RNA 3D Hub //

5AA0 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_5AA0_0031/AA/123:128No text annotation
homologous
HL_4WF9_003
HL_75660.6
HL_5AA0_0061/AA/194:201No text annotation
geometric
HL_4WF9_011
HL_75660.6
HL_5AA0_0181/AA/564:577No text annotation
HL_5AA0_0231/AA/744:753No text annotation
homologous
HL_7A0S_022
HL_50204.1
HL_5AA0_0241/AA/779:785UNCG variation
homologous
HL_7A0S_023
HL_51020.1
HL_5AA0_0271/AA/955:962GNRA
homologous
HL_4WF9_027
HL_34789.1
HL_5AA0_0391/AA/1612:1619No text annotation
homologous
HL_4WF9_038
HL_28592.1
HL_5AA0_0441/AA/1779:1785No text annotation
geometric
HL_2Y8W_001
NA
HL_5AA0_0481/AA/1950:1956Mini UNCG
geometric
HL_5T16_002
HL_12626.1
HL_5AA0_0611/AA/2551:2557No text annotation
homologous
HL_4WF9_058
HL_48677.1
HL_5AA0_0661/AA/2819:2827No text annotation
homologous
HL_7RQB_068
NA
HL_5AA0_1161/AB/34:48No text annotation
homologous
HL_5J7L_215
NA
HL_5AA0_0791/BA/379:384GNRA
homologous
HL_5J7L_010
NA
HL_5AA0_0881/BA/862:867GNRA
homologous
HL_4LFB_019
HL_34789.1
HL_5AA0_0891/BA/897:902GNRA
homologous
HL_4LFB_020
HL_34789.1

Problematic loops

#loop idProblemSequence
HL_5AA0_001No text annotation
HL_5AA0_002No text annotation
HL_5AA0_004No text annotation
HL_5AA0_005No text annotation
HL_5AA0_007No text annotation
HL_5AA0_008tRNA D-loop
HL_5AA0_125No text annotation
HL_5AA0_009No text annotation
HL_5AA0_111No text annotation
HL_5AA0_010No text annotation
HL_5AA0_011No text annotation
HL_5AA0_012T-loop with unstacked turn
HL_5AA0_013No text annotation
HL_5AA0_014No text annotation
HL_5AA0_015GNRA
HL_5AA0_016GNRA
HL_5AA0_112No text annotation
HL_5AA0_017No text annotation
HL_5AA0_019No text annotation
HL_5AA0_020GNRA
HL_5AA0_021No text annotation
HL_5AA0_022No text annotation
HL_5AA0_025No text annotation
HL_5AA0_113No text annotation
HL_5AA0_026No text annotation
HL_5AA0_028No text annotation
HL_5AA0_114No text annotation
HL_5AA0_029No text annotation
HL_5AA0_030No text annotation
HL_5AA0_031Externally structured
HL_5AA0_032No text annotation
HL_5AA0_033Pseudoknot geometry with 3' bulge
HL_5AA0_034No text annotation
HL_5AA0_126GNRA
HL_5AA0_035No text annotation
HL_5AA0_036No text annotation
HL_5AA0_037No text annotation
HL_5AA0_038UNCG
HL_5AA0_127Pseudoknot geometry with 3' bulge
HL_5AA0_040No text annotation
HL_5AA0_041UNCG
HL_5AA0_042No text annotation
HL_5AA0_043No text annotation
HL_5AA0_045No text annotation
HL_5AA0_046GNRA
HL_5AA0_047No text annotation
HL_5AA0_049No text annotation
HL_5AA0_050No text annotation
HL_5AA0_051No text annotation
HL_5AA0_052No text annotation
HL_5AA0_053No text annotation
HL_5AA0_054No text annotation
HL_5AA0_055Pseudoknot geometry
HL_5AA0_056GNRA with extra cWW
HL_5AA0_057GNRA
HL_5AA0_058No text annotation
HL_5AA0_059No text annotation
HL_5AA0_060No text annotation
HL_5AA0_115tRNA anticodon loop
HL_5AA0_062GNRA
HL_5AA0_063No text annotation
HL_5AA0_064No text annotation
HL_5AA0_065No text annotation
HL_5AA0_067GNRA
HL_5AA0_068No text annotation
HL_5AA0_069GNRA
HL_5AA0_070No text annotation
HL_5AA0_128No text annotation
HL_5AA0_117No text annotation
HL_5AA0_071No text annotation
HL_5AA0_072GNRA
HL_5AA0_073No text annotation
HL_5AA0_118No text annotation
HL_5AA0_074Mini UNCG
HL_5AA0_075GNRA related
HL_5AA0_076GNRA
HL_5AA0_077No text annotation
HL_5AA0_078UNCG
HL_5AA0_080UNCG
HL_5AA0_081GNRA
HL_5AA0_082No text annotation
HL_5AA0_083No text annotation
HL_5AA0_119No text annotation
HL_5AA0_084No text annotation
HL_5AA0_085GNRA
HL_5AA0_086No text annotation
HL_5AA0_087Mini UNCG
HL_5AA0_090No text annotation
HL_5AA0_091GNRA
HL_5AA0_092No text annotation
HL_5AA0_093GNRA
HL_5AA0_094T-loop related
HL_5AA0_095No text annotation
HL_5AA0_120No text annotation
HL_5AA0_096GNRA
HL_5AA0_097No text annotation
HL_5AA0_121No text annotation
HL_5AA0_098T-loop with 3 stacked bulged bases
HL_5AA0_099No text annotation
HL_5AA0_100UNCG
HL_5AA0_101GNRA
HL_5AA0_102tRNA D-loop
HL_5AA0_122No text annotation
HL_5AA0_103No text annotation
HL_5AA0_123No text annotation
HL_5AA0_104T-loop with 2 stacked bulged bases
HL_5AA0_105No text annotation
HL_5AA0_106tRNA anticodon loop
HL_5AA0_124No text annotation
HL_5AA0_107T-loop with 2 stacked bulged bases
HL_5AA0_108tRNA D-loop
HL_5AA0_109tRNA anticodon loop
HL_5AA0_110T-loop with 2 stacked bulged bases

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_5AA0_0061/AA/188:194,
1/AA/201:208		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7RQB_006
NA
IL_5AA0_0301/AA/998:1002,
1/AA/1153:1157		UAA/GAN
geometric
IL_5TBW_048
NA
IL_5AA0_1751/AA/1423:1429,
1/AA/1564:1575		No text annotation
IL_5AA0_0611/AA/1798:1804,
1/AA/1813:1821		Kink-turn related
homologous
IL_4WF9_069
IL_17069.6
IL_5AA0_0631/AA/1841:1842,
1/AA/1898:1901		Major groove intercalation
homologous
IL_4WF9_071
IL_78536.1
IL_5AA0_0671/AA/1934:1945,
1/AA/1961:1964		No text annotation
homologous
IL_7A0S_072
IL_04332.3
IL_5AA0_0691/AA/2054:2056,
1/AA/2612:2615		No text annotation
homologous
IL_4WF9_079
IL_80025.1
IL_5AA0_0911/AA/2680:2684,
1/AA/2725:2727		C-loop
homologous
IL_4WF9_101
IL_63596.12
IL_5AA0_1031/AB/34:38,
1/AB/44:48		No text annotation
homologous
IL_8C3A_147
NA
IL_5AA0_1381/BA/922:923,
1/BA/1393:1395		Single bulged A
homologous
IL_4LFB_035
IL_14190.1

Problematic loops

#loop idProblemSequence
IL_5AA0_001No text annotation
IL_5AA0_002Single bulged A
IL_5AA0_003Minor groove platform
IL_5AA0_004Kink-turn
IL_5AA0_005No text annotation
IL_5AA0_0077x6 Sarcin-Ricin; G-bulge
IL_5AA0_008Multiple bulged bases
IL_5AA0_169No text annotation
IL_5AA0_009No text annotation
IL_5AA0_010Isolated non-canonical cWW pair
IL_5AA0_184No text annotation
IL_5AA0_170No text annotation
IL_5AA0_011Isolated non-canonical cWW pair
IL_5AA0_171No text annotation
IL_5AA0_012No text annotation
IL_5AA0_013No text annotation
IL_5AA0_014Isolated non-canonical cWW pair
IL_5AA0_015Isolated non-canonical cWW pair
IL_5AA0_172No text annotation
IL_5AA0_016tHW-tHW cross-strand stack
IL_5AA0_017Single bulged A
IL_5AA0_018Triple sheared
IL_5AA0_019Major groove platform with extra cWW
IL_5AA0_020Single stack bend
IL_5AA0_021No text annotation
IL_5AA0_022Stack outside cWW
IL_5AA0_023No text annotation
IL_5AA0_024No text annotation
IL_5AA0_025Minor groove platform related
IL_5AA0_026C-loop
IL_5AA0_027Isolated cWS basepair
IL_5AA0_028No text annotation
IL_5AA0_029Single bulged C
IL_5AA0_031No text annotation
IL_5AA0_032Single bulged U
IL_5AA0_033No text annotation
IL_5AA0_034Isolated non-canonical cWW pair
IL_5AA0_173No text annotation
IL_5AA0_035No text annotation
IL_5AA0_174No text annotation
IL_5AA0_036No text annotation
IL_5AA0_037No text annotation
IL_5AA0_038Single bulged G
IL_5AA0_185No text annotation
IL_5AA0_039No text annotation
IL_5AA0_040Kink-turn
IL_5AA0_041Intercalated cWW
IL_5AA0_186C-loop
IL_5AA0_042C-loop with extra cWW pair
IL_5AA0_043UAA/GAN
IL_5AA0_044tSH-tHW-tHS
IL_5AA0_045No text annotation
IL_5AA0_046No text annotation
IL_5AA0_047No text annotation
IL_5AA0_048tSH-tHW
IL_5AA0_049Single stack bend
IL_5AA0_050No text annotation
IL_5AA0_051No text annotation
IL_5AA0_052No text annotation
IL_5AA0_187Single bulged A
IL_5AA0_053No text annotation
IL_5AA0_054Isolated non-canonical cWW pair
IL_5AA0_055No text annotation
IL_5AA0_056No text annotation
IL_5AA0_057tSH-tSH-tHH-tHS
IL_5AA0_058No text annotation
IL_5AA0_059Single bulged A
IL_5AA0_060No text annotation
IL_5AA0_062No text annotation
IL_5AA0_064Major groove minor groove platform; mini C-loop
IL_5AA0_065UAA/GAN with extra stack
IL_5AA0_066Triple sheared
IL_5AA0_068Major groove platform
IL_5AA0_070Single bulged U
IL_5AA0_071Minor groove platform
IL_5AA0_072Isolated tHS basepair with bulges
IL_5AA0_073No text annotation
IL_5AA0_074Isolated non-canonical cWW pair
IL_5AA0_075No text annotation
IL_5AA0_076No text annotation
IL_5AA0_077No text annotation
IL_5AA0_078Isolated tHS basepair with bulges
IL_5AA0_079Double sheared
IL_5AA0_080Major groove platform
IL_5AA0_081Major groove platform
IL_5AA0_176No text annotation
IL_5AA0_082No text annotation
IL_5AA0_083Double sheared with non-canonical cWW
IL_5AA0_084Major groove platform
IL_5AA0_085Isolated non-canonical cWW with bulges
IL_5AA0_086No text annotation
IL_5AA0_087No text annotation
IL_5AA0_088Single bulged A
IL_5AA0_089No text annotation
IL_5AA0_090Isolated non-canonical cWW pair
IL_5AA0_092No text annotation
IL_5AA0_093Multiple bulged bases
IL_5AA0_094Isolated non-canonical cWW pair
IL_5AA0_095UAA/GAN with extra cWW
IL_5AA0_096Single bulged C
IL_5AA0_097No text annotation
IL_5AA0_098No text annotation
IL_5AA0_188tHS double platform
IL_5AA0_099Isolated non-canonical cWW pair
IL_5AA0_100Major groove intercalation
IL_5AA0_101No text annotation
IL_5AA0_189No text annotation
IL_5AA0_102No text annotation
IL_5AA0_104Bacterial 5S Loop E
IL_5AA0_105Single bulged G
IL_5AA0_106Intercalated cWW
IL_5AA0_107No text annotation
IL_5AA0_108Minor groove platform
IL_5AA0_109Multiple bulged bases
IL_5AA0_110Isolated non-canonical cWW pair
IL_5AA0_111Multiple bulged bases
IL_5AA0_112No text annotation
IL_5AA0_113tWH-tWH-tHW-tHW
IL_5AA0_114No text annotation
IL_5AA0_177Isolated non-canonical cWW pair
IL_5AA0_115Kink-turn with non-sequential stacking
IL_5AA0_116No text annotation
IL_5AA0_117C-loop
IL_5AA0_118Single bulged U
IL_5AA0_178No text annotation
IL_5AA0_119C-loop
IL_5AA0_120Single bulged G
IL_5AA0_121No text annotation
IL_5AA0_1226x5 Sarcin-Ricin; G-bulge
IL_5AA0_123No text annotation
IL_5AA0_124SSU/LSU pseudoknot
IL_5AA0_125Kink-turn related
IL_5AA0_126tSH-tHW-tHS-cWW
IL_5AA0_179tSH-tHW-tHS
IL_5AA0_127Major groove platform
IL_5AA0_128Major groove minor groove platform; mini C-loop
IL_5AA0_129No text annotation
IL_5AA0_130Major groove platform; stack outside cWW
IL_5AA0_131Major groove platform
IL_5AA0_132Tandem non-canonical cWW pairs
IL_5AA0_133Triple non-canonical cWW pairs
IL_5AA0_134Kink-turn
IL_5AA0_135Left turn
IL_5AA0_136tSH-tHW-tHS
IL_5AA0_1378x6 Sarcin-Ricin with inserted Y; G-bulge
IL_5AA0_139Single bulged G
IL_5AA0_140Minor groove platform
IL_5AA0_141Minor groove platform
IL_5AA0_142No text annotation
IL_5AA0_143No text annotation
IL_5AA0_144Isolated cWS basepair
IL_5AA0_145Minor groove platform
IL_5AA0_146Single bulged U
IL_5AA0_147Isolated non-canonical cWW pair
IL_5AA0_148No text annotation
IL_5AA0_180No text annotation
IL_5AA0_149No text annotation
IL_5AA0_150No text annotation
IL_5AA0_151No text annotation
IL_5AA0_152180 degree turn
IL_5AA0_153Double sheared with non-canonical cWW
IL_5AA0_190No text annotation
IL_5AA0_154No text annotation
IL_5AA0_155No text annotation
IL_5AA0_156No text annotation
IL_5AA0_157No text annotation
IL_5AA0_181No text annotation
IL_5AA0_158Isolated non-canonical cWW pair
IL_5AA0_159No text annotation
IL_5AA0_182No text annotation
IL_5AA0_160Triple sheared related
IL_5AA0_191UAA/GAN variation
IL_5AA0_161Isolated non-canonical cWW pair
IL_5AA0_183No text annotation
IL_5AA0_162No text annotation
IL_5AA0_163Isolated non-canonical cWW contact
IL_5AA0_164No text annotation
IL_5AA0_165No text annotation
IL_5AA0_166Tandem non-canonical cWW pairs
IL_5AA0_167Isolated non-canonical cWW pair
IL_5AA0_168No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_5AA0_0281/BA/586:588,
1/BA/651:654,
1/BA/754:755		No text annotation
geometric
J3_1KUQ_001
J3_01633.1
J3_5AA0_0291/BA/586:588,
1/BA/651:655,
1/BA/751:755		No text annotation
homologous
J3_4LFB_015
J3_17385.5
J3_5AA0_0101/BA/826:829,
1/BA/857:861,
1/BA/868:874		No text annotation
homologous
J3_4LFB_001
J3_02285.1
J4_5AA0_0011/AA/47:54,
1/AA/116:121,
1/AA/130:131,
1/AA/148:178		No text annotation
J4_5AA0_0031/AA/1270:1276,
1/AA/1294:1295,
1/AA/1645:1648,
1/AA/2009:2010		No text annotation
homologous
J4_9DFE_003
J4_64571.6
J4_5AA0_0061/AA/1772:1775,
1/AA/1789:1792,
1/AA/1827:1830,
1/AA/1975:1979		No text annotation
J4_5AA0_0071/AA/1833:1835,
1/AA/1905:1909,
1/AA/1922:1945,
1/AA/1961:1972		No text annotation
J4_5AA0_0081/AA/2285:2289,
1/AA/2343:2347,
1/AA/2370:2372,
1/AA/2381:2383		No text annotation
homologous
J4_7A0S_009
J4_98139.1
J4_5AA0_0151/BA/569:577,
1/BA/764:769,
1/BA/810:821,
1/BA/879:881		No text annotation
J5_5AA0_0021/AA/584:589,
1/AA/668:671,
1/AA/809:812,
1/AA/1195:1198,
1/AA/1247:1256		No text annotation
J5_5AA0_0091/AA/1667:1683,
1/AA/1705:1707,
1/AA/1751:1752,
1/AA/1756:1764,
1/AA/1988:1993		No text annotation
J5_5AA0_0041/AA/2057:2064,
1/AA/2446:2455,
1/AA/2496:2507,
1/AA/2582:2588,
1/AA/2606:2611		No text annotation
J5_5AA0_0051/AA/2074:2077,
1/AA/2243:2246,
1/AA/2258:2259,
1/AA/2281:2282,
1/AA/2427:2435		No text annotation
homologous
J5_7A0S_007
J5_39529.2
J6_5AA0_0021/AA/2074:2077,
1/AA/2243:2246,
1/AA/2258:2259,
1/AA/2281:2284,
1/AA/2384:2395,
1/AA/2421:2435		No text annotation
J10_5AA0_0011/AA/4:15,
1/AA/525:533,
1/AA/560:564,
1/AA/577:579,
1/AA/1261:1269,
1/AA/2011:2023,
1/AA/2040:2043,
1/AA/2625:2630,
1/AA/2788:2811,
1/AA/2889:2899		No text annotation

Problematic loops

#loop idProblemSequence
J3_5AA0_018No text annotation
J3_5AA0_019No text annotation
J3_5AA0_036No text annotation
J3_5AA0_020No text annotation
J3_5AA0_021No text annotation
J3_5AA0_001No text annotation
J3_5AA0_002No text annotation
J3_5AA0_003No text annotation
J3_5AA0_004No text annotation
J3_5AA0_005No text annotation
J3_5AA0_022No text annotation
J3_5AA0_006No text annotation
J3_5AA0_023No text annotation
J3_5AA0_007No text annotation
J3_5AA0_008No text annotation
J3_5AA0_024No text annotation
J3_5AA0_025No text annotation
J3_5AA0_037No text annotation
J3_5AA0_009No text annotation
J3_5AA0_026No text annotation
J3_5AA0_027No text annotation
J3_5AA0_030No text annotation
J3_5AA0_011No text annotation
J3_5AA0_012No text annotation
J3_5AA0_013No text annotation
J3_5AA0_014No text annotation
J3_5AA0_031No text annotation
J3_5AA0_015No text annotation
J3_5AA0_038No text annotation
J3_5AA0_032No text annotation
J3_5AA0_033No text annotation
J3_5AA0_039No text annotation
J3_5AA0_016No text annotation
J3_5AA0_017No text annotation
J3_5AA0_034No text annotation
J3_5AA0_035No text annotation
J3_5AA0_040No text annotation
J4_5AA0_002No text annotation
J4_5AA0_004No text annotation
J4_5AA0_014No text annotation
J4_5AA0_005No text annotation
J4_5AA0_009No text annotation
J4_5AA0_010No text annotation
J4_5AA0_011No text annotation
J4_5AA0_012No text annotation
J4_5AA0_013No text annotation
J4_5AA0_016No text annotation
J5_5AA0_001No text annotation
J5_5AA0_008No text annotation
J5_5AA0_003No text annotation
J5_5AA0_006No text annotation
J5_5AA0_007No text annotation
J6_5AA0_003No text annotation
J6_5AA0_001No text annotation
J7_5AA0_001No text annotation

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