Sulftransferase Interface Protein  Common  Interfaces  Database
(ProtCID)
2NLQ Crystal

Pfam assignments have been used previously to catalogue the physical interaction of different domain families within the PDB. With a larger and more accurate set of assignments, we have investigated the number of such interactions that are now present in the biological assemblies of the PDB. An interaction is defined if there are at least 5 pairs of residues with any atomic distance < 5Å, or at least 10 pairs of residues with C-beta/C-alpha distance < 12Å and at least one atomic distance < 5Å.

Interaction Type #Interactions
Inter-Chain: Same-Pfam 3,499
Inter-Chain: Diff-Pfam Pairs 3,958
Intra-Chain: Same_Pfam 383
Intra-Chain: Diff-Pfam Pairs 3,240
Same-Pfams (Inter and/or Intra) 3,576
Diff-Pfam Pairs (Inter and/or Intra) 6,132
#Pfam in diff interactions 3,982
#Pfams in same or diff interactions 5,263

The interactions in biological assemblies provide more accurate estimates of our structural knowledge of how proteins interact with each other, and how this information might be used to investigate protein-protein interaction networks. In the following Table, we show the Pfams that interact with 30 or more other Pfams within the PDB. Several of these are domains which typically bind short peptides from other proteins, including MHC_I, Pkinase, WD40, and efhand domains. Many are also repeat modules that serve as protein-protein interaction scaffolds.

PFAM #Pfam #Entries #Intra-Chain Pfams #Inter-Chain Pfams
V-set 178 1,575 8 177
Ras 77 206 2 75
MHC_I 69 516 2 69
Crp 67 86 57 30
Pkinase 52 480 17 41
ubiquitin 47 99 13 36
Trypsin 46 519 9 43
EF_hand_5 42 209 12 37
WD40 40 166 15 27
fn3 36 70 16 28
efhand 35 314 23 22
I-set 35 152 18 25
Arm 35 62 12 26
HEAT_2 33 61 19 16
C1-set 32 1756 5 32
Fer4_7 30 66 12 21