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All interfaces > All interologs > Interface groups > group63 > 4Y4O_1d_1a

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Licorice
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RNA

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Licorice
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Chain
Chain (with hetatm)
Chainbow
Hydrophobicity
Electrostatics (surface only)
Conservation*

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Rim - Core

Contacts -

4Y4O_1d
4Y4O_1a
Distance
Base Pair
Hbond nuc:res
Base Stacking
Residue conservation
1d:2 [GLY] 1a:404 [U] 3.3 61.65
1d:2 [GLY] 1a:405 [U] 2.64 1a:499 [A] base:BB 61.65
1d:2 [GLY] 1a:499 [A] 3.79 1a:405 [U] 61.65
1d:2 [GLY] 1a:546 [G] 4.84 61.65
1d:2 [GLY] 1a:547 [A] 3.06 1a:498 [U] 61.65
1d:3 [ARG] 1a:404 [U] 4.73 74.9
1d:3 [ARG] 1a:405 [U] 3.29 1a:499 [A] 74.9
1d:3 [ARG] 1a:406 [G] 2.82 1a:436 [C] sugar:SC 74.9
1d:3 [ARG] 1a:407 [G] 2.89 1a:435 [C] 74.9
1d:3 [ARG] 1a:547 [A] 4.85 1a:498 [U] 74.9
1d:4 [TYR] 1a:546 [G] 3.83 56.42
1d:5 [ILE] 1a:405 [U] 3.69 1a:499 [A] 22.16
1d:5 [ILE] 1a:406 [G] 3.44 1a:436 [C] 22.16
1d:5 [ILE] 1a:407 [G] 4.6 1a:435 [C] 22.16
1d:6 [GLY] 1a:430 [A] 4.75 1a:414 [A] 45.3
1d:7 [PRO] 1a:428 [G] 3.71 1a:413 [G] 65.18
1d:7 [PRO] 1a:430 [A] 3.68 1a:414 [A] 65.18
1d:8 [VAL] 1a:430 [A] 3.09 1a:414 [A] 77.69
1d:9 [CYS] 1a:429 [U] 3.4 1a:431 [A] 8.07
1d:9 [CYS] 1a:430 [A] 2.7 1a:414 [A] 8.07
1d:10 [ARG] 1a:427 [U] 3.19 1a:416 [G] 82.08
1d:10 [ARG] 1a:428 [G] 2.68 1a:413 [G] 82.08
1d:10 [ARG] 1a:429 [U] 3.91 1a:431 [A] 82.08
1d:10 [ARG] 1a:430 [A] 4.24 1a:414 [A] 82.08
1d:10 [ARG] 1a:541 [G] 4.82 1a:504 [C] 82.08
1d:10 [ARG] 1a:542 [G] 2.51 1a:503 [C] 82.08
1d:10 [ARG] 1a:543 [C] 3.23 1a:502 [G] 82.08
1d:13 [ARG] 1a:426 [G] 4.4 1a:417 [C] 94.24
1d:13 [ARG] 1a:427 [U] 2.15 1a:416 [G] 94.24
1d:13 [ARG] 1a:428 [G] 4.76 1a:413 [G] 94.24
1d:13 [ARG] 1a:429 [U] 3.47 1a:431 [A] 94.24
1d:14 [ARG] 1a:511 [C] 4.26 1a:540 [G] 79.64
1d:14 [ARG] 1a:542 [G] 3.33 1a:503 [C] 79.64
1d:14 [ARG] 1a:543 [C] 3.0 1a:502 [G] 79.64
1d:21 [LEU] 1a:408 [A] 3.58 1a:434 [U] 51.64
1d:22 [LYS] 1a:408 [A] 3.37 1a:434 [U] 58.58
1d:22 [LYS] 1a:409 [G] 3.02 1a:433 [C] 58.58
1d:22 [LYS] 1a:410 [G] 3.33 1a:432 [A] base:SC 58.58
1d:22 [LYS] 1a:429 [U] 2.68 1a:431 [A] sugar:SC 58.58
1d:22 [LYS] 1a:430 [A] 3.46 1a:414 [A] 58.58
1d:23 [GLY] 1a:409 [G] 3.99 1a:433 [C] 44.11
1d:24 [GLU] 1a:408 [A] 4.52 1a:434 [U] 45.02
1d:24 [GLU] 1a:409 [G] 3.31 1a:433 [C] 45.02
1d:25 [ARG] 1a:409 [G] 3.12 1a:433 [C] 60.55
1d:25 [ARG] 1a:410 [G] 3.17 1a:432 [A] 60.55
1d:25 [ARG] 1a:411 [A] 2.41 60.55
1d:25 [ARG] 1a:429 [U] 3.63 1a:431 [A] 60.55
1d:26 [CYS] 1a:409 [G] 4.8 1a:433 [C] 27.5
1d:30 [LYS] 1a:409 [G] 4.64 1a:433 [C] 73.82
1d:30 [LYS] 1a:410 [G] 2.25 1a:432 [A] 73.82
1d:30 [LYS] 1a:411 [A] 2.64 73.82
1d:30 [LYS] 1a:412 [A] 3.92 73.82
1d:32 [ALA] 1a:429 [U] 3.85 1a:431 [A] 33.96
1d:34 [GLU] 1a:412 [A] 4.58 2.17
1d:35 [ARG] 1a:411 [A] 4.59 63.68
1d:35 [ARG] 1a:412 [A] 2.73 63.68
1d:35 [ARG] 1a:413 [G] 3.28 1a:428 [G] 63.68
1d:36 [ARG] 1a:412 [A] 4.76 71.84
1d:36 [ARG] 1a:413 [G] 3.81 1a:428 [G] 71.84
1d:36 [ARG] 1a:426 [G] 3.02 1a:417 [C] 71.84
1d:36 [ARG] 1a:427 [U] 3.1 1a:416 [G] 71.84
1d:36 [ARG] 1a:428 [G] 3.28 1a:413 [G] sugar:SC 71.84
1d:36 [ARG] 1a:429 [U] 2.65 1a:431 [A] 71.84
1d:38 [TYR] 1a:425 [G] 3.88 1a:418 [C] 21.1
1d:38 [TYR] 1a:426 [G] 2.24 1a:417 [C] 21.1
1d:40 [PRO] 1a:426 [G] 4.4 1a:417 [C] 72.55
1d:40 [PRO] 1a:427 [U] 3.46 1a:416 [G] 72.55
1d:40 [PRO] 1a:542 [G] 3.57 1a:503 [C] 72.55
1d:40 [PRO] 1a:543 [C] 4.23 1a:502 [G] 72.55
1d:41 [GLY] 1a:426 [G] 3.18 1a:417 [C] 83.92
1d:41 [GLY] 1a:427 [U] 3.1 1a:416 [G] 83.92
1d:41 [GLY] 1a:541 [G] 3.5 1a:504 [C] 83.92
1d:41 [GLY] 1a:542 [G] 3.78 1a:503 [C] 83.92
1d:42 [GLN] 1a:418 [C] 4.31 1a:425 [G] 54.9
1d:42 [GLN] 1a:419 [C] 3.8 1a:424 [G] 54.9
1d:42 [GLN] 1a:425 [G] 4.67 1a:418 [C] 54.9
1d:42 [GLN] 1a:426 [G] 3.15 1a:417 [C] 54.9
1d:42 [GLN] 1a:512 [U] 3.22 1a:539 [A] sugar:SC 54.9
1d:42 [GLN] 1a:540 [G] 3.34 1a:511 [C] base:SC 54.9
1d:42 [GLN] 1a:541 [G] 3.02 1a:504 [C] sugar:BB 54.9
1d:43 [HIS] 1a:511 [C] 3.07 1a:540 [G] base:SC 81.85
1d:43 [HIS] 1a:512 [U] 3.42 1a:539 [A] 81.85
1d:43 [HIS] 1a:540 [G] 4.21 1a:511 [C] 81.85
1d:43 [HIS] 1a:541 [G] 4.86 1a:504 [C] 81.85
1d:45 [GLN] 1a:425 [G] 2.81 1a:418 [C] 38.62
1d:45 [GLN] 1a:426 [G] 3.17 1a:417 [C] 38.62
1d:46 [LYS] 1a:511 [C] 4.23 1a:540 [G] 57.56
1d:46 [LYS] 1a:512 [U] 2.95 1a:539 [A] 57.56
1d:49 [ARG] 1a:510 [A] 4.59 1a:508 [C] 54.23
1d:49 [ARG] 1a:511 [C] 2.9 1a:540 [G] 54.23
1d:52 [SER] 1a:509 [A] 2.78 92.94
1d:54 [TYR] 1a:508 [C] 3.85 1a:510 [A] 79.9
1d:54 [TYR] 1a:509 [A] 3.31 79.9
1d:55 [ALA] 1a:509 [A] 3.52 69.08
1d:55 [ALA] 1a:510 [A] 4.83 1a:508 [C] 69.08
1d:57 [ARG] 1a:8 [A] 4.49 79.42
1d:58 [LEU] 1a:509 [A] 3.12 92.01
1d:58 [LEU] 1a:543 [C] 4.86 1a:502 [G] 92.01
1d:58 [LEU] 1a:544 [G] 4.13 1a:501 [C] 92.01
1d:59 [ARG] 1a:509 [A] 4.75 25.07
1d:59 [ARG] 1a:543 [C] 3.66 1a:502 [G] 25.07
1d:59 [ARG] 1a:544 [G] 2.89 1a:501 [C] 25.07
1d:61 [LYS] 1a:544 [G] 4.68 1a:501 [C] 97.49
1d:61 [LYS] 1a:545 [C] 2.56 1a:500 [G] 97.49
1d:62 [GLN] 1a:543 [C] 4.88 1a:502 [G] 94.71
1d:62 [GLN] 1a:544 [G] 2.66 1a:501 [C] 94.71
1d:62 [GLN] 1a:545 [C] 3.23 1a:500 [G] 94.71
1d:65 [ARG] 1a:545 [C] 2.77 1a:500 [G] 78.86
1d:65 [ARG] 1a:546 [G] 4.15 78.86
1d:66 [ARG] 1a:543 [C] 4.85 1a:502 [G] 8.07
1d:66 [ARG] 1a:544 [G] 2.87 1a:501 [C] 8.07
1d:71 [SER] 1a:546 [G] 3.89 63.86
1d:72 [GLU] 1a:545 [C] 3.1 1a:500 [G] 84.12
1d:72 [GLU] 1a:546 [G] 3.17 84.12
1d:73 [ARG] 1a:400 [C] 3.84 1a:42 [G] 70.22
1d:73 [ARG] 1a:401 [C] 3.06 1a:41 [G] 70.22
1d:73 [ARG] 1a:545 [C] 4.78 1a:500 [G] 70.22
1d:73 [ARG] 1a:546 [G] 3.12 70.22
1d:73 [ARG] 1a:549 [C] 5.0 1a:35 [G] 70.22
1d:74 [GLN] 1a:402 [G] 3.4 1a:40 [C] 85.26
1d:74 [GLN] 1a:403 [C] 2.7 1a:39 [G] 85.26
1d:76 [ARG] 1a:28 [G] 3.9 1a:555 [C] 59.51
1d:77 [ASN] 1a:401 [C] 2.95 1a:41 [G] 56.23
1d:77 [ASN] 1a:402 [G] 4.93 1a:40 [C] 56.23
1d:84 [LYS] 1a:613 [C] 4.65 1a:627 [G] 54.01
1d:85 [LYS] 1a:613 [C] 4.44 1a:627 [G] 3.2
1d:85 [LYS] 1a:614 [A] 3.12 1a:626 [U] 3.2
1d:87 [GLY] 1a:5 [U] 4.28 62.44
1d:112 [VAL] 1a:408 [A] 3.85 1a:434 [U] 36.61
1d:113 [SER] 1a:407 [G] 3.49 1a:435 [C] 91.93
1d:113 [SER] 1a:408 [A] 2.27 1a:434 [U] 91.93
1d:115 [ARG] 1a:406 [G] 4.87 1a:436 [C] 35.44
1d:115 [ARG] 1a:407 [G] 2.73 1a:435 [C] 35.44
1d:115 [ARG] 1a:408 [A] 3.55 1a:434 [U] 35.44
1d:116 [GLN] 1a:407 [G] 3.08 1a:435 [C] sugar:SC 64.74
1d:116 [GLN] 1a:408 [A] 3.22 1a:434 [U] sugar:SC 64.74
1d:118 [ARG] 1a:403 [C] 4.87 1a:39 [G] 97.31
1d:118 [ARG] 1a:404 [U] 3.13 97.31
1d:119 [GLN] 1a:405 [U] 4.7 1a:499 [A] 98.89
1d:119 [GLN] 1a:406 [G] 2.74 1a:436 [C] base:SC, base:SC 98.89
1d:119 [GLN] 1a:407 [G] 2.85 1a:435 [C] 98.89
1d:119 [GLN] 1a:437 [U] 3.53 1a:495 [A] 98.89
1d:119 [GLN] 1a:495 [A] 3.25 1a:437 [U] 98.89
1d:122 [ARG] 1a:403 [C] 2.93 1a:39 [G] 79.97
1d:122 [ARG] 1a:404 [U] 3.54 79.97
1d:122 [ARG] 1a:619 [U] 4.56 79.97
1d:123 [HIS] 1a:437 [U] 2.93 1a:495 [A] base:SC 98.97
1d:123 [HIS] 1a:438 [G] 3.39 1a:496 [A] 98.97
1d:123 [HIS] 1a:439 [A] 4.32 1a:494 [U] 98.97
1d:123 [HIS] 1a:495 [A] 3.5 1a:437 [U] 98.97
1d:125 [HIS] 1a:437 [U] 2.67 1a:495 [A] 85.74
1d:125 [HIS] 1a:438 [G] 2.56 1a:496 [A] 85.74
1d:132 [ARG] 1a:488 [C] 4.97 1a:446 [G] 58.17
1d:132 [ARG] 1a:489 [C] 2.68 1a:445 [G] 58.17
1d:132 [ARG] 1a:490 [G] 2.85 1a:444 [C] 58.17
1d:132 [ARG] 1a:619 [U] 3.53 58.17
1d:133 [VAL] 1a:619 [U] 3.37 79.13
1d:134 [ASP] 1a:619 [U] 2.34 base:BB, base:SC 74.43
1d:135 [LEU] 1a:402 [G] 4.28 1a:40 [C] 76.36
1d:135 [LEU] 1a:403 [C] 4.6 1a:39 [G] 76.36
1d:135 [LEU] 1a:619 [U] 3.24 76.36
1d:135 [LEU] 1a:620 [C] 3.46 76.36
1d:136 [PRO] 1a:403 [C] 3.52 1a:39 [G] 84.31
1d:136 [PRO] 1a:404 [U] 4.21 84.31
1d:137 [SER] 1a:402 [G] 3.34 1a:40 [C] 95.21
1d:137 [SER] 1a:403 [C] 2.48 1a:39 [G] 95.21
1d:137 [SER] 1a:620 [C] 4.22 95.21
1d:138 [TYR] 1a:619 [U] 4.23 52.39
1d:138 [TYR] 1a:620 [C] 3.83 52.39
1d:139 [ARG] 1a:620 [C] 4.51 6.51
1d:141 [ARG] 1a:615 [C] 4.76 1a:625 [G] 57.89
1d:141 [ARG] 1a:616 [G] 2.5 1a:624 [C] 57.89
1d:152 [SER] 1a:438 [G] 4.99 1a:496 [A] 59.49
1d:155 [LEU] 1a:436 [C] 3.7 1a:406 [G] 32.78
1d:155 [LEU] 1a:437 [U] 3.54 1a:495 [A] 32.78
1d:156 [GLU] 1a:436 [C] 3.72 1a:406 [G] 5.08
1d:156 [GLU] 1a:437 [U] 3.69 1a:495 [A] 5.08
1d:157 [LEU] 1a:436 [C] 4.0 1a:406 [G] 2.49
1d:205 [GLU] 1a:8 [A] 2.79 base:BB 93.12
1d:206 [PHE] 1a:8 [A] 4.73 65.28
1d:208 [SER] 1a:8 [A] 2.56 base:SC 89.21
1d:209 [ARG] 1a:8 [A] 3.71 84.2
1d:209 [ARG] 1a:26 [A] 3.38 1a:558 [G] sugar:SC 84.2
1d:209 [ARG] 1a:27 [G] 4.87 1a:556 [C] 84.2
1d:209 [ARG] 1a:507 [C] 4.96 1a:524 [G] 84.2
1d:209 [ARG] 1a:508 [C] 2.94 1a:510 [A] 84.2

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*Conservation was calculated using Rate4Site
NB: conservation is missing (completly white) for a very small minority of cases in which no homologous sequences were found (e.g. synthetic proteins 7D3J_A & 7EU9_A)

Properties of this interface

Interolog group ID Structure ID Structure description
 UniProt ID
 		ECOD label(s)
 		RFAM label(s)
 		Is ribosome? RCSB PDB link
group63 4Y4O_1d_1a 1d: 30s ribosomal protein s4, Thermus thermophilus (strain hb8 / atcc 27634 / dsm 579) (natural) 1a: 16s ribosomal RNA, Thermus thermophilus hb8 (natural) P80373 Alpha-L RNA-binding motif Bacterial small subunit ribosomal RNA ✔

Interologs

Total number of interologs for this interface: 3

Interface 1 Interface 2 Percentage conservation
 		Interface TM-score
 		Interface RMSD
 		Percentage identity
 		Common ECOD label(s)
 		Common RFAM label(s)
 		Explore both interfaces
4Y4O_1d_1a 7RYG_d_a 0.61 0.91 4.08 0.44 Alpha-L RNA-binding motif Bacterial small subunit ribosomal RNA compare
4Y4O_1d_1a 6S0X_d_a 0.36 0.95 4.96 0.39 Alpha-L RNA-binding motif Bacterial small subunit ribosomal RNA compare
4Y4O_1d_1a 7K00_D_A 0.73 0.98 1.52 0.45 Alpha-L RNA-binding motif Bacterial small subunit ribosomal RNA compare