Movie generated with PyMOL

A: b.47.1.2 (red/blue)

View b.47.1.2 in Scoppi
PDB: 1acb (Search literature with GoPubMed)
FA: Eukaryotic proteases
SF: Trypsin-like serine proteases
SP: Cow (Bos taurus)/Rat (Rattus norvegicus)

B: d.40.1.1 (yellow)

View d.40.1.1 in Scoppi
PDB: 1acb (Search literature with GoPubMed)
FA: CI-2 family of serine protease inhibitors
SF: CI-2 family of serine protease inhibitors
SP: Leech (Hirudo medicinalis)

C: e.1.1.1 (green)

View e.1.1.1 in Scoppi
PDB: 1k9o (Search literature with GoPubMed)
FA: Serpins
SF: Serpins
SP: Tobacco hornworm (Manduca sexta)
com Center of mass, domain b.47.1.2
com Center of mass, domain d.40.1.1
com Center of mass of interface atoms, domain d.40.1.1
com Center of mass, domain e.1.1.1
com Center of mass of interface atoms, domain e.1.1.1

Geometric Parameters

RMSD A1-A2 0.93
Shared interface atoms 223 (91.0%)
Angle between green and yellow interface: 8.18
Angle between green and yellow domain: 10.32
Distance between center of mass of green and yellow interface (in Angstrom): 2.55
Distance between center of mass of green and yellow domain (in Angstrom) 25.82

Sequence Alignment of domain b.47.1.2



cgvpaiqpvlsglivngeeavpgswpwqvslqdktgFHFCggslinenwvvtaaHCGvttsdvvvagefdqgsssekiqk
-------------ivggytcqensvpyqvsln--sgYHFCggslindqwvvsaaHC-yksriqvrlgehninvlegneqf
                                    :###              ##                         

lkiakvfknskynslt-InnditllklstaasfsqtvsavclpsasddfaagttcvttgwgLtr--YanTpdrlqqaslp
vnaakiikhpnfdRKTL-nndimliklsspvklnarvatvalp--sscapagtqclisgwgntlSSGVnEpdllqcldap
             ___                                             _    ._ .           

llsntnckkyWgtKikdamicag--asgvsSCMGDSggplvckkngawtlvgiVSWGSStCststpgvyarvtalvnwvq
llpqadceasypgKitdnmvcvgfleggkDSCQGDAggpvvc----ngelqgiVSWGYGCalpdnpGVytkvcnyvdwiq
          _  #               _##.##:                 ####..__     __             

qtlaan
dtiaan
Aligned interface residues 
. : #
 21 (65%)
Aligned, similar interface residues (with positive BLOSUM value) 
: #
 16 (50%)
Raw BLOSUM-Score for the latter residues 99
Meaning
    
Capital letters
 Residue interacts with domain A 
#
 Identical interacting residues 
:
 Residues are similar and interact 
.
 Residues are not similar and interact 
_
 Only one residue interacts
   

Sequences of domain d.40.1.1 and e.1.1.1



ksfpevvgktvdqareyftlhypqydvyflpeGSPVTLDLRYnRvRvFynpgtnvvnhVpHvg 


getdlqkilresndqftaqmfsevvkanpgqnvvlsafsvlpplgqlalasvgeshdellralalpndnvtkdvfadlnr 
gvravkgvdlkmaskiyvakglelnddfaavsrdvfgsevqnvdfvksveaagainkwvedqtnnriknlvdpdaldett 
rsvlvnaiyfkgswkdkfVkERtmdrdfhvskdktikvptmigkkdvryadvpeldakmiemsyegdqasmiiilpnqvd 
gitaleqklkdpkalsraeerlynteveitlpkfkietttdlkevlsnmnikklftpgaarlenllktkesltvdaaiqk 
afievneegaeAAAAnAfGIVPKSLILypevhidrpfyfelkidgipmfngkviep

Similarities between domain d.40.1.1 and e.1.1.1

Residue PairAtom MatchesBLOSUMScoreAvg.-Distance
Leu47-Leu355 ca cb bb bb bb sc sc sc sc sc 4 12.25 0.53
Val43-Val351 ca cb bb bb bb sc sc sc 4 9.27 1.02
Asp46-Ser354 ca cb bb bb bb sc sc sc sc sc 0 8.22 0.53
Leu45-Lys353 ca cb bb bb bb sc sc sc sc sc -2 8.11 0.57
Thr44-Pro352 ca cb bb bb bb sc sc sc sc -1 7.10 0.63
Arg48-Ile356 ca cb bb bb bb sc sc sc -3 6.77 0.46
Tyr49-Leu357 ca cb bb bb bb sc sc sc sc sc sc sc -1 6.25 1.44
Val66-Val189 bb 4 4.04 2.89
Arg53-Ala347 sc sc sc sc sc -1 2.08 1.75
His68-Val189 sc sc -3 1.34 1.00
Pro42-Gly349 bb sc -2 0.74 1.90
Pro42-Ile350 ca cb bb -3 0.82 2.18
Pro42-Val351 bb -2 0.56 1.31
Arg51-Ile356 sc -3 0.42 1.75
Ser41-Gly349 bb 0 0.24 2.28
Phe55-Ala342 bb bb -2 0.21 2.69
Total Score 68.40
SymbolAtom match between
ca C-alpha atoms within 3 A
cb C-beta atoms within 3 A
bb backbone atoms within 3 A
sc side chain atoms within 2 A
The score for each residue pair is simply its BLOSUM score (if positive) + the sum of atom pair scores.
The latter are between 0 and 1, with 0 for 3A distance or above
and 1 for exact coordinate matches, linearly interpolated.