 69 70 71 90 P A A 5 distorted distorted 76 91 92 93 112 P G A 6 distorted distorted 98 113 114 115 139 P A A 7 140 P A A 7 183 P A A 8 184 P A A 8 211 P A A 9 distorted distorted 197 212 213 214 233 P A A 10 distorted distorted 219 234 235 236 255 P G A 11 distorted distorted 241 256 257 258 278 P G A 12 distorted distorted 263 279 280 281 318 P DC B 14 distorted distorted 307 319 320 321 337 P DT B 15 distorted distorted 326 338 339 340 357 P DT B 16 distorted distorted 345 358 359 360 377 P DT B 17 distorted distorted 365 378 379 380 397 P DT B 18 distorted distorted 385 398 399 400 417 P DC B 19 distorted distorted 405 418 419 420 436 P DT B 20 distorted distorted 425 437 438 439 456 P DT B 21 distorted distorted 444 457 458 459 476 P DT B 22 distorted distorted 464 477 478 479 496 P DT B 23 distorted distorted 484 497 498 499 516 P DA B 24 distorted distorted 504 517 518 519 ---------------------------------------------------------------------------------