Interface analysis
Style
Protein
CartoonLicorice
Surface
RNA
CartoonLicorice
Surface
Color
ChainChain (with hetatm)
Chainbow
Hydrophobicity Electrostatics (surface only) Conservation*
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InterfaceRNA
Protein
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Interface
show as licoriceshow Accessibility
Rim - Core
Contacts -
| 5DDP_D
|
5DDP_A
|
Distance
|
Base Pair
|
Hbond nuc:res
|
Base Stacking
|
Residue conservation
|
|---|---|---|---|---|---|---|
| D:4 [GLU] | A:39 [C] | 3.54 | 36.91 | |||
| D:10 [THR] | A:40 [A] | 4.46 | 89.28 | |||
| D:12 [TYR] | A:38 [G] | 3.3 | base:SC | 85.3 | ||
| D:12 [TYR] | A:39 [C] | 3.52 | base/AA stacks | 85.3 | ||
| D:14 [ASN] | A:37 [U] | 3.77 | 59.09 | |||
| D:14 [ASN] | A:38 [G] | 3.22 | base:SC | 59.09 | ||
| D:15 [ASN] | A:37 [U] | 2.54 | base:SC | 95.83 | ||
| D:15 [ASN] | A:38 [G] | 2.91 | base:BB | 95.83 | ||
| D:16 [LEU] | A:38 [G] | 4.29 | 79.23 | |||
| D:18 [GLU] | A:35 [A] | 4.4 | 47.48 | |||
| D:18 [GLU] | A:36 [U] | 2.86 | base:SC | 47.48 | ||
| D:18 [GLU] | A:37 [U] | 3.94 | 47.48 | |||
| D:18 [GLU] | A:38 [G] | 2.74 | base:SC | 47.48 | ||
| D:19 [LYS] | A:31 [G] | 4.58 | A:48 [C] | 49.98 | ||
| D:21 [LYS] | A:29 [A] | 4.94 | A:50 [U] | 60.09 | ||
| D:21 [LYS] | A:30 [G] | 3.2 | A:49 [C] | 60.09 | ||
| D:21 [LYS] | A:31 [G] | 3.23 | A:48 [C] | 60.09 | ||
| D:22 [LYS] | A:30 [G] | 3.91 | A:49 [C] | 36.36 | ||
| D:43 [LEU] | A:40 [A] | 3.58 | 12.51 | |||
| D:43 [LEU] | A:41 [C] | 3.49 | 12.51 | |||
| D:45 [SER] | A:44 [C] | 3.26 | 5.44 | |||
| D:46 [ARG] | A:29 [A] | 4.87 | A:50 [U] | 53.88 | ||
| D:46 [ARG] | A:30 [G] | 2.72 | A:49 [C] | 53.88 | ||
| D:46 [ARG] | A:31 [G] | 4.9 | A:48 [C] | 53.88 | ||
| D:46 [ARG] | A:44 [C] | 4.59 | 53.88 | |||
| D:46 [ARG] | A:45 [G] | 4.76 | A:34 [C] | 53.88 | ||
| D:47 [SER] | A:44 [C] | 3.89 | 69.66 | |||
| D:47 [SER] | A:45 [G] | 3.35 | A:34 [C] | 69.66 | ||
| D:48 [LEU] | A:35 [A] | 3.74 | 42.01 | |||
| D:48 [LEU] | A:36 [U] | 4.44 | 42.01 | |||
| D:48 [LEU] | A:38 [G] | 5.0 | 42.01 | |||
| D:48 [LEU] | A:44 [C] | 4.76 | 42.01 | |||
| D:48 [LEU] | A:45 [G] | 2.77 | A:34 [C] | 42.01 | ||
| D:49 [LYS] | A:38 [G] | 2.84 | sugar:BB | 50.67 | ||
| D:49 [LYS] | A:39 [C] | 3.9 | 50.67 | |||
| D:49 [LYS] | A:40 [A] | 3.08 | 50.67 | |||
| D:49 [LYS] | A:45 [G] | 4.88 | A:34 [C] | 50.67 | ||
| D:50 [MET] | A:38 [G] | 3.38 | 52.33 | |||
| D:50 [MET] | A:39 [C] | 3.46 | 52.33 | |||
| D:50 [MET] | A:40 [A] | 3.41 | 52.33 | |||
| D:51 [ARG] | A:35 [A] | 2.77 | base:SC | 83.46 | ||
| D:51 [ARG] | A:36 [U] | 3.41 | 83.46 | |||
| D:51 [ARG] | A:38 [G] | 3.15 | 83.46 | |||
| D:51 [ARG] | A:45 [G] | 2.87 | A:34 [C] | base:SC, base:SC | 83.46 | |
| D:52 [GLY] | A:38 [G] | 3.37 | 94.15 | |||
| D:53 [GLN] | A:38 [G] | 3.16 | base/AA stacks | 89.23 | ||
| D:53 [GLN] | A:39 [C] | 3.74 | 89.23 | |||
| D:55 [PHE] | A:39 [C] | 3.5 | 85.57 | |||
| D:55 [PHE] | A:40 [A] | 3.42 | base/AA stacks | 85.57 | ||
| D:79 [LYS] | A:37 [U] | 2.51 | base:SC | 73.23 | ||
| D:84 [GLN] | A:39 [C] | 2.81 | base:SC | 16.84 | ||
| D:85 [TYR] | A:39 [C] | 2.89 | base:BB | 53.23 | ||
| D:86 [ALA] | A:39 [C] | 3.54 | 95.02 | |||
| D:86 [ALA] | A:40 [A] | 4.02 | 95.02 | |||
| D:87 [LYS] | A:39 [C] | 2.97 | base:BB | 60.42 | ||
| D:88 [THR] | A:39 [C] | 4.76 | 52.32 | |||
| D:88 [THR] | A:40 [A] | 2.96 | base:BB | 52.32 | ||
| D:88 [THR] | A:41 [C] | 4.31 | 52.32 | |||
| D:89 [ASP] | A:40 [A] | 3.24 | 37.36 | |||
| D:89 [ASP] | A:41 [C] | 3.02 | base:BB | 37.36 | ||
| D:90 [SER] | A:40 [A] | 2.37 | base:SC, base:SC | 88.79 | ||
| D:90 [SER] | A:41 [C] | 3.53 | 88.79 | |||
| D:91 [ASP] | A:41 [C] | 3.01 | base:BB | base/AA stacks | 68.07 | |
| D:91 [ASP] | A:42 [U] | 3.83 | 68.07 | |||
| D:92 [ILE] | A:41 [C] | 3.99 | 40.2 |
Export the table of contacts
*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 | 5DDP_D_A | D: U1 small nuclear ribonucleoprotein a, Homo sapiens (genetically engineered) A: RNA (61-mer), Synechococcus elongatus (natural) | P09012 | RNA-binding domain, RBD | Glutamine riboswitch | ✘ |
|
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 | 5DDP_D_A | 0.93 | 0.72 | 0.43 | 0.69 | RNA-binding domain, RBD | compare | |
| 1URN_A_P | 5DDP_D_A | 0.97 | 0.95 | 0.36 | 0.83 | RNA-binding domain, RBD | compare | |
| 4PR6_A_B | 5DDP_D_A | 0.93 | 0.72 | 0.39 | 0.69 | RNA-binding domain, RBD | compare | |
| 3MXH_P_R | 5DDP_D_A | 0.95 | 0.68 | 0.89 | 0.69 | RNA-binding domain, RBD | compare | |
| 1A9N_B_Q | 5DDP_D_A | 0.81 | 0.82 | 0.42 | 0.46 | RNA-binding domain, RBD | compare | |
| 1M5O_C_B | 5DDP_D_A | 0.95 | 0.72 | 0.25 | 0.77 | RNA-binding domain, RBD | compare | |
| 4PKD_B_V | 5DDP_D_A | 0.98 | 0.71 | 0.29 | 0.85 | RNA-binding domain, RBD | compare | |
| 2NZ4_A_P | 5DDP_D_A | 0.96 | 0.73 | 0.46 | 0.85 | RNA-binding domain, RBD | compare | |
| 1SJ3_P_R | 5DDP_D_A | 0.97 | 0.72 | 0.57 | 0.82 | RNA-binding domain, RBD | compare | |
| 5DDP_D_A | 6F4G_B_C | 0.82 | 0.81 | 0.36 | 0.46 | RNA-binding domain, RBD | compare | |
| 5DDP_D_A | 6F4H_A_B | 0.92 | 0.96 | 0.33 | 0.68 | RNA-binding domain, RBD | compare | |
| 5DDP_D_A | 7DCO_R_G | 0.74 | 0.54 | 2.57 | 0.21 | compare |