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All interfaces > All interologs > Interface groups > group113 > 4YBB_DW_DB

Interface analysis

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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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Interface

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Rim - Core

Contacts -

4YBB_DW
4YBB_DB
Distance
Base Pair
Hbond nuc:res
Base Stacking
Residue conservation
DW:9 [ARG] DB:75 [G] 3.16 DB:101 [A] 96.75
DW:9 [ARG] DB:76 [G] 2.62 DB:100 [G] 96.75
DW:12 [GLN] DB:75 [G] 3.8 DB:101 [A] 40.29
DW:12 [GLN] DB:76 [G] 2.94 DB:100 [G] 40.29
DW:13 [GLY] DB:76 [G] 3.0 DB:100 [G] 92.07
DW:13 [GLY] DB:77 [U] 4.36 DB:99 [A] 92.07
DW:13 [GLY] DB:98 [G] 3.42 DB:78 [A] 92.07
DW:14 [LYS] DB:77 [U] 3.61 DB:99 [A] 81.48
DW:14 [LYS] DB:78 [A] 4.15 DB:98 [G] 81.48
DW:14 [LYS] DB:79 [G] 2.7 DB:97 [C] base:SC, base:SC 81.48
DW:14 [LYS] DB:80 [U] 3.26 DB:96 [G] 81.48
DW:14 [LYS] DB:97 [C] 4.29 DB:79 [G] 81.48
DW:14 [LYS] DB:98 [G] 2.97 DB:78 [A] base:BB 81.48
DW:15 [GLY] DB:94 [A] 4.6 DB:82 [U] 59.86
DW:15 [GLY] DB:95 [U] 4.93 DB:81 [G] 59.86
DW:17 [SER] DB:76 [G] 3.11 DB:100 [G] 78.74
DW:17 [SER] DB:77 [U] 3.64 DB:99 [A] 78.74
DW:18 [ARG] DB:77 [U] 4.28 DB:99 [A] 83.74
DW:18 [ARG] DB:78 [A] 3.26 DB:98 [G] 83.74
DW:18 [ARG] DB:79 [G] 4.5 DB:97 [C] 83.74
DW:18 [ARG] DB:92 [C] 3.83 DB:84 [G] 83.74
DW:18 [ARG] DB:93 [C] 2.8 DB:83 [G] 83.74
DW:19 [ARG] DB:93 [C] 4.92 DB:83 [G] 66.66
DW:19 [ARG] DB:94 [A] 2.52 DB:82 [U] 66.66
DW:19 [ARG] DB:95 [U] 2.96 DB:81 [G] 66.66
DW:21 [ARG] DB:76 [G] 2.86 DB:100 [G] 98.98
DW:21 [ARG] DB:77 [U] 2.79 DB:99 [A] 98.98
DW:27 [PRO] DB:76 [G] 4.1 DB:100 [G] 99.0
DW:28 [ALA] DB:75 [G] 4.09 DB:101 [A] 89.77
DW:29 [ILE] DB:74 [U] 3.49 DB:102 [G] 86.51
DW:29 [ILE] DB:75 [G] 3.56 DB:101 [A] 86.51
DW:31 [TYR] DB:73 [A] 3.51 DB:103 [U] 97.71
DW:31 [TYR] DB:74 [U] 3.72 DB:102 [G] 97.71
DW:31 [TYR] DB:103 [U] 2.71 DB:73 [A] sugar:SC 97.71
DW:31 [TYR] DB:104 [A] 3.35 DB:72 [G] 97.71
DW:32 [GLY] DB:104 [A] 3.69 DB:72 [G] 92.43
DW:33 [GLY] DB:104 [A] 4.83 DB:72 [G] 51.48
DW:37 [PRO] DB:73 [A] 3.92 DB:103 [U] 58.59
DW:37 [PRO] DB:74 [U] 3.17 DB:102 [G] 58.59
DW:39 [ALA] DB:75 [G] 4.62 DB:101 [A] 61.39
DW:75 [GLN] DB:103 [U] 2.89 DB:73 [A] sugar:SC 71.11
DW:75 [GLN] DB:104 [A] 3.83 DB:72 [G] 71.11
DW:76 [ASP] DB:102 [G] 4.15 DB:74 [U] 76.93
DW:76 [ASP] DB:103 [U] 4.59 DB:73 [A] 76.93
DW:78 [GLN] DB:75 [G] 3.67 DB:101 [A] 95.02
DW:78 [GLN] DB:76 [G] 2.86 DB:100 [G] base:SC, sugar:SC 95.02
DW:78 [GLN] DB:77 [U] 3.82 DB:99 [A] 95.02
DW:87 [GLN] DB:76 [G] 4.27 DB:100 [G] 46.83
DW:87 [GLN] DB:77 [U] 4.99 DB:99 [A] 46.83
DW:88 [HIS] DB:75 [G] 2.7 DB:101 [A] sugar:SC 99.0
DW:88 [HIS] DB:76 [G] 3.1 DB:100 [G] 99.0
DW:90 [ASP] DB:75 [G] 3.0 DB:101 [A] base:SC 98.98
DW:90 [ASP] DB:102 [G] 4.34 DB:74 [U] 98.98
DW:90 [ASP] DB:103 [U] 4.45 DB:73 [A] 98.98
DW:92 [VAL] DB:104 [A] 4.79 DB:72 [G] 44.8

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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
group113 4YBB_DW_DB DW: 50s ribosomal protein l25, Escherichia coli (strain k12) (natural) DB: 5s rRNA, Escherichia coli k-12 (natural) P68919 Ribosomal protein L25-like 5S ribosomal RNA ✔

Interologs

Total number of interologs for this interface: 7

Interface 1 Interface 2 Percentage conservation
 		Interface TM-score
 		Interface RMSD
 		Percentage identity
 		Common ECOD label(s)
 		Common RFAM label(s)
 		Explore both interfaces
1DFU_P_M,N 4YBB_DW_DB 0.97 0.83 0.3 0.53 Ribosomal protein L25-like compare
1FEU_A_B,C 4YBB_DW_DB 0.68 0.54 1.06 0.25 Ribosomal protein L25-like compare
4Y4O_1Z_1B 4YBB_DW_DB 0.66 0.87 1.58 0.26 Ribosomal protein L25-like 5S ribosomal RNA compare
4YBB_DW_DB 6S0Z_T_B 0.64 0.91 2.15 0.39 Ribosomal protein L25-like 5S ribosomal RNA compare
4YBB_DW_DB 6YSI_R_5 0.92 0.97 0.56 0.83 Ribosomal protein L25-like 5S ribosomal RNA compare
4YBB_DW_DB 7ASM_T_B 0.61 0.9 2.27 0.38 Ribosomal protein L25-like 5S ribosomal RNA compare
4YBB_DW_DB 7RYG_U_B 0.91 0.93 1.12 0.86 Ribosomal protein L25-like 5S ribosomal RNA compare