39 protein-protein interfaces by MolSurfer

Instructions:
  • Use menu File--Open to switch between the interfaces;
  • Use menu View to switch between the properties to be displayed on the 2D map;
  • Use Mouse to move/drag/click across the map to navigate in the 3D structure;
  • To adjust the range for displaying properties on 2D map, click left/right mouse button on the color bar;
  • Use features of WebMol while viewing 3D - stereo, colouring, selecting etc;
  • Use menu File--Quit when done.


  • Details of interface mapping for a demo:
  • Interfaces were chosen that have a) 3D x-ray crystal structures available in the PDB; b) a detailed description of the protein-protein interaction properties available in the literature (Suggestions for additions to this set of  protein-protein interfaces are appreciated);
  • Each PDB file was split into 2 parts giving coordinates of the first and the second proteins forming the interface;
  • A quasi rectangular mesh of ca 1 Å spacing was generated on the analytically defined interface between these 2 proteins;
  • Points for which the sum of the distances to the closest atoms of proteins 1 and 2 exceeds 6 Å were deleted;
  • Heteroatoms were added which lie within 3 Å of any interface point;
  • The properties of each protein were projected onto every point of the interface; these are the properties assigned to the closest atom to the point;
  • Electrostatic potential of each (isolated) protein was computed with the UHBD program by solving FD LPBE and the potential values were interpolated at each interface point.
  • Additionally, the changes in binding free energy upon alanine mutation were assigned to each side-chain atom of the corresponding residue.  This property is included for interfaces for which these data are available for at least one of the proteins.  See the recent compilation by A. Bogan and K. Thorn
  • Residue hydrophobicities are assigned according to the residue name and following the parameters in Eisenberg D., Weiss R.M., Terwilliger T.C. and Wilcox W. (1982) Farad. Symp. Chem. Soc., 17, 109-120, namely:

  •   ALA   0.25       GLN  -0.69       LEU   0.53       SER  -0.26
      ARG  -1.80       GLU  -0.62       LYS  -1.10       THR  -0.18
      ASN  -0.64       GLY   0.16       MET   0.26       TRP   0.37
      ASP  -0.72       HIS  -0.40       PHE   0.61       TYP   0.02
      CYS   0.04       ILE   0.73       PRO  -0.07       VAL   0.54
      none of the above                 0.00
  • Atomic hydrophobicities are assigned according to the atom name and follow  Eisenberg D., Wesson M., Yamashita M. (1989) Chem. Scrip., 29A, 217-221, namely:

  •   'NZ  LYS'  -38       'OE1 GLU'  -37         'C'    18
      'NH1 ARG'  -38       'OE2 GLU'  -37         'S'     5
      'NH2 ARG'  -38       'OD1 ASP'  -37         'O'    -9
                           'OD2 ASP'  -37         'N'    -9
      none of the above    0
  • Atomic radii are also from the previous reference, namely:

  •   'C'    1.9 A
      'S'    1.8 A
      'O'    1.4 A
      'N'    1.7 A
      none of the above    1.9 A
    Listing of complexes:
    code R protein 1 aa protein 2 aa wat, het
    1acb 2.0 A-chymotrypsin
    Oxen
    245 Eglin C
    Leech
    70 142W
    1atn 2.8 Deoxyribonuclease-I
    Bovine
    373 Actin
    Rabbit
    260 3NAG+1ATP+4CA
    1bql 2.6 Fab HyHEL-5
    Mouse
    212+
    215
    Lysozyme
    Bobwhite-Quail
    129 86W
    1brs 2.0 Barnase
    BacillusA_EC
    110*3 Barstar
    BL21
    89*3 513W
    1cho 1.8 A-chymotrypsin
    Bovine
    245 OMTKY3
    Turkey
    56 221W
    1cse 1.2 SubtilisinCarlsberg
    BacillusS
    274 Eglin C
    Leech
    71 432W+2CA
    1dvf 1.9 Fab D1.3
    Mouse_EC
    108+
    116
    Fab E5.2
    Mouse_EC
    107+
    120
    157W+3ZN
    1fbi 3.0 Fab F9.13.7
    Mouse
    (214+
    221)*2
    Lysozyme
    Guineafowl
    129*2 -
    1fc2 2.8 Ig FC 224 Protein A
    human
    58 9S+1SO4
    1fdl 2.5 Fab D1.3
    Mouse_EC
    214+
    218
    Lysozyme
    Hen
    129 -
    1gla 2.6 Glycerol Kinase
    EC
    168 Factor III
    EC
    501 1GOL
    1jhl 2.4 Fab D11.15
    Murine_EC
    108+
    116
    Lysozyme
    Pheasant
    129 -
    1lpa 3.0 Lipase
    Human
    449 Colipase
    Pig
    449 BNG+CA+PLC
    1mah 3.2 Acetylcholinesterase
    Mouse
    543 Fasciculin 2
    Mouse
    61 1S
    1mlc 2.1 Fab D44.1
    Mouse
    (214+
    218)*2
    Lysozyme
    Hen
    129*2 210W
    1nca 2.5 Neuraminidase NC41 389 Fab IV A
    NoddyTern...
    214+
    221
    72W+8S+CA
    1ppf 1.8 Leukocyte Elastase
    Human
    218 OMTKY3
    Turkey
    56 272W+4S
    1tab 2.3 Trypsin
    Bovine
    223 BBI
    AdzukiBeans...
    82 140W
    1tec 2.2 Thermitase
    Thermoactinomyces
    279 Eglin C
    Leech
    70 208W+2CA+NA
    1tgs 1.8 Trypsinogen
    Bovine
    229 PSTI
    Porcine
    56 152W+CA+SO4
    1tpa 1.9 AnhydroTrypsin 223 BPTI 58 159W+CA
    1vfb 1.8 Fab D1.3
    Mouse_EC
    107+
    116
    Lysozyme
    Hen
    129 48W
    2kai 2.5 Kallikrein A
    Porcine
    80+
    152
    BPTI 58 10W
    2pcb 2.8 Cyt CP
    Yeast
    296(*2) Cyt C
    Horse
    296 337W
    2ptc 1.9 B-trypsin 223 BPTI 58 157W+CA
    2sec 1.8 Subtilisin Carlsberg
    Bacillus S
    274 Eglin C
    Leech
    71 170W+3CA
    2sic 1.8 Subtilisin BPN
    Bacillus A
    275 SI
    Streptomyces
    107 258W+2CA
    2sni 2.1 Subtilisin Novo
    BacillusA
    275 CI2
    Barley
    83 168W+2CA
    2tgp 1.9 Trypsinogen
    Bovine
    229 BPTI 58 138W+2SO4+1CA
    2tpi 2.1 Trypsinogen
    Bovine
    229
    +2
    BPTI 59 139W+HG
    3hfl 2.65 Fab HyHEL-5
    Mouse
    212+
    215
    Lysozyme
    Chicken
    129 82W
    3hfm 3.0 Fab HyHEL-10
    Mouse
    214+
    215
    Lysozyme
    Chicken
    129 1W
    3hhr 2.8 hGH 190 hGH bp 203(*2) -
    3sgb 1.8 Serine Proteinase B
    Streptomyces G
    185 OMTKY3
    Turkey
    56 182W
    4cpa 2.5 COXA
    Bovine
    307 COXI
    Potato...
    38 1ZN
    4ins 1.5 Insulin
    Pig
    21+30 Insulin
    Pig
    21+30 350W+2ZN
    4sgb 2.1 Serine Proteinase B
    Streptomyces G
    185 PCI1
    Potato...
    51 179W+2SO4+CA
    4tpi 2.2 Trypsinogen
    Bovine
    229
    +2
    BPTI_M 59 155W+2SO4+CA
    6rlx 1.5 Relaxin
    Human
    24+28 Relaxin
    Human
    24+28 73W



     
     

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