6YBW Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6YBW_001 | 1/A/7:17 | No text annotation | homologous HL_4V88_186 NA | |
| HL_6YBW_002 | 1/A/69:80 | Mini UNCG | geometric HL_4YAZ_004 HL_90436.1 | |
| HL_6YBW_003 | 1/A/156:162 | GNRA related | homologous HL_4V88_188 NA | |
| HL_6YBW_005 | 1/A/288:295 | T-loop with 1 bulged base | homologous HL_4V88_191 NA | |
| HL_6YBW_006 | 1/A/322:329 | Externally structured | geometric HL_8C3A_022 NA | |
| HL_6YBW_007 | 1/A/377:387 | No text annotation | ||
| HL_6YBW_008 | 1/A/416:421 | No text annotation | homologous HL_4V88_194 NA | |
| HL_6YBW_009 | 1/A/441:452 | No text annotation | homologous HL_4V88_195 NA | |
| HL_6YBW_010 | 1/A/462:467 | UNCG | homologous HL_4V88_196 NA | |
| HL_6YBW_011 | 1/A/498:504 | No text annotation | homologous HL_4V88_197 NA | |
| HL_6YBW_013 | 1/A/569:581 | No text annotation | homologous HL_4V88_199 NA | |
| HL_6YBW_014 | 1/A/618:623 | GNRA variation | homologous HL_4V88_200 NA | |
| HL_6YBW_017 | 1/A/820:828 | No text annotation | homologous HL_4V88_203 NA | |
| HL_6YBW_018 | 1/A/833:841 | No text annotation | ||
| HL_6YBW_028 | 1/A/881:905 | No text annotation | ||
| HL_6YBW_019 | 1/A/885:901 | No text annotation | ||
| HL_6YBW_020 | 1/A/957:966 | No text annotation | homologous HL_4V88_206 NA | |
| HL_6YBW_021 | 1/A/994:999 | GNRA | homologous HL_4V88_207 NA | |
| HL_6YBW_022 | 1/A/1054:1064 | No text annotation | homologous HL_4V88_208 NA | |
| HL_6YBW_024 | 1/A/1141:1146 | GNRA | homologous HL_4V88_210 NA | |
| HL_6YBW_025 | 1/A/1178:1183 | GNRA | homologous HL_4V88_211 NA | |
| HL_6YBW_027 | 1/A/1847:1852 | GNRA variation | homologous HL_4V88_222 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6YBW_004 | No text annotation | ||
| HL_6YBW_012 | Externally structured | ||
| HL_6YBW_015 | No text annotation | ||
| HL_6YBW_016 | No text annotation | ||
| HL_6YBW_023 | No text annotation | ||
| HL_6YBW_029 | No text annotation | ||
| HL_6YBW_026 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6YBW_001 | 1/A/23:25, 1/A/649:651 | Isolated non-canonical cWW pair | geometric IL_3MEI_002 NA | |
| IL_6YBW_003 | 1/A/34:36, 1/A/519:521 | Isolated non-canonical cWW pair | homologous IL_4V88_385 NA | |
| IL_6YBW_004 | 1/A/37:40, 1/A/514:518 | Double sheared | geometric IL_4WF9_016 IL_58355.1 | |
| IL_6YBW_005 | 1/A/41:47, 1/A/479:481 | No text annotation | homologous IL_4V88_387 NA | |
| IL_6YBW_006 | 1/A/49:51, 1/A/476:477 | Minor groove platform | homologous IL_4V88_388 NA | |
| IL_6YBW_007 | 1/A/57:62, 1/A/86:88 | No text annotation | homologous IL_4V88_389 NA | |
| IL_6YBW_008 | 1/A/63:68, 1/A/81:85 | No text annotation | homologous IL_4V88_390 NA | |
| IL_6YBW_009 | 1/A/108:110, 1/A/351:353 | Isolated non-canonical cWW pair | geometric IL_1ZX7_006 IL_71625.1 | |
| IL_6YBW_069 | 1/A/108:115, 1/A/348:353 | No text annotation | ||
| IL_6YBW_010 | 1/A/110:112, 1/A/349:351 | Isolated non-canonical cWW pair | geometric IL_4WF9_042 IL_01003.1 | |
| IL_6YBW_011 | 1/A/112:115, 1/A/348:349 | Multiple bulged bases | geometric IL_4V88_392 NA | |
| IL_6YBW_070 | 1/A/116:121, 1/A/343:347 | No text annotation | homologous IL_8P9A_382 IL_31545.1 | |
| IL_6YBW_071 | 1/A/145:151, 1/A/167:174 | No text annotation | homologous IL_8C3A_402 NA | |
| IL_6YBW_072 | 1/A/152:154, 1/A/164:166 | No text annotation | homologous IL_8P9A_384 IL_23751.1 | |
| IL_6YBW_016 | 1/A/188:192, 1/A/207:211 | Double sheared with non-canonical cWW | geometric IL_5J7L_274 NA | |
| IL_6YBW_017 | 1/A/216:219, 1/A/302:309 | Tandem non-canonical cWW pairs | geometric IL_1GID_008 NA | |
| IL_6YBW_019 | 1/A/312:314, 1/A/336:337 | Single bulged A | homologous IL_4V88_399 NA | |
| IL_6YBW_020 | 1/A/317:319, 1/A/332:333 | No text annotation | ||
| IL_6YBW_021 | 1/A/359:364, 1/A/396:403 | Kink-turn with non-sequential stacking | homologous IL_4V88_402 NA | |
| IL_6YBW_022 | 1/A/366:371, 1/A/393:394 | No text annotation | geometric IL_5Y58_001 IL_45649.1 | |
| IL_6YBW_023 | 1/A/411:413, 1/A/424:429 | No text annotation | homologous IL_4V88_404 NA | |
| IL_6YBW_024 | 1/A/437:439, 1/A/454:456 | Isolated cWH basepair | homologous IL_4V88_405 NA | |
| IL_6YBW_025 | 1/A/459:461, 1/A/468:470 | Isolated near basepair | homologous IL_4V88_406 NA | |
| IL_6YBW_026 | 1/A/487:489, 1/A/511:512 | Single bulged U | homologous IL_4V88_407 NA | |
| IL_6YBW_073 | 1/A/491:495, 1/A/508:509 | C-loop | homologous IL_8C3A_416 NA | |
| IL_6YBW_028 | 1/A/495:496, 1/A/506:508 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_6YBW_029 | 1/A/527:534, 1/A/549:558 | No text annotation | ||
| IL_6YBW_031 | 1/A/563:565, 1/A/585:592 | No text annotation | homologous IL_8C3A_420 NA | |
| IL_6YBW_032 | 1/A/566:569, 1/A/581:584 | Tandem non-canonical cWW pairs | geometric IL_6JDV_001 IL_71194.1 | |
| IL_6YBW_033 | 1/A/599:606, 1/A/636:637 | SSU/LSU pseudoknot | geometric IL_4V88_413 NA | |
| IL_6YBW_034 | 1/A/606:608, 1/A/635:636 | Single bulged U | homologous IL_4V88_414 NA | |
| IL_6YBW_035 | 1/A/611:617, 1/A/624:632 | Kink-turn related | homologous IL_4V88_415 NA | |
| IL_6YBW_074 | 1/A/663:665, 1/A/1162:1164 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 NA | |
| IL_6YBW_075 | 1/A/665:671, 1/A/1161:1162 | No text annotation | homologous IL_8C3A_426 NA | |
| IL_6YBW_036 | 1/A/673:675, 1/A/1030:1032 | Isolated non-canonical cWW pair | homologous IL_4V88_417 NA | |
| IL_6YBW_037 | 1/A/676:680, 1/A/1025:1029 | tSH-tHW-tHS | homologous IL_4V88_418 NA | |
| IL_6YBW_040 | 1/A/802:803, 1/A/860:863 | Major groove minor groove platform; mini C-loop | homologous IL_4V88_423 NA | |
| IL_6YBW_041 | 1/A/805:807, 1/A/856:858 | Isolated non-canonical cWW pair | homologous IL_4V88_424 NA | |
| IL_6YBW_042 | 1/A/807:815, 1/A/849:856 | No text annotation | geometric IL_4V88_425 NA | |
| IL_6YBW_043 | 1/A/874:876, 1/A/910:912 | Isolated non-canonical cWW pair | geometric IL_5Y85_006 IL_01003.1 | |
| IL_6YBW_044 | 1/A/877:879, 1/A/907:909 | Isolated non-canonical cWW pair | geometric IL_5J7L_061 NA | |
| IL_6YBW_045 | 1/A/922:923, 1/A/1019:1022 | Major groove platform; stack outside cWW | homologous IL_4V88_428 NA | |
| IL_6YBW_076 | 1/A/925:926, 1/A/1015:1017 | Single bulged U | geometric IL_6UFH_004 NA | |
| IL_6YBW_077 | 1/A/928:931, 1/A/1010:1013 | Tandem non-canonical cWW pairs | homologous IL_8P9A_419 IL_15225.1 | |
| IL_6YBW_048 | 1/A/931:935, 1/A/1007:1010 | Tandem non-canonical cWW pairs | homologous IL_4V88_431 NA | |
| IL_6YBW_049 | 1/A/942:945, 1/A/981:984 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_6YBW_050 | 1/A/952:956, 1/A/967:974 | Kink-turn | homologous IL_4V88_434 NA | |
| IL_6YBW_051 | 1/A/1042:1047, 1/A/1071:1073 | Other IL | geometric IL_4V88_435 NA | |
| IL_6YBW_052 | 1/A/1047:1051, 1/A/1067:1071 | tSH-tHW-tHS | homologous IL_4V88_436 NA | |
| IL_6YBW_053 | 1/A/1091:1093, 1/A/1152:1158 | No text annotation | homologous IL_4V88_437 NA | |
| IL_6YBW_054 | 1/A/1098:1101, 1/A/1131:1134 | Tandem non-canonical cWW pairs | homologous IL_4V88_438 NA | |
| IL_6YBW_055 | 1/A/1101:1103, 1/A/1129:1131 | Isolated non-canonical cWW pair | geometric IL_4V9F_105 IL_01003.1 | |
| IL_6YBW_056 | 1/A/1108:1110, 1/A/1123:1124 | Minor groove platform | geometric IL_4V88_412 NA | |
| IL_6YBW_057 | 1/A/1168:1175, 1/A/1186:1191 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4V88_440 NA | |
| IL_6YBW_058 | 1/A/1700:1702, 1/A/1833:1836 | No text annotation | homologous IL_4V88_463 NA | |
| IL_6YBW_059 | 1/A/1702:1705, 1/A/1829:1833 | No text annotation | homologous IL_8P9A_453 IL_25873.1 | |
| IL_6YBW_060 | 1/A/1706:1708, 1/A/1826:1828 | Isolated non-canonical cWW pair | geometric IL_1UN6_005 IL_01003.1 | |
| IL_6YBW_061 | 1/A/1708:1711, 1/A/1822:1826 | No text annotation | ||
| IL_6YBW_062 | 1/A/1714:1716, 1/A/1817:1819 | Isolated non-canonical cWW pair | homologous IL_4V88_467 NA | |
| IL_6YBW_063 | 1/A/1717:1720, 1/A/1813:1816 | Double sheared | homologous IL_4V88_468 NA | |
| IL_6YBW_065 | 1/A/1729:1731, 1/A/1803:1805 | Isolated non-canonical cWW pair | homologous IL_4V88_470 NA | |
| IL_6YBW_066 | 1/A/1733:1736, 1/A/1798:1801 | Double sheared | homologous IL_4V88_471 NA | |
| IL_6YBW_067 | 1/A/1739:1741, 1/A/1793:1795 | Isolated non-canonical cWW pair | geometric IL_4E48_002 IL_01003.1 | |
| IL_6YBW_068 | 1/A/1742:1746, 1/A/1788:1792 | Triple sheared | homologous IL_4V88_474 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6YBW_002 | Isolated non-canonical cWW pair | ||
| IL_6YBW_012 | No text annotation | ||
| IL_6YBW_013 | No text annotation | ||
| IL_6YBW_014 | No text annotation | ||
| IL_6YBW_015 | Tandem non-canonical cWW pairs | ||
| IL_6YBW_018 | No text annotation | ||
| IL_6YBW_027 | No text annotation | ||
| IL_6YBW_030 | No text annotation | ||
| IL_6YBW_038 | No text annotation | ||
| IL_6YBW_039 | Isolated non-canonical cWW pair | ||
| IL_6YBW_046 | Isolated non-canonical cWW pair | ||
| IL_6YBW_047 | No text annotation | ||
| IL_6YBW_064 | Single bulged U |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6YBW_001 | 1/A/40:41, 1/A/481:487, 1/A/512:514 | No text annotation | geometric J3_4V88_078 NA | |
| J3_6YBW_006 | 1/A/40:47, 1/A/479:487, 1/A/512:514 | No text annotation | homologous J3_8P9A_069 J3_63856.1 | |
| J3_6YBW_002 | 1/A/682:685, 1/A/917:922, 1/A/1022:1023 | No text annotation | ||
| J3_6YBW_007 | 1/A/682:685, 1/A/917:923, 1/A/1019:1023 | No text annotation | ||
| J3_6YBW_003 | 1/A/816:819, 1/A/829:831, 1/A/843:848 | No text annotation | homologous J3_4V88_032 NA | |
| J3_6YBW_004 | 1/A/938:941, 1/A/985:993, 1/A/1000:1004 | No text annotation | homologous J3_4V88_033 NA | |
| J3_6YBW_005 | 1/A/1094:1096, 1/A/1136:1140, 1/A/1147:1151 | No text annotation | ||
| J4_6YBW_001 | 1/A/98:106, 1/A/355:357, 1/A/405:409, 1/A/431:432 | No text annotation | homologous J4_8P9A_021 J4_15241.2 | |
| J4_6YBW_002 | 1/A/671:673, 1/A/1032:1037, 1/A/1078:1089, 1/A/1160:1161 | No text annotation | homologous J4_8P9A_022 J4_14595.1 | |
| J5_6YBW_001 | 1/A/30:34, 1/A/521:527, 1/A/558:563, 1/A/592:595, 1/A/641:644 | No text annotation | homologous J5_8C3A_018 NA | |
| J5_6YBW_002 | 1/A/30:34, 1/A/521:527, 1/A/558:565, 1/A/585:595, 1/A/641:644 | No text annotation | ||
| J5_6YBW_003 | 1/A/53:56, 1/A/89:96, 1/A/434:436, 1/A/457:459, 1/A/470:474 | No text annotation | homologous J5_8C3A_020 NA | |
| J5_6YBW_004 | 1/A/123:129, 1/A/183:185, 1/A/214:215, 1/A/310:312, 1/A/337:341 | No text annotation |
Problematic loops
No problematic loops
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