ID code: '2GYN' 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' --------------------------------------------------------------------------------- 8 C1' G A 1 alpha beta 4 24 9 7 42 C1' C A 2 alpha beta 38 55 43 41 72 C1' C A 3 alpha beta 68 85 73 71 102 C1' T A 4 alpha beta 98 118 103 101 134 C1' A A 5 alpha beta 130 149 135 133 166 C1' T A 6 alpha beta 162 182 167 165 198 C1' T A 7 alpha beta 194 214 199 197 230 C1' A A 8 alpha beta 226 245 231 229 262 C1' G A 9 alpha beta 258 278 263 261 295 C1' C A 10 alpha beta 291 308 296 294 325 C1' G A 11 alpha beta 321 342 326 324 357 C1' C B 12 alpha beta 353 370 358 356 388 C1' G B 13 alpha beta 384 404 389 387 421 C1' C B 14 alpha beta 417 434 422 420 451 C1' T B 15 alpha beta 447 467 452 450 483 C1' A B 16 alpha beta 479 498 484 482 515 C1' A B 17 alpha beta 511 530 516 514 547 C1' T B 18 alpha beta 543 563 548 546 579 C1' A B 19 alpha beta 575 594 580 578 611 C1' G B 20 alpha beta 607 627 612 610 644 C1' G B 21 alpha beta 640 660 645 643 677 C1' C B 22 alpha beta 673 691 678 676 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 8 5 30 31 41 C2' C A 2 OK OK 42 39 60 61 71 C2' C A 3 OK OK 72 69 90 91 101 C2' T A 4 OK OK 102 99 116 117 133 C2' A A 5 OK OK 134 131 154 155 165 C2' T A 6 OK OK 166 163 180 181 197 C2' T A 7 OK OK 198 195 212 213 229 C2' A A 8 OK OK 230 227 250 251 261 C2' G A 9 OK OK 262 259 283 284 294 C2' C A 10 OK OK 295 292 313 314 324 C2' G A 11 OK OK 325 322 347 348 356 C2' C B 12 OK OK 357 354 376 377 387 C2' G B 13 OK OK 388 385 409 410 420 C2' C B 14 OK OK 421 418 439 440 450 C2' T B 15 OK OK 451 448 465 466 482 C2' A B 16 OK OK 483 480 503 504 514 C2' A B 17 OK OK 515 512 535 536 546 C2' T B 18 OK OK 547 544 561 562 578 C2' A B 19 OK OK 579 576 599 600 610 C2' G B 20 OK OK 611 608 632 633 643 C2' G B 21 OK OK 644 641 665 666 676 C2' C B 22 OK OK 677 674 696 697 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 23 6 7 39 C3' C A 2 OK OK 37 54 40 41 69 C3' C A 3 OK OK 67 84 70 71 99 C3' T A 4 OK OK 97 115 100 101 131 C3' A A 5 OK OK 129 148 132 133 163 C3' T A 6 OK OK 161 179 164 165 195 C3' T A 7 OK OK 193 211 196 197 227 C3' A A 8 OK OK 225 244 228 229 259 C3' G A 9 OK OK 257 277 260 261 292 C3' C A 10 OK OK 290 307 293 294 322 C3' G A 11 OK OK 320 340 323 324 354 C3' C B 12 OK OK 352 369 355 356 385 C3' G B 13 OK OK 383 403 386 387 418 C3' C B 14 OK OK 416 433 419 420 448 C3' T B 15 OK OK 446 464 449 450 480 C3' A B 16 OK OK 478 497 481 482 512 C3' A B 17 OK OK 510 529 513 514 544 C3' T B 18 OK OK 542 560 545 546 576 C3' A B 19 OK OK 574 593 577 578 608 C3' G B 20 OK OK 606 626 609 610 641 C3' G B 21 OK OK 639 659 642 643 674 C3' C B 22 OK OK 672 689 675 676 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 22 2 4 37 C4' C A 2 OK OK 39 53 36 38 67 C4' C A 3 OK OK 69 83 66 68 97 C4' T A 4 OK OK 99 114 96 98 129 C4' A A 5 OK OK 131 147 128 130 161 C4' T A 6 OK OK 163 178 160 162 193 C4' T A 7 OK OK 195 210 192 194 225 C4' A A 8 OK OK 227 243 224 226 257 C4' G A 9 OK OK 259 276 256 258 290 C4' C A 10 OK OK 292 306 289 291 320 C4' G A 11 OK OK 322 339 319 321 352 C4' C B 12 OK OK 354 368 351 353 383 C4' G B 13 OK OK 385 402 382 384 416 C4' C B 14 OK OK 418 432 415 417 446 C4' T B 15 OK OK 448 463 445 447 478 C4' A B 16 OK OK 480 496 477 479 510 C4' A B 17 OK OK 512 528 509 511 542 C4' T B 18 OK OK 544 559 541 543 574 C4' A B 19 OK OK 576 592 573 575 606 C4' G B 20 OK OK 608 625 605 607 639 C4' G B 21 OK OK 641 658 638 640 672 C4' C B 22 OK OK 674 688 671 673 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 20 21 3 36 C5' C A 2 OK OK 35 51 52 37 66 C5' C A 3 OK OK 65 81 82 67 96 C5' T A 4 OK OK 95 112 113 97 128 C5' A A 5 OK OK 127 145 146 129 160 C5' T A 6 OK OK 159 176 177 161 192 C5' T A 7 OK OK 191 208 209 193 224 C5' A A 8 OK OK 223 241 242 225 256 C5' G A 9 OK OK 255 274 275 257 289 C5' C A 10 OK OK 288 304 305 290 319 C5' G A 11 OK OK 318 337 338 320 351 C5' C B 12 OK OK 350 366 367 352 382 C5' G B 13 OK OK 381 400 401 383 415 C5' C B 14 OK OK 414 430 431 416 445 C5' T B 15 OK OK 444 461 462 446 477 C5' A B 16 OK OK 476 494 495 478 509 C5' A B 17 OK OK 508 526 527 510 541 C5' T B 18 OK OK 540 557 558 542 573 C5' A B 19 OK OK 572 590 591 574 605 C5' G B 20 OK OK 604 623 624 606 638 C5' G B 21 OK OK 637 656 657 639 671 C5' C B 22 OK OK 670 686 687 672 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P C A 2 distorted distorted 6 33 34 35 62 P C A 3 distorted distorted 40 63 64 65 92 P T A 4 distorted distorted 70 93 94 95 124 P A A 5 distorted distorted 100 125 126 127 156 P T A 6 distorted distorted 132 157 158 159 188 P T A 7 distorted distorted 164 189 190 191 220 P A A 8 distorted distorted 196 221 222 223 252 P G A 9 distorted distorted 228 253 254 255 285 P C A 10 distorted distorted 260 286 287 288 315 P G A 11 distorted distorted 293 316 317 318 378 P G B 13 distorted distorted 355 379 380 381 411 P C B 14 distorted distorted 386 412 413 414 441 P T B 15 distorted distorted 419 442 443 444 473 P A B 16 distorted distorted 449 474 475 476 505 P A B 17 distorted distorted 481 506 507 508 537 P T B 18 distorted distorted 513 538 539 540 569 P A B 19 distorted distorted 545 570 571 572 601 P G B 20 distorted distorted 577 602 603 604 634 P G B 21 distorted distorted 609 635 636 637 667 P C B 22 distorted distorted 642 668 669 670 ---------------------------------------------------------------------------------