2VQE Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_2VQE_001 | 1/A/12:22 | No text annotation | homologous HL_4LFB_001 HL_31940.1 | |
| HL_2VQE_002 | 1/A/80:89 | No text annotation | homologous HL_4LFB_002 HL_46665.1 | |
| HL_2VQE_003 | 1/A/158:163 | GNRA | homologous HL_4LFB_003 HL_34789.1 | |
| HL_2VQE_004 | 1/A/190B:190G | No text annotation | homologous HL_4LFB_004 HL_89167.1 | |
| HL_2VQE_005 | 1/A/201:216 | Mini UNCG | homologous HL_4LFB_005 HL_90436.1 | |
| HL_2VQE_006 | 1/A/259:267 | GNRA related | homologous HL_4LFB_006 HL_36455.1 | |
| HL_2VQE_007 | 1/A/296:301 | GNRA | homologous HL_4LFB_007 HL_34789.1 | |
| HL_2VQE_008 | 1/A/320:333 | No text annotation | homologous HL_4LFB_008 HL_39665.1 | |
| HL_2VQE_009 | 1/A/342:347 | UNCG | homologous HL_4LFB_009 HL_61337.1 | |
| HL_2VQE_010 | 1/A/379:384 | GNRA | homologous HL_4LFB_010 HL_34789.1 | |
| HL_2VQE_011 | 1/A/419:424 | UNCG | homologous HL_4LFB_011 HL_61337.1 | |
| HL_2VQE_012 | 1/A/458:474 | GNRA | homologous HL_4LFB_012 HL_34789.1 | |
| HL_2VQE_013 | 1/A/522:527 | GNRA variation | homologous HL_4LFB_033 HL_34789.1 | |
| HL_2VQE_014 | 1/A/617:623 | GNRA-like with tWH | homologous HL_4LFB_014 HL_92337.1 | |
| HL_2VQE_015 | 1/A/689:698 | No text annotation | homologous HL_4LFB_015 HL_38491.1 | |
| HL_2VQE_016 | 1/A/726:731 | GNRA | homologous HL_4LFB_016 HL_34789.1 | |
| HL_2VQE_017 | 1/A/786:796 | No text annotation | homologous HL_4LFB_017 HL_38491.1 | |
| HL_2VQE_018 | 1/A/838:848 | Mini UNCG | homologous HL_4LFB_018 HL_90436.1 | |
| HL_2VQE_019 | 1/A/862:867 | GNRA | homologous HL_4LFB_019 HL_34789.1 | |
| HL_2VQE_020 | 1/A/897:902 | GNRA | homologous HL_4LFB_020 HL_34789.1 | |
| HL_2VQE_021 | 1/A/963:972 | No text annotation | homologous HL_4LFB_021 HL_97521.1 | |
| HL_2VQE_022 | 1/A/1012:1017 | GNRA | homologous HL_4LFB_022 HL_34789.1 | |
| HL_2VQE_023 | 1/A/1030:1031 | No text annotation | homologous HL_4LFB_023 NA | |
| HL_2VQE_024 | 1/A/1076:1081 | GNRA | homologous HL_4LFB_024 HL_34789.1 | |
| HL_2VQE_025 | 1/A/1089:1096 | T-loop related | homologous HL_4LFB_025 HL_63894.1 | |
| HL_2VQE_026 | 1/A/1134:1140 | No text annotation | geometric HL_4LFB_026 HL_92935.1 | |
| HL_2VQE_027 | 1/A/1165:1171 | GNRA | homologous HL_4LFB_027 HL_34789.1 | |
| HL_2VQE_028 | 1/A/1265:1270 | GNRA | homologous HL_4LFB_028 HL_34789.1 | |
| HL_2VQE_029 | 1/A/1314:1323 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_93658.1 | |
| HL_2VQE_030 | 1/A/1356:1366 | No text annotation | homologous HL_4LFB_030 HL_86432.1 | |
| HL_2VQE_031 | 1/A/1449:1454 | UNCG | homologous HL_4LFB_031 HL_61337.1 | |
| HL_2VQE_032 | 1/A/1515:1520 | GNRA | homologous HL_4LFB_032 HL_34789.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_2VQE_034 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_2VQE_001 | 1/A/30:32, 1/A/552:553 | Single bulged G | homologous IL_4LFB_001 IL_28408.1 | |
| IL_2VQE_002 | 1/A/44:45, 1/A/396:398 | Single bulged A | homologous IL_4LFB_002 IL_14190.1 | |
| IL_2VQE_003 | 1/A/47:52, 1/A/359:361 | No text annotation | geometric IL_4LFB_003 IL_68149.1 | |
| IL_2VQE_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform | homologous IL_4LFB_004 IL_34520.1 | |
| IL_2VQE_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | homologous IL_4LFB_005 IL_71421.1 | |
| IL_2VQE_006 | 1/A/67:69, 1/A/99:102 | Isolated non-canonical cWW pair | homologous IL_4LFB_006 IL_01003.1 | |
| IL_2VQE_007 | 1/A/129:131, 1/A/231:232 | Multiple bulged bases | homologous IL_4LFB_007 IL_75289.1 | |
| IL_2VQE_008 | 1/A/132:136, 1/A/227:230 | No text annotation | homologous IL_4LFB_008 IL_60988.1 | |
| IL_2VQE_009 | 1/A/148:153, 1/A/168:174 | tWH-tWH-tHW-tHW | homologous IL_4LFB_009 IL_00680.1 | |
| IL_2VQE_010 | 1/A/186:188, 1/A/190K:191 | Isolated non-canonical cWW pair | homologous IL_4LFB_010 IL_01003.1 | |
| IL_2VQE_011 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | homologous IL_4LFB_011 IL_46174.4 | |
| IL_2VQE_012 | 1/A/249:252, 1/A/274:275 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_2VQE_013 | 1/A/292:293, 1/A/304:308 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_2VQE_014 | 1/A/367:369, 1/A/392:393 | Single bulged U | homologous IL_4LFB_014 IL_97561.1 | |
| IL_2VQE_015 | 1/A/371:375, 1/A/389:390 | C-loop | homologous IL_5J7L_018 NA | |
| IL_2VQE_016 | 1/A/375:376, 1/A/387:389 | Single bulged G | homologous IL_5J7L_019 NA | |
| IL_2VQE_017 | 1/A/409:416, 1/A/427:433 | No text annotation | homologous IL_4LFB_017 IL_62329.1 | |
| IL_2VQE_018 | 1/A/446:450, 1/A/483:488 | 6x5 Sarcin-Ricin; G-bulge | homologous IL_4LFB_018 IL_82100.1 | |
| IL_2VQE_019 | 1/A/450:455, 1/A/477:483 | No text annotation | homologous IL_4LFB_019 IL_31561.1 | |
| IL_2VQE_020 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | homologous IL_4LFB_020 IL_11411.1 | |
| IL_2VQE_021 | 1/A/515:521, 1/A/528:536 | Kink-turn related | homologous IL_4LFB_021 IL_52042.1 | |
| IL_2VQE_022 | 1/A/569:575, 1/A/880:881 | No text annotation | homologous IL_4LFB_022 IL_20847.1 | |
| IL_2VQE_023 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS | homologous IL_4LFB_023 IL_05821.1 | |
| IL_2VQE_024 | 1/A/594:596, 1/A/644:645 | Major groove platform | homologous IL_4LFB_024 IL_48076.7 | |
| IL_2VQE_025 | 1/A/597:598, 1/A/640:643 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_029 NA | |
| IL_2VQE_026 | 1/A/605:612, 1/A/628:633 | No text annotation | homologous IL_4LFB_026 IL_04211.1 | |
| IL_2VQE_027 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW | geometric IL_5J7L_031 NA | |
| IL_2VQE_028 | 1/A/657:658, 1/A/747:749 | Major groove platform | homologous IL_4LFB_028 IL_48076.7 | |
| IL_2VQE_029 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | homologous IL_4LFB_029 IL_15225.1 | |
| IL_2VQE_060 | 1/A/673:677, 1/A/713:717 | Triple non-canonical cWW pairs | homologous IL_4LFB_065 IL_71154.1 | |
| IL_2VQE_031 | 1/A/683:688, 1/A/699:707 | Kink-turn | homologous IL_4LFB_031 IL_95727.1 | |
| IL_2VQE_032 | 1/A/774:778, 1/A/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_2VQE_033 | 1/A/779:783, 1/A/799:803 | tSH-tHW-tHS | homologous IL_4LFB_033 IL_05821.1 | |
| IL_2VQE_034 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4LFB_034 IL_84044.1 | |
| IL_2VQE_035 | 1/A/922:923, 1/A/1393:1395 | Single bulged A | homologous IL_4LFB_035 IL_14190.1 | |
| IL_2VQE_036 | 1/A/925:927, 1/A/1390:1391 | Single bulged G | homologous IL_4LFB_036 IL_28408.1 | |
| IL_2VQE_037 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform | homologous IL_4LFB_037 IL_61370.1 | |
| IL_2VQE_038 | 1/A/953:954, 1/A/1226:1228 | Minor groove platform | homologous IL_4LFB_038 IL_34520.1 | |
| IL_2VQE_039 | 1/A/1048:1050, 1/A/1208:1209 | Single bulged U | homologous IL_4LFB_042 IL_97561.1 | |
| IL_2VQE_040 | 1/A/1052:1056, 1/A/1204:1206 | Isolated cWS basepair | homologous IL_4LFB_044 IL_82453.1 | |
| IL_2VQE_041 | 1/A/1057:1058, 1/A/1199:1203 | Minor groove platform | homologous IL_4LFB_045 IL_24264.1 | |
| IL_2VQE_042 | 1/A/1060:1061, 1/A/1195:1197 | Single bulged U | homologous IL_4LFB_046 IL_97561.1 | |
| IL_2VQE_043 | 1/A/1061:1063, 1/A/1193:1195 | Isolated non-canonical cWW pair | homologous IL_4LFB_047 IL_68118.1 | |
| IL_2VQE_044 | 1/A/1124:1127, 1/A/1145:1149 | No text annotation | ||
| IL_2VQE_046 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation | homologous IL_4LFB_051 IL_12056.1 | |
| IL_2VQE_047 | 1/A/1255:1258, 1/A/1277:1282 | 180 degree turn | homologous IL_4LFB_052 IL_08849.1 | |
| IL_2VQE_048 | 1/A/1259:1260, 1/A/1274:1276 | Not an internal loop | homologous IL_4LFB_053 NA | |
| IL_2VQE_061 | 1/A/1259:1262, 1/A/1273:1276 | Double sheared | homologous IL_4LFB_067 IL_58355.1 | |
| IL_2VQE_049 | 1/A/1260:1262, 1/A/1273:1274 | Minor groove platform | homologous IL_4LFB_054 IL_34520.1 | |
| IL_2VQE_050 | 1/A/1303:1308, 1/A/1329:1334 | No text annotation | homologous IL_4LFB_055 IL_57885.1 | |
| IL_2VQE_051 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation | homologous IL_4LFB_056 IL_18228.1 | |
| IL_2VQE_052 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation | homologous IL_4LFB_068 IL_25873.1 | |
| IL_2VQE_053 | 1/A/1405:1407, 1/A/1494:1496 | Isolated non-canonical cWW pair | homologous IL_4LFB_069 IL_01003.1 | |
| IL_2VQE_054 | 1/A/1407:1409, 1/A/1491:1494 | No text annotation | homologous IL_4LFB_070 IL_29925.1 | |
| IL_2VQE_055 | 1/A/1412:1414, 1/A/1486:1488 | Isolated non-canonical cWW pair | homologous IL_4LFB_059 IL_01003.1 | |
| IL_2VQE_056 | 1/A/1416:1419, 1/A/1481:1484 | Double sheared | homologous IL_4LFB_060 IL_58355.1 | |
| IL_2VQE_057 | 1/A/1431:1435, 1/A/1466:1469 | UAA/GAN variation | homologous IL_4LFB_062 IL_77691.6 | |
| IL_2VQE_058 | 1/A/1435:1437, 1/A/1464:1466 | Isolated non-canonical cWW pair | homologous IL_4LFB_063 IL_01003.1 | |
| IL_2VQE_059 | 1/A/1440:1447, 1/A/1459:1461 | No text annotation | homologous IL_4LFB_064 IL_93811.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_2VQE_030 | No text annotation | ||
| IL_2VQE_045 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_2VQE_010 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation | geometric J3_4LFB_010 J3_58657.1 | |
| J3_2VQE_014 | 1/A/46:52, 1/A/359:367, 1/A/393:395 | No text annotation | homologous J3_4LFB_014 J3_63856.1 | |
| J3_2VQE_011 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | geometric J3_4LFB_011 J3_01633.1 | |
| J3_2VQE_015 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | homologous J3_4LFB_015 J3_17385.5 | |
| J3_2VQE_012 | 1/A/672:673, 1/A/717:725, 1/A/732:734 | No text annotation | homologous J3_4LFB_012 J3_74074.1 | |
| J3_2VQE_001 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_4LFB_001 J3_02285.1 | |
| J3_2VQE_002 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_85722.1 | |
| J3_2VQE_003 | 1/A/943:946, 1/A/1235:1237, 1/A/1337:1340 | No text annotation | homologous J3_4LFB_003 J3_44359.1 | |
| J3_2VQE_004 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation | homologous J3_4LFB_004 J3_88451.1 | |
| J3_2VQE_005 | 1/A/990:997, 1/A/1044:1047, 1/A/1210:1215 | No text annotation | homologous J3_4LFB_016 J3_28881.1 | |
| J3_2VQE_018 | 1/A/1001:1006, 1/A/1023:1028, 1/A/1033:1040 | No text annotation | ||
| J3_2VQE_007 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | homologous J3_4LFB_007 J3_01343.1 | |
| J3_2VQE_017 | 1/A/1073:1074, 1/A/1083:1086, 1/A/1099:1102 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J3_2VQE_019 | 1/A/1116:1118, 1/A/1155:1161, 1/A/1175:1184 | No text annotation | homologous J3_4LFB_018 J3_40706.1 | |
| J3_2VQE_009 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J4_2VQE_001 | 1/A/115:122, 1/A/239:240, 1/A/286:289, 1/A/311:312 | No text annotation | homologous J4_4LFB_001 J4_90044.1 | |
| J4_2VQE_002 | 1/A/142:144, 1/A/178:183, 1/A/194:198, 1/A/219:221 | No text annotation | homologous J4_4LFB_002 J4_88771.1 | |
| J4_2VQE_003 | 1/A/575:577, 1/A/764:769, 1/A/810:821, 1/A/879:880 | No text annotation | homologous J4_4LFB_003 J4_14595.1 | |
| J5_2VQE_001 | 1/A/36:39, 1/A/403:406, 1/A/436:442, 1/A/492:500, 1/A/545:548 | No text annotation | homologous J5_4LFB_001 J5_70703.1 | |
| J5_2VQE_002 | 1/A/58:61, 1/A/106:113, 1/A/314:316, 1/A/337:339, 1/A/350:354 | No text annotation | homologous J5_4LFB_002 J5_58574.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_2VQE_006 | No text annotation | ||
| J3_2VQE_016 | No text annotation | ||
| J3_2VQE_013 | No text annotation | ||
| J3_2VQE_008 | No text annotation |
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