ID code: '2KRP' 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' C A 1 alpha beta 4 24 10 7 40 C1' U A 2 alpha beta 35 55 41 38 70 C1' C A 3 alpha beta 65 85 71 68 101 C1' G A 4 alpha beta 96 119 102 99 135 C1' G A 5 alpha beta 130 153 136 133 169 C1' C A 6 alpha beta 164 184 170 167 200 C1' U A 7 alpha beta 195 215 201 198 230 C1' A A 8 alpha beta 225 247 231 228 263 C1' C A 9 alpha beta 258 278 264 261 294 C1' G A 10 alpha beta 289 312 295 292 328 C1' A A 11 alpha beta 323 345 329 326 361 C1' A A 12 alpha beta 356 378 362 359 394 C1' C A 13 alpha beta 389 409 395 392 425 C1' C A 14 alpha beta 420 440 426 423 456 C1' G A 15 alpha beta 451 474 457 454 490 C1' A A 16 alpha beta 485 507 491 488 523 C1' G A 17 alpha beta 518 542 524 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK OK 9 5 22 8 38 C2' U A 2 OK OK 40 36 53 39 68 C2' C A 3 OK OK 70 66 83 69 99 C2' G A 4 OK OK 101 97 117 100 133 C2' G A 5 OK OK 135 131 151 134 167 C2' C A 6 OK OK 169 165 182 168 198 C2' U A 7 OK OK 200 196 213 199 228 C2' A A 8 OK OK 230 226 245 229 261 C2' C A 9 OK OK 263 259 276 262 292 C2' G A 10 OK OK 294 290 310 293 326 C2' A A 11 OK OK 328 324 343 327 359 C2' A A 12 OK OK 361 357 376 360 392 C2' C A 13 OK OK 394 390 407 393 423 C2' C A 14 OK OK 425 421 438 424 454 C2' G A 15 OK OK 456 452 472 455 488 C2' A A 16 OK OK 490 486 505 489 521 C2' G A 17 OK OK 523 519 540 522 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 21 6 7 36 C3' U A 2 OK OK 34 52 37 38 66 C3' C A 3 OK OK 64 82 67 68 97 C3' G A 4 OK OK 95 116 98 99 131 C3' G A 5 OK OK 129 150 132 133 165 C3' C A 6 OK OK 163 181 166 167 196 C3' U A 7 OK OK 194 212 197 198 226 C3' A A 8 OK OK 224 244 227 228 259 C3' C A 9 OK OK 257 275 260 261 290 C3' G A 10 OK OK 288 309 291 292 324 C3' A A 11 OK OK 322 342 325 326 357 C3' A A 12 OK OK 355 375 358 359 390 C3' C A 13 OK OK 388 406 391 392 421 C3' C A 14 OK OK 419 437 422 423 452 C3' G A 15 OK OK 450 471 453 454 486 C3' A A 16 OK OK 484 504 487 488 519 C3' G A 17 OK OK 517 538 520 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 20 2 4 34 C4' U A 2 OK OK 36 51 33 35 64 C4' C A 3 OK OK 66 81 63 65 95 C4' G A 4 OK OK 97 115 94 96 129 C4' G A 5 OK OK 131 149 128 130 163 C4' C A 6 OK OK 165 180 162 164 194 C4' U A 7 OK OK 196 211 193 195 224 C4' A A 8 OK OK 226 243 223 225 257 C4' C A 9 OK OK 259 274 256 258 288 C4' G A 10 OK OK 290 308 287 289 322 C4' A A 11 OK OK 324 341 321 323 355 C4' A A 12 OK OK 357 374 354 356 388 C4' C A 13 OK OK 390 405 387 389 419 C4' C A 14 OK OK 421 436 418 420 450 C4' G A 15 OK OK 452 470 449 451 484 C4' A A 16 OK OK 486 503 483 485 517 C4' G A 17 OK OK 519 537 516 518 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 OK OK 1 18 19 3 33 C5' U A 2 OK OK 32 49 50 34 63 C5' C A 3 OK OK 62 79 80 64 94 C5' G A 4 OK OK 93 113 114 95 128 C5' G A 5 OK OK 127 147 148 129 162 C5' C A 6 OK OK 161 178 179 163 193 C5' U A 7 OK OK 192 209 210 194 223 C5' A A 8 OK OK 222 241 242 224 256 C5' C A 9 OK OK 255 272 273 257 287 C5' G A 10 OK OK 286 306 307 288 321 C5' A A 11 OK OK 320 339 340 322 354 C5' A A 12 OK OK 353 372 373 355 387 C5' C A 13 OK OK 386 403 404 388 418 C5' C A 14 OK OK 417 434 435 419 449 C5' G A 15 OK OK 448 468 469 450 483 C5' A A 16 OK OK 482 501 502 484 516 C5' G A 17 OK OK 515 535 536 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P U A 2 distorted distorted 6 30 31 32 59 P C A 3 distorted distorted 37 60 61 62 90 P G A 4 distorted distorted 67 91 92 93 124 P G A 5 distorted distorted 98 125 126 127 158 P C A 6 distorted distorted 132 159 160 161 189 P U A 7 distorted distorted 166 190 191 192 219 P A A 8 distorted distorted 197 220 221 222 252 P C A 9 distorted distorted 227 253 254 255 283 P G A 10 distorted distorted 260 284 285 286 317 P A A 11 distorted distorted 291 318 319 320 350 P A A 12 distorted distorted 325 351 352 353 383 P C A 13 distorted distorted 358 384 385 386 414 P C A 14 distorted distorted 391 415 416 417 445 P G A 15 distorted distorted 422 446 447 448 479 P A A 16 distorted distorted 453 480 481 482 512 P G A 17 distorted distorted 487 513 514 515 ---------------------------------------------------------------------------------