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All interfaces > All interologs > Interface groups > group141 > 4PKD_B_V

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Chain
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Hydrophobicity
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Conservation*

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Rim - Core

Contacts -

4PKD_B
4PKD_V
Distance
Base Pair
Hbond nuc:res
Base Stacking
Residue conservation
B:11 [THR] V:70 [A] 4.58 95.54
B:13 [TYR] V:68 [G] 3.3 84.86
B:13 [TYR] V:69 [C] 3.35 base/AA stacks 84.86
B:15 [ASN] V:67 [U] 3.72 69.01
B:15 [ASN] V:68 [G] 2.93 base:SC 69.01
B:16 [ASN] V:67 [U] 2.67 base:SC 98.92
B:16 [ASN] V:68 [G] 2.83 base:BB 98.92
B:17 [LEU] V:68 [G] 4.13 84.68
B:19 [GLU] V:65 [A] 4.52 54.19
B:19 [GLU] V:66 [U] 3.09 base:SC 54.19
B:19 [GLU] V:67 [U] 4.77 54.19
B:19 [GLU] V:68 [G] 2.7 base:SC 54.19
B:22 [LYS] V:59 [GTP] 3.32 V:80 [C] 55.04
B:22 [LYS] V:60 [G] 3.65 V:79 [C] 55.04
B:23 [LYS] V:59 [GTP] 3.39 V:80 [C] 13.55
B:24 [ASP] V:59 [GTP] 4.49 V:80 [C] 17.95
B:44 [LEU] V:70 [A] 3.69 58.08
B:44 [LEU] V:71 [C] 4.3 58.08
B:46 [SER] V:73 [C] 4.92 16.25
B:46 [SER] V:74 [C] 3.07 16.25
B:47 [ARG] V:59 [GTP] 2.77 V:80 [C] 55.93
B:47 [ARG] V:74 [C] 4.35 55.93
B:47 [ARG] V:75 [G] 4.83 V:64 [C] 55.93
B:48 [SER] V:74 [C] 3.84 64.45
B:48 [SER] V:75 [G] 3.51 V:64 [C] 64.45
B:49 [LEU] V:65 [A] 3.74 6.48
B:49 [LEU] V:66 [U] 4.5 6.48
B:49 [LEU] V:68 [G] 4.81 6.48
B:49 [LEU] V:75 [G] 3.17 V:64 [C] 6.48
B:50 [LYS] V:68 [G] 2.9 sugar:BB 59.03
B:50 [LYS] V:70 [A] 3.83 59.03
B:50 [LYS] V:71 [C] 4.59 59.03
B:51 [MET] V:68 [G] 4.9 76.21
B:51 [MET] V:69 [C] 4.26 76.21
B:51 [MET] V:70 [A] 3.52 76.21
B:52 [ARG] V:65 [A] 2.98 base:SC 88.8
B:52 [ARG] V:66 [U] 3.59 88.8
B:52 [ARG] V:68 [G] 3.24 88.8
B:52 [ARG] V:75 [G] 3.06 V:64 [C] base:SC, base:SC 88.8
B:53 [GLY] V:68 [G] 3.48 97.65
B:54 [GLN] V:68 [G] 3.1 base/AA stacks 97.55
B:54 [GLN] V:69 [C] 3.65 97.55
B:56 [PHE] V:69 [C] 3.56 73.28
B:56 [PHE] V:70 [A] 3.35 base/AA stacks 73.28
B:80 [LYS] V:67 [U] 2.82 base:SC 86.18
B:85 [GLN] V:69 [C] 3.66 39.98
B:86 [TYR] V:69 [C] 3.02 base:BB 67.32
B:87 [ALA] V:69 [C] 3.55 90.25
B:87 [ALA] V:70 [A] 4.12 90.25
B:88 [LYS] V:69 [C] 3.14 base:BB, sugar:SC 64.74
B:89 [THR] V:69 [C] 4.55 48.02
B:89 [THR] V:70 [A] 2.91 base:SC, base:BB 48.02
B:89 [THR] V:71 [C] 3.66 48.02
B:90 [ASP] V:70 [A] 3.62 44.29
B:90 [ASP] V:71 [C] 3.21 base:BB 44.29
B:91 [SER] V:70 [A] 2.87 base:SC, base:SC 91.37
B:91 [SER] V:71 [C] 3.65 91.37
B:92 [ASP] V:71 [C] 3.06 base:BB, base:BB base/AA stacks 57.54
B:92 [ASP] V:72 [U] 4.41 57.54
B:129 [GLU] V:84 [A] 4.97 V:110 [U] 3.51
B:132 [MET] V:85 [G] 3.59 V:109 [U] 36.49
B:132 [MET] V:86 [A] 4.13 V:108 [U] 36.49
B:136 [ARG] V:86 [A] 2.81 V:108 [U] 39.72
B:136 [ARG] V:102 [G] 4.1 39.72
B:136 [ARG] V:103 [G] 3.04 V:92 [U] 39.72
B:139 [LYS] V:87 [U] 4.33 V:107 [U] 50.83
B:139 [LYS] V:101 [A] 4.01 50.83
B:139 [LYS] V:102 [G] 2.76 50.83
B:143 [ARG] V:100 [A] 2.79 base:SC, base:SC 26.09
B:143 [ARG] V:101 [A] 3.28 26.09
B:147 [VAL] V:100 [A] 3.95 4.35
B:154 [TRP] V:96 [C] 4.04 11.98
B:154 [TRP] V:97 [A] 2.78 11.98
B:156 [PRO] V:97 [A] 4.34 56.18
B:159 [ASP] V:97 [A] 2.42 sugar:SC 13.96
B:159 [ASP] V:98 [C] 4.87 13.96
B:161 [ASN] V:97 [A] 3.14 sugar:SC 19.66
B:161 [ASN] V:98 [C] 3.47 19.66
B:162 [ALA] V:97 [A] 3.53 36.45
B:163 [GLN] V:97 [A] 4.69 10.04
B:169 [THR] V:97 [A] 4.98 85.47
B:171 [PHE] V:95 [U] 3.4 81.96
B:171 [PHE] V:96 [C] 3.3 base/AA stacks 81.96
B:173 [ALA] V:95 [U] 3.56 44.11
B:174 [ARG] V:93 [G] 3.78 75.43
B:174 [ARG] V:94 [A] 4.88 75.43
B:174 [ARG] V:95 [U] 2.58 75.43
B:175 [VAL] V:93 [G] 2.72 base:BB, base:BB 76.45
B:176 [ASN] V:93 [G] 3.46 73.38
B:177 [TYR] V:93 [G] 2.88 base:BB base/AA stacks 13.58
B:177 [TYR] V:94 [A] 4.1 13.58
B:178 [ASP] V:93 [G] 4.84 29.92
B:196 [ARG] V:97 [A] 4.45 52.76
B:198 [HIS] V:97 [A] 3.33 72.92
B:200 [VAL] V:97 [A] 3.93 76.06
B:200 [VAL] V:98 [C] 3.55 76.06
B:201 [TYR] V:98 [C] 3.39 47.98
B:202 [SER] V:98 [C] 3.5 82.29
B:203 [LYS] V:98 [C] 2.9 sugar:BB 57.56
B:204 [ARG] V:98 [C] 3.12 base:SC 27.21
B:204 [ARG] V:99 [G] 3.72 base/AA stacks 27.21
B:209 [ARG] V:93 [G] 4.81 55.45
B:209 [ARG] V:94 [A] 4.82 55.45
B:209 [ARG] V:98 [C] 3.4 55.45
B:209 [ARG] V:99 [G] 3.23 55.45
B:209 [ARG] V:100 [A] 3.56 55.45
B:210 [GLY] V:93 [G] 3.89 70.41
B:211 [TYR] V:96 [C] 3.61 71.4
B:211 [TYR] V:97 [A] 3.58 71.4
B:211 [TYR] V:98 [C] 3.84 71.4
B:211 [TYR] V:99 [G] 2.33 71.4
B:213 [PHE] V:96 [C] 3.46 98.08
B:213 [PHE] V:97 [A] 3.3 base/AA stacks 98.08
B:237 [ARG] V:93 [G] 3.46 sugar:SC base/AA stacks 56.35
B:240 [LEU] V:95 [U] 3.39 11.06
B:242 [ASP] V:95 [U] 2.8 base:SC 72.06
B:242 [ASP] V:96 [C] 3.7 72.06
B:243 [VAL] V:96 [C] 2.9 base:BB 23.5
B:244 [GLU] V:96 [C] 3.5 79.77
B:244 [GLU] V:97 [A] 3.1 base:SC, base:SC 79.77
B:245 [ARG] V:95 [U] 4.97 64.32
B:245 [ARG] V:96 [C] 2.99 base:BB 64.32
B:246 [GLY] V:96 [C] 3.07 base:BB 48.67
B:247 [ARG] V:97 [A] 3.77 68.08
B:252 [TRP] V:95 [U] 3.73 41.11
B:252 [TRP] V:96 [C] 2.89 sugar:SC base/AA stacks 41.11
B:254 [PRO] V:96 [C] 3.78 78.09
B:254 [PRO] V:97 [A] 3.56 78.09
B:255 [ARG] V:94 [A] 3.66 base/AA stacks 73.2
B:255 [ARG] V:96 [C] 3.16 73.2
B:255 [ARG] V:100 [A] 3.06 73.2
B:256 [ARG] V:97 [A] 3.45 80.41
B:256 [ARG] V:99 [G] 3.11 base/AA stacks 80.41
B:256 [ARG] V:100 [A] 3.41 80.41
B:258 [GLY] V:100 [A] 3.62 77.71
B:260 [GLY] V:95 [U] 3.75 73.77
B:260 [GLY] V:96 [C] 3.88 73.77
B:261 [LEU] V:94 [A] 4.48 11.7
B:261 [LEU] V:95 [U] 3.16 sugar:BB 11.7
B:261 [LEU] V:96 [C] 4.7 11.7
B:262 [GLY] V:95 [U] 3.65 72.88
B:263 [GLY] V:95 [U] 4.56 64.54
B:264 [THR] V:92 [U] 4.14 V:103 [G] 32.91
B:264 [THR] V:93 [G] 2.61 32.91
B:264 [THR] V:94 [A] 3.38 sugar:SC 32.91
B:264 [THR] V:95 [U] 4.78 32.91
B:264 [THR] V:103 [G] 4.69 V:92 [U] 32.91
B:265 [ARG] V:92 [U] 3.15 V:103 [G] base/AA stacks 52.42
B:265 [ARG] V:93 [G] 2.73 52.42
B:265 [ARG] V:94 [A] 3.28 base/AA stacks 52.42
B:265 [ARG] V:102 [G] 3.0 base:BB, base:BB 52.42
B:265 [ARG] V:103 [G] 3.63 V:92 [U] 52.42
B:266 [ARG] V:102 [G] 3.42 32.67
B:266 [ARG] V:103 [G] 4.52 V:92 [U] 32.67
B:267 [GLY] V:102 [G] 4.73 78.48
B:267 [GLY] V:103 [G] 3.68 V:92 [U] 78.48
B:267 [GLY] V:104 [U] 3.4 V:91 [A] 78.48

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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
group141 4PKD_B_V B: U1 small nuclear ribonucleoprotein a,u1 small nuclear ribonucleoprotein 70 kda, Sus scrofa (genetically engineered) V: U1 snRNA stem-loops 1 and 2 (55-mer), Homo sapiens (synthetic) Q06AA4 RNA-binding domain, RBD ✘

Interologs

Total number of interologs for this interface: 12

Interface 1 Interface 2 Percentage conservation
 		Interface TM-score
 		Interface RMSD
 		Percentage identity
 		Common ECOD label(s)
 		Common RFAM label(s)
 		Explore both interfaces
1DRZ_A_B 4PKD_B_V 0.93 0.66 0.31 0.71 RNA-binding domain, RBD compare
1URN_A_P 4PKD_B_V 0.93 0.92 0.29 0.83 RNA-binding domain, RBD compare
3MXH_P_R 4PKD_B_V 0.84 0.6 0.68 0.69 RNA-binding domain, RBD compare
1A9N_B_Q 4PKD_B_V 0.75 0.85 0.6 0.5 RNA-binding domain, RBD compare
1M5O_C_B 4PKD_B_V 0.89 0.65 0.3 0.79 RNA-binding domain, RBD compare
4PKD_B_V 4PR6_A_B 0.94 0.66 0.3 0.69 RNA-binding domain, RBD compare
4PKD_B_V 6F4H_A_B 0.88 0.94 0.45 0.65 RNA-binding domain, RBD compare
4PKD_B_V 5DDP_D_A 0.98 0.71 0.29 0.85 RNA-binding domain, RBD compare
4PKD_B_V 6SQN_A_X 0.96 0.94 0.34 0.8 RNA-binding domain, RBD compare
4PKD_B_V 6F4G_B_C 0.81 0.81 0.46 0.5 RNA-binding domain, RBD compare
2NZ4_A_P 4PKD_B_V 0.94 0.52 0.55 0.69 RNA-binding domain, RBD compare
1SJ3_P_R 4PKD_B_V 0.95 0.66 0.28 0.82 RNA-binding domain, RBD compare