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Contact Molecules for Homologous Proteins

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PID QueryLength Homolgous Sequence in PDB UniProt Query TITLE
2691701 207 46 P51149(RAB7A_HUMAN) RecName: Full=Ras-related protein Rab-7a ; EC=3.6.5.2 ;
QUERYSEQ 
MTSRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIP
YFETSAKEAINVEQAFQTIARNALKQETEVELYNEFPEPIKLDKNDRAKASAESCSC
[BLAST file for PDB] (plain) (bar) (multiple alignment) [BLAST for UniProt: (plain) (bar) (multiple alignment) (PSSM file) ]

Statistics of sites in view of Disease classification

All 600882 Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) LB/B (likely benign or benign)
Number of sites 207 4 1
Buired or ExposedBuried 41.6 (%) [79] 25.0 (%) [1] 0.0 (%) [0]
Exposed 58.4 (%) [111] 75.0 (%) [3] 100.0 (%) [1]
Ave relacc 32.5 % 30.8 % 56.1 %
SD relacc 28.92 % 16.91 % 0.00 %
Contact Molhetero 36.7 (%) [76] 0.0 (%) [0] 100.0 (%) [1]
nucleotide 0.0 (%) [0] 0.0 (%) [0] 0.0 (%) [0]
compound 19.8 (%) [41] 50.0 (%) [2] 0.0 (%) [0]
metal 16.4 (%) [34] 50.0 (%) [2] 0.0 (%) [0]
otherpoly 0.0 (%) [0] 0.0 (%) [0] 0.0 (%) [0]
homo 15.5 (%) [32] 0.0 (%) [0] 100.0 (%) [1]
precipitant 11.6 (%) [24] 50.0 (%) [2] 0.0 (%) [0]
Number of variants 5 4 1
N_Freq(AAvariant)==0 % 25.0 % [1] 0.0 % [0]
N_Freq(AAvariant)>0 % 75.0 % [3] 100.0 % [1]
Ave Freq(AAvariant) 1.0 % 17.0 %
SD Freq(AAvariant) 0.71 % 0.00 %

Site Table for OMIM:600882 Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) [4 variants]

4 sites 129,157,161,162
  [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
129LSe 44.4 1vg8_D compound GTP GDP GNP 
LMIVKARCDEFHPQST
 L->F:(1.0 %):LP/P Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) dbSNP:rs1219090 [MIM:600882]
157KTe 41.0 1vg8_D compound GTP GDP GNP 2UK 2UH 2UJ 
KLARTMSEFIQV
 BINDING /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565" ECO:0000269|PubMed:20028791" BINDING /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565" ECO:0000269|PubMed:20028791" K->N:(0.0 %):LP/P Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) dbSNP:rs1219090 [MIM:600882]
161NSe 35.8 1vg8_D metal CL UNX precipitant 
NGSHRTCDEKLQ
 N->T:(2.0 %):LP/P Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) dbSNP:rs1219090 [MIM:600882]
162VHb 2.0 1vg8_D metal CL UNX precipitant 
VILFTAEKMY
 V->M:(1.0 %):LP/P Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) dbSNP:rs1219090 [MIM:600882]

Site Table for OMIM:LB/B [1 variants]

1 sites 32
  [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
32K e 56.1 1vg8_D hetero G0SGS3_CHATD homo 
ERKQTSAHDIGNPVCLMY
 K->E:(17.0 %):LB/B - dbSNP:rs1154975