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  
d3iam6-  (  15 )    eregilfttleklvawgrSnslwpatfgla---ccaieMmas----tda-
d4u9hs-  (   3 )                     gprrpsvvYlHnaectgcSesvlrAfepyidtl
                                              bb      aaaaa           

                             60        70        80        90        100 
d3iam6-  (  74 )    --------------------------------qadVMIVAgrLsk-----
d4u9hs-  (  36 )    ildtlsldYHetimaaagdaaeaaleqavnsphgFiAvvEGGiPtaanGi
                                                        bbbb          

                             110       120       130       140       150 
d3iam6-  (  87 )    -------kmapvMrrvweqmpdpkWVISMGacAssGgmfn---nyaivqn
d4u9hs-  (  86 )    ygkvanhtmldiCsrilpkA---qaviAYGtcAtfGGvqaakpnptgAkG
                             aaaaaaa         bbbb aaaa                

                             160       170       180       190       200 
d3iam6-  ( 127 )    Vds----vVpVDvyvpgcpPrpealiyAvmqLqkkVrgqayne-------
d4u9hs-  ( 133 )    vndAlkhlgvkAiniAGcpPnpynlvgtivyylknkaaPeldslnRPtmf
                                bbb      aaaaaaaaaaaaaa               

                             210       220       230       240       250 
d3iam6-  ( 166 )    --------------------------------------------------
d4u9hs-  ( 183 )    FgqtvheqcprlphfdagefApsfeseearkgwclyelGckGpvtmnncP
                                                                      

                             260       270       280   
d3iam6-  ( 166 )    ------------rgerl--ppvaa           
d4u9hs-  ( 233 )    kikfnqtnWpvdaghPciGcSepdFwdamtpfyqn

Domains
Outliers

Domain ID	Name	Family	Source	Domain	STRING-DB
d3iam6- # 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 d3iam6- # 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	Nq06-like	Thermus thermophilus HB8 [TaxId: 300852]		view
d4u9hs- # 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 d4u9hs- # 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	Nickel-iron hydrogenase, small subunit	Desulfovibrio vulgaris [TaxId: 883]		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

									10										20										30										40										50										60										70										80										90										100										110										120										130										140										150										160										170										180										190										200										210										220										230										240										250										260										270										280
E	R	E	G	I	L	F	T	T	L	E	K	L	V	A	W	G	R	S	N	S	L	W	P	A	T	F	G	L	A	-	-	-	C	C	A	I	E	M	M	A	S	-	-	-	-	T	D	A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	Q	A	D	V	M	I	V	A	G	R	L	S	K	-	-	-	-	-	-	-	-	-	-	-	-	K	M	A	P	V	M	R	R	V	W	E	Q	M	P	D	P	K	W	V	I	S	M	G	A	C	A	S	S	G	G	M	F	N	-	-	-	N	Y	A	I	V	Q	N	V	D	S	-	-	-	-	V	V	P	V	D	V	Y	V	P	G	C	P	P	R	P	E	A	L	I	Y	A	V	M	Q	L	Q	K	K	V	R	G	Q	A	Y	N	E	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	R	G	E	R	L	-	-	P	P	V	A	A	-	-	-	-	-	-	-	-	-	-	-
-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	G	P	R	R	P	S	V	V	Y	L	H	N	A	E	C	T	G	C	S	E	S	V	L	R	A	F	E	P	Y	I	D	T	L	I	L	D	T	L	S	L	D	Y	H	E	T	I	M	A	A	A	G	D	A	A	E	A	A	L	E	Q	A	V	N	S	P	H	G	F	I	A	V	V	E	G	G	I	P	T	A	A	N	G	I	Y	G	K	V	A	N	H	T	M	L	D	I	C	S	R	I	L	P	K	A	-	-	-	Q	A	V	I	A	Y	G	T	C	A	T	F	G	G	V	Q	A	A	K	P	N	P	T	G	A	K	G	V	N	D	A	L	K	H	L	G	V	K	A	I	N	I	A	G	C	P	P	N	P	Y	N	L	V	G	T	I	V	Y	Y	L	K	N	K	A	A	P	E	L	D	S	L	N	R	P	T	M	F	F	G	Q	T	V	H	E	Q	C	P	R	L	P	H	F	D	A	G	E	F	A	P	S	F	E	S	E	E	A	R	K	G	W	C	L	Y	E	L	G	C	K	G	P	V	T	M	N	N	C	P	K	I	K	F	N	Q	T	N	W	P	V	D	A	G	H	P	C	I	G	C	S	E	P	D	F	W	D	A	M	T	P	F	Y	Q	N

Member	Chain	UniProtKB	GO term

									10										20										30										40										50										60										70										80										90										100										110										120										130										140										150										160										170										180										190										200										210										220										230										240										250										260										270										280
E	R	E	G	I	L	F	T	T	L	E	K	L	V	A	W	G	R	S	N	S	L	W	P	A	T	F	G	L	A	-	-	-	C	C	A	I	E	M	M	A	S	-	-	-	-	T	D	A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	Q	A	D	V	M	I	V	A	G	R	L	S	K	-	-	-	-	-	-	-	-	-	-	-	-	K	M	A	P	V	M	R	R	V	W	E	Q	M	P	D	P	K	W	V	I	S	M	G	A	C	A	S	S	G	G	M	F	N	-	-	-	N	Y	A	I	V	Q	N	V	D	S	-	-	-	-	V	V	P	V	D	V	Y	V	P	G	C	P	P	R	P	E	A	L	I	Y	A	V	M	Q	L	Q	K	K	V	R	G	Q	A	Y	N	E	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	R	G	E	R	L	-	-	P	P	V	A	A	-	-	-	-	-	-	-	-	-	-	-
-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	G	P	R	R	P	S	V	V	Y	L	H	N	A	E	C	T	G	C	S	E	S	V	L	R	A	F	E	P	Y	I	D	T	L	I	L	D	T	L	S	L	D	Y	H	E	T	I	M	A	A	A	G	D	A	A	E	A	A	L	E	Q	A	V	N	S	P	H	G	F	I	A	V	V	E	G	G	I	P	T	A	A	N	G	I	Y	G	K	V	A	N	H	T	M	L	D	I	C	S	R	I	L	P	K	A	-	-	-	Q	A	V	I	A	Y	G	T	C	A	T	F	G	G	V	Q	A	A	K	P	N	P	T	G	A	K	G	V	N	D	A	L	K	H	L	G	V	K	A	I	N	I	A	G	C	P	P	N	P	Y	N	L	V	G	T	I	V	Y	Y	L	K	N	K	A	A	P	E	L	D	S	L	N	R	P	T	M	F	F	G	Q	T	V	H	E	Q	C	P	R	L	P	H	F	D	A	G	E	F	A	P	S	F	E	S	E	E	A	R	K	G	W	C	L	Y	E	L	G	C	K	G	P	V	T	M	N	N	C	P	K	I	K	F	N	Q	T	N	W	P	V	D	A	G	H	P	C	I	G	C	S	E	P	D	F	W	D	A	M	T	P	F	Y	Q	N

									10										20										30										40										50										60										70										80										90										100										110										120										130										140										150										160										170										180										190										200										210										220										230										240										250										260										270										280
E	R	E	G	I	L	F	T	T	L	E	K	L	V	A	W	G	R	S	N	S	L	W	P	A	T	F	G	L	A	-	-	-	C	C	A	I	E	M	M	A	S	-	-	-	-	T	D	A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	Q	A	D	V	M	I	V	A	G	R	L	S	K	-	-	-	-	-	-	-	-	-	-	-	-	K	M	A	P	V	M	R	R	V	W	E	Q	M	P	D	P	K	W	V	I	S	M	G	A	C	A	S	S	G	G	M	F	N	-	-	-	N	Y	A	I	V	Q	N	V	D	S	-	-	-	-	V	V	P	V	D	V	Y	V	P	G	C	P	P	R	P	E	A	L	I	Y	A	V	M	Q	L	Q	K	K	V	R	G	Q	A	Y	N	E	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	R	G	E	R	L	-	-	P	P	V	A	A	-	-	-	-	-	-	-	-	-	-	-
-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	G	P	R	R	P	S	V	V	Y	L	H	N	A	E	C	T	G	C	S	E	S	V	L	R	A	F	E	P	Y	I	D	T	L	I	L	D	T	L	S	L	D	Y	H	E	T	I	M	A	A	A	G	D	A	A	E	A	A	L	E	Q	A	V	N	S	P	H	G	F	I	A	V	V	E	G	G	I	P	T	A	A	N	G	I	Y	G	K	V	A	N	H	T	M	L	D	I	C	S	R	I	L	P	K	A	-	-	-	Q	A	V	I	A	Y	G	T	C	A	T	F	G	G	V	Q	A	A	K	P	N	P	T	G	A	K	G	V	N	D	A	L	K	H	L	G	V	K	A	I	N	I	A	G	C	P	P	N	P	Y	N	L	V	G	T	I	V	Y	Y	L	K	N	K	A	A	P	E	L	D	S	L	N	R	P	T	M	F	F	G	Q	T	V	H	E	Q	C	P	R	L	P	H	F	D	A	G	E	F	A	P	S	F	E	S	E	E	A	R	K	G	W	C	L	Y	E	L	G	C	K	G	P	V	T	M	N	N	C	P	K	I	K	F	N	Q	T	N	W	P	V	D	A	G	H	P	C	I	G	C	S	E	P	D	F	W	D	A	M	T	P	F	Y	Q	N

									10										20										30										40										50										60										70										80										90										100										110										120										130										140										150										160										170										180										190										200										210										220										230										240										250										260										270										280
E	R	E	G	I	L	F	T	T	L	E	K	L	V	A	W	G	R	S	N	S	L	W	P	A	T	F	G	L	A	-	-	-	C	C	A	I	E	M	M	A	S	-	-	-	-	T	D	A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	Q	A	D	V	M	I	V	A	G	R	L	S	K	-	-	-	-	-	-	-	-	-	-	-	-	K	M	A	P	V	M	R	R	V	W	E	Q	M	P	D	P	K	W	V	I	S	M	G	A	C	A	S	S	G	G	M	F	N	-	-	-	N	Y	A	I	V	Q	N	V	D	S	-	-	-	-	V	V	P	V	D	V	Y	V	P	G	C	P	P	R	P	E	A	L	I	Y	A	V	M	Q	L	Q	K	K	V	R	G	Q	A	Y	N	E	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	R	G	E	R	L	-	-	P	P	V	A	A	-	-	-	-	-	-	-	-	-	-	-
-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	G	P	R	R	P	S	V	V	Y	L	H	N	A	E	C	T	G	C	S	E	S	V	L	R	A	F	E	P	Y	I	D	T	L	I	L	D	T	L	S	L	D	Y	H	E	T	I	M	A	A	A	G	D	A	A	E	A	A	L	E	Q	A	V	N	S	P	H	G	F	I	A	V	V	E	G	G	I	P	T	A	A	N	G	I	Y	G	K	V	A	N	H	T	M	L	D	I	C	S	R	I	L	P	K	A	-	-	-	Q	A	V	I	A	Y	G	T	C	A	T	F	G	G	V	Q	A	A	K	P	N	P	T	G	A	K	G	V	N	D	A	L	K	H	L	G	V	K	A	I	N	I	A	G	C	P	P	N	P	Y	N	L	V	G	T	I	V	Y	Y	L	K	N	K	A	A	P	E	L	D	S	L	N	R	P	T	M	F	F	G	Q	T	V	H	E	Q	C	P	R	L	P	H	F	D	A	G	E	F	A	P	S	F	E	S	E	E	A	R	K	G	W	C	L	Y	E	L	G	C	K	G	P	V	T	M	N	N	C	P	K	I	K	F	N	Q	T	N	W	P	V	D	A	G	H	P	C	I	G	C	S	E	P	D	F	W	D	A	M	T	P	F	Y	Q	N