Contact Molecules for Homologous Proteins | ||||
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PID | QueryLength | Homolgous Sequence in PDB | UniProt Query | TITLE |
2624989 | 215 | 29 | P09429(HMGB1_HUMAN) | RecName: Full=High mobility group protein B1;AltName: Full=High mobility group protein 1; Short=HMG-1; |
QUERYSEQ |
MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK LKEKYEKDIAAYRAKGKPDAAKKGVVKAEKSKKKKEEEEDEEDEEDEEEEEDEEDEDEEEDDDDE |
All | LB/B (likely benign or benign) | US (uncertain significance) | ||
Number of sites | 215 | 1 | 3 | |
Buired or Exposed | Buried | 15.8 (%) [27] | 0.0 (%) [0] | 0.0 (%) [0] |
Exposed | 84.2 (%) [144] | 100.0 (%) [1] | 100.0 (%) [2] | |
Ave relacc | 51.0 % | 44.2 % | 37.4 % | |
SD relacc | 27.58 % | 0.00 % | 13.54 % | |
Contact Mol | hetero | 15.8 (%) [34] | 100.0 (%) [1] | 33.3 (%) [1] |
nucleotide | 20.9 (%) [45] | 0.0 (%) [0] | 33.3 (%) [1] | |
compound | 0.0 (%) [0] | 0.0 (%) [0] | 0.0 (%) [0] | |
metal | 0.0 (%) [0] | 0.0 (%) [0] | 0.0 (%) [0] | |
otherpoly | 0.0 (%) [0] | 0.0 (%) [0] | 0.0 (%) [0] | |
homo | 2.3 (%) [5] | 0.0 (%) [0] | 0.0 (%) [0] | |
precipitant | 2.8 (%) [6] | 0.0 (%) [0] | 0.0 (%) [0] | |
Number of variants | 4 | 1 | 3 | |
N_Freq(AAvariant)==0 % | 0.0 % [0] | 0.0 % [0] | ||
N_Freq(AAvariant)>0 % | 100.0 % [1] | 100.0 % [3] | ||
Ave Freq(AAvariant) | 7.0 % | 26.7 % | ||
SD Freq(AAvariant) | 0.00 % | 18.55 % |
1 sites | 156 |
[n]:site number of query sequence. [a]:amino acid of query sequence. [s]:predicted secondary structure. [e]:predicted exposed/buried. [acc]:predicted relative accesssibility(%). [pdb]:PDB code of homologous structure. [contact_mols]:predicted binding molecules [observed aa]:Observed amino acids among homologous sequences. [feature table]:UniProt Feature Table [variant]:UniProt Human Variant.
n | a | s | e | acc | pdb | contact_mols | observed aa | feature table | variant |
156 | E | H | e | 44.2 | 2yrq_A | hetero RAGE_HUMAN | EKMDQNTYAGILFHR |
REGION /note="Binding to AGER/RAGE" DNA_BIND /note="HMG box 2" REGION /note="Binding to AGER/RAGE" DNA_BIND /note="HMG box 2" | E->Q:(7.0 %):LB/B - |
3 sites | 11,149,190 |
[n]:site number of query sequence. [a]:amino acid of query sequence. [s]:predicted secondary structure. [e]:predicted exposed/buried. [acc]:predicted relative accesssibility(%). [pdb]:PDB code of homologous structure. [contact_mols]:predicted binding molecules [observed aa]:Observed amino acids among homologous sequences. [feature table]:UniProt Feature Table [variant]:UniProt Human Variant.
n | a | s | e | acc | pdb | contact_mols | observed aa | feature table | variant |
11 | G | e | 23.8 | 2yrq_A | nucleotide | RGAPHQSVDEFIKLNT |
SITE /note="Cleavage; by thrombin:thrombomodulin" REGION /note="LPS binding (delipidated)" DNA_BIND /note="HMG box 1" REGION /note="Sufficient for interaction with HAVCR2" SITE /note="Cleavage; by thrombin:thrombomodulin" REGION /note="LPS binding (delipidated)" DISORDER predicted by DISOPRED DNA_BIND /note="HMG box 1" REGION /note="Sufficient for interaction with HAVCR2" | G->R:(51.0 %):US Gastric-carcinoma cell line | |
149 | A | H | e | 50.9 | 2yrq_A | hetero RAGE_HUMAN | AEQKSRDVNTGILM |
DNA_BIND /note="HMG box 2" DNA_BIND /note="HMG box 2" | A->E:(23.0 %):US Gastric-carcinoma cell line |
190 | D | - | - | - | - | DEKAG |
COMPBIAS /note="Acidic residues" REGION /note="Disordered" COMPBIAS /note="Acidic residues" DISORDER predicted by DISOPRED REGION /note="Disordered" | D->G:(6.0 %):US Gastric-carcinoma cell line |