PASS2.8 - Home

solvent inaccessible: UPPER CASE X
solvent accesible: lower case x
alpha helix: red x

beta strand: blue x
3 - 10 helix: maroon x
hydrogen bond to main chain amide: bold x

hydrogen bond to mainchain carbonyl: underline x
disulphide bond: cedilla
positive phi: italic x

                             10        20        30        40        50  
d2cpta1  (   8 )    msstspnlqkAidlAskAaqedkagnyeeAlqlYqhAvqyFlhvvkyeaq
d4a5xa-  (  10 )         pqstaAatvLkrAveldsesrypqAlvcYqeGIdlLlqvlk-gtk
d5fvka-  (   1 )    m-stgdFltkGielVqkAidldtatqyeeAytAYynGLdyLmlAlk-yek
                          aaaaaaaaaaaaaaaaa   aaaaaaaaaaaaaaaaaaaa    

                             60        70        80        90        100 
d2cpta1  (  58 )    gdkakqsirakCteyldrAeklkeylknkekkaqkpvkegqpspadekgn
d4a5xa-  (  54 )    dntkrcnlrekIskymdrAenIkkyldqe                     
d5fvka-  (  49 )    npkskdlirakfteylnrAeqLkkhleseeanaa                
                     aaaaaaaaaaaaaaaaaaaaaaaaaaa                      

                        
d2cpta1  ( 108 )    dsdg
d4a5xa-                 
d5fvka-

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d2cpta1 # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d2cpta1 # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	Vacuolar sorting protein 4b (VPS4B, SKD1 protein)	MIT domain	Human (Homo sapiens) [TaxId: 9606]	view
d4a5xa- # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d4a5xa- # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	automated matches	automated matches	Human (Homo sapiens) [TaxId: 9606]	view
d5fvka- # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d5fvka- # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]	view

No outliers

Feature	Download
Superfamily
Distance Matrix
Conserved Interactions
Cusp Results
Alistat - Alignment Statistics
SMotif - Conserved Structural Motifs
MeanRMS
PCSSE Details
Absolutely Conserved Residues
Highly Conserved Residues

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M	S	S	T	S	P	N	L	Q	K	A	I	D	L	A	S	K	A	A	Q	E	D	K	A	G	N	Y	E	E	A	L	Q	L	Y	Q	H	A	V	Q	Y	F	L	H	V	V	K	Y	E	A	Q	G	D	K	A	K	Q	S	I	R	A	K	C	T	E	Y	L	D	R	A	E	K	L	K	E	Y	L	K	N	K	E	K	K	A	Q	K	P	V	K	E	G	Q	P	S	P	A	D	E	K	G	N	D	S	D	G
-	-	-	-	-	P	Q	S	T	A	A	A	T	V	L	K	R	A	V	E	L	D	S	E	S	R	Y	P	Q	A	L	V	C	Y	Q	E	G	I	D	L	L	L	Q	V	L	K	-	G	T	K	D	N	T	K	R	C	N	L	R	E	K	I	S	K	Y	M	D	R	A	E	N	I	K	K	Y	L	D	Q	E	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
M	-	S	T	G	D	F	L	T	K	G	I	E	L	V	Q	K	A	I	D	L	D	T	A	T	Q	Y	E	E	A	Y	T	A	Y	Y	N	G	L	D	Y	L	M	L	A	L	K	-	Y	E	K	N	P	K	S	K	D	L	I	R	A	K	F	T	E	Y	L	N	R	A	E	Q	L	K	K	H	L	E	S	E	E	A	N	A	A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Member	Chain	UniProtKB	GO term

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-	-	-	-	-	P	Q	S	T	A	A	A	T	V	L	K	R	A	V	E	L	D	S	E	S	R	Y	P	Q	A	L	V	C	Y	Q	E	G	I	D	L	L	L	Q	V	L	K	-	G	T	K	D	N	T	K	R	C	N	L	R	E	K	I	S	K	Y	M	D	R	A	E	N	I	K	K	Y	L	D	Q	E	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
M	-	S	T	G	D	F	L	T	K	G	I	E	L	V	Q	K	A	I	D	L	D	T	A	T	Q	Y	E	E	A	Y	T	A	Y	Y	N	G	L	D	Y	L	M	L	A	L	K	-	Y	E	K	N	P	K	S	K	D	L	I	R	A	K	F	T	E	Y	L	N	R	A	E	Q	L	K	K	H	L	E	S	E	E	A	N	A	A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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M	S	S	T	S	P	N	L	Q	K	A	I	D	L	A	S	K	A	A	Q	E	D	K	A	G	N	Y	E	E	A	L	Q	L	Y	Q	H	A	V	Q	Y	F	L	H	V	V	K	Y	E	A	Q	G	D	K	A	K	Q	S	I	R	A	K	C	T	E	Y	L	D	R	A	E	K	L	K	E	Y	L	K	N	K	E	K	K	A	Q	K	P	V	K	E	G	Q	P	S	P	A	D	E	K	G	N	D	S	D	G
-	-	-	-	-	P	Q	S	T	A	A	A	T	V	L	K	R	A	V	E	L	D	S	E	S	R	Y	P	Q	A	L	V	C	Y	Q	E	G	I	D	L	L	L	Q	V	L	K	-	G	T	K	D	N	T	K	R	C	N	L	R	E	K	I	S	K	Y	M	D	R	A	E	N	I	K	K	Y	L	D	Q	E	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
M	-	S	T	G	D	F	L	T	K	G	I	E	L	V	Q	K	A	I	D	L	D	T	A	T	Q	Y	E	E	A	Y	T	A	Y	Y	N	G	L	D	Y	L	M	L	A	L	K	-	Y	E	K	N	P	K	S	K	D	L	I	R	A	K	F	T	E	Y	L	N	R	A	E	Q	L	K	K	H	L	E	S	E	E	A	N	A	A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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M	S	S	T	S	P	N	L	Q	K	A	I	D	L	A	S	K	A	A	Q	E	D	K	A	G	N	Y	E	E	A	L	Q	L	Y	Q	H	A	V	Q	Y	F	L	H	V	V	K	Y	E	A	Q	G	D	K	A	K	Q	S	I	R	A	K	C	T	E	Y	L	D	R	A	E	K	L	K	E	Y	L	K	N	K	E	K	K	A	Q	K	P	V	K	E	G	Q	P	S	P	A	D	E	K	G	N	D	S	D	G
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M	-	S	T	G	D	F	L	T	K	G	I	E	L	V	Q	K	A	I	D	L	D	T	A	T	Q	Y	E	E	A	Y	T	A	Y	Y	N	G	L	D	Y	L	M	L	A	L	K	-	Y	E	K	N	P	K	S	K	D	L	I	R	A	K	F	T	E	Y	L	N	R	A	E	Q	L	K	K	H	L	E	S	E	E	A	N	A	A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-