Interfaces

Classifications of Interfaces

Definition of Interfaces and Interface Residues

  • If two subunits (SCOPe domains) form a protein complex, each subunit loses solvent-accessible surface area (ASA). Interface residues are defined as residues that lose >1 Å2 of ASA upon formation of an interface. We have calculated the ASA of each residue using the program DSSP. We calculated the ASA of each residue using a program, DSSP.
  • If each interacting surface of two subunits has >10 interface residues, then the interacting surface is defined as an interface.

Browse OLIGAMI Hierarchy

  1. Secondary structure–based classification
  2. Interchain disulfide bond–based classification
  3. Intermolecular β-sheet–based classification

1. Secondary structure–based classification

  • We defined the seven interacting area types according to the fractions of secondary structures for interface residues. Then, the interface class is defined based on the two interacting area types. The secondary structures were defined using the program DSSP.
Interacting area typeDefinition
H (Helix) typefH ≥ 3fE and fH ≥ 3fN
E (Strand) typefE ≥ 3fH and fE ≥ 3fN
N (No structure) classfN ≥ 3fH and fN ≥ 3fE
HE type{3fN ≤ fH < 3fE} or {3fN ≤ fE < 3fH}
HN type{3fE ≤ fH < 3fN} or {3fE ≤ fN < 3fH}
EN type{3fH ≤ fE < 3fN} or {3fH ≤ fN < 3fE}
HEN typeOthers

fH : Fraction of the interface residues occurring in helical structures
fE : Fraction of the interface residues occurring in the strand structures
fN : fN = 1 - fH - fE
- Helical structure : H in DSSP output
- Strand structure : E in DSSP output
Interface class Number of domain pairs
H:H12300
E:E2943
N:N18427
H:E94
H:N3633
E:N566
H:HE155
H:HN16747
H:EN1663
E:HE200
E:HN242
E:EN3195
N:HN14972
N:EN8331
N:HE391
HE:HE679
HN:HN50696
EN:EN22651
HE:HN368
HE:EN821
HN:EN5208
H:HEN1468
E:HEN338
N:HEN3310
HE:HEN666
HN:HEN5608
EN:HEN6251
HEN:HEN12957

2. Interchain disulfide–bond based classification

  • Users can browse the oligomers according to the number of interchain disulfide bonds of an interface. We extracted the disulfide bond pairs between chains from the DSSP outputs.
Number of interchain disulfide bonds per interface Number of entries
12100
2225
315
41
51

3. Intermolecular β-sheet–based classification Intermolecular

  • Users can browse the oligomers according to the number of hydrogen bonds within an intermolecular -sheet of an interface. We extracted the hydrogen bond pairs between -strands of different chains. The hydrogen bond information was obtained from column BP1 or BP2 in the DSSP outputs.
Number of H-bonds on intermolecular β-sheet per interface Number of entries
16008
24779
35049
43319
53393
62112
71990
81427
91090
10720
11567
12525
13236
14200
15138
16132
17133
18236
1979
2075
2142
2259
2344
2458
2527
2615
2721
2816
2917
3012
3110
328
3313
346
356
Number of H-bonds on intermolecular β-sheet per interface Number of entries
3613
378
383
396
406
4110
425
4311
4416
451
462
474
482
492
501
512
524
534
541
553
562
576
585
596
604
613
624
632
642
662
672
681
691
811
841
881
891
901
PDL