Contacts of the strand formed by residues 130 - 140 (chain I) in PDB entry 2WQT


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ILE 130 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110I  LEU*     4.4    19.5    -      -       +      -
    111I  VAL      3.7     5.2    -      -       -      +
    112I  LEU*     4.7     4.3    -      -       +      +
    113I  ASN*     3.3     6.3    +      -       -      +
    126I  LEU*     3.6    19.1    -      -       +      +
    127I  TYR*     3.3    20.9    +      -       +      +
    128I  ASN      4.9     0.7    -      -       -      +
    129I  ALA*     1.3    76.5    -      -       -      +
    131I  GLU*     1.3    63.0    +      -       -      +
    132I  TRP      3.6    24.2    -      -       -      +
    133I  VAL*     4.1     5.6    -      -       +      -
    173I  PRO*     3.4    35.4    -      -       +      +
    178I  LEU*     5.2     2.5    -      -       +      -
    205I  LEU*     3.6    40.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 131 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128H  ASN*     3.1    32.1    +      -       -      +
    111I  VAL*     2.6    27.0    +      -       -      +
    112I  LEU      3.9    11.2    -      -       -      +
    113I  ASN*     3.3    24.7    +      -       -      +
    129I  ALA      3.5     0.4    +      -       -      -
    130I  ILE*     1.3    76.5    -      -       -      +
    132I  TRP*     1.3    70.9    +      -       +      +
    172I  ARG*     3.2    40.2    +      -       -      +
    173I  PRO*     3.8     4.7    -      -       -      +
    225I  GLY*     5.3     2.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 132 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  ASP      5.6     2.0    -      -       -      -
    127H  TYR*     4.7    15.3    -      +       +      -
    128H  ASN*     2.7    39.8    -      -       +      +
    173H  PRO*     5.0     8.3    -      -       +      -
    174H  ALA*     3.7    34.1    -      -       +      -
    109I  ALA      3.9     0.2    -      -       -      +
    110I  LEU*     3.5     3.8    -      -       -      -
    111I  VAL*     3.0    44.0    +      -       +      +
    130I  ILE*     3.6     6.1    -      -       -      +
    131I  GLU*     1.3    99.8    -      -       +      +
    133I  VAL*     1.3    63.2    +      -       -      +
    134I  LEU*     4.2    15.7    -      -       +      -
    170I  ALA*     3.7    27.8    -      -       +      -
    171I  GLN      3.4    23.3    -      -       -      -
    172I  ARG*     3.3    38.6    -      -       -      -
    173I  PRO*     5.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108I  ILE*     4.2    10.5    -      -       +      -
    109I  ALA      3.4     2.9    -      -       -      -
    110I  LEU*     3.8    14.4    -      -       +      -
    130I  ILE*     4.1     9.0    -      -       +      -
    132I  TRP*     1.3    77.0    -      -       -      +
    134I  LEU*     1.3    63.1    +      -       -      +
    170I  ALA      4.0     0.2    -      -       -      -
    171I  GLN*     2.9    37.6    +      -       -      +
    173I  PRO*     4.0    18.4    -      -       +      -
    176I  LEU*     3.6    33.9    -      -       +      -
    178I  LEU*     4.0    21.8    -      -       +      -
    252I  ILE*     4.3    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  ASP*     4.8     6.1    -      -       +      +
    127H  TYR*     3.9    23.6    -      -       +      -
    108I  ILE*     3.8     2.8    -      -       -      +
    109I  ALA*     2.8    54.3    +      -       +      +
    111I  VAL*     3.9    25.8    -      -       +      -
    132I  TRP*     4.2     8.5    -      -       +      -
    133I  VAL*     1.3    79.4    -      -       -      +
    135I  PRO*     1.4    75.0    -      -       +      +
    166I  ILE*     4.0    22.7    -      -       +      -
    167I  GLY      4.4     2.2    -      -       -      +
    169I  PRO      4.4     4.3    -      -       -      +
    170I  ALA*     3.9    24.2    -      -       +      -
    227I  ILE*     5.0     3.4    -      -       +      -
    252I  ILE*     4.1     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 135 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107I  GLU      3.9     5.2    -      -       -      +
    108I  ILE*     5.0     0.2    -      -       -      -
    134I  LEU*     1.4    91.9    -      -       +      +
    136I  ALA*     1.3    58.8    +      -       -      +
    166I  ILE*     3.8     2.1    -      -       -      +
    167I  GLY      2.9    26.9    +      -       -      -
    168I  GLY      3.5    26.7    -      -       -      +
    169I  PRO      3.9     9.2    -      -       -      +
    249I  ILE*     3.8    20.9    -      -       +      -
    252I  ILE*     3.8    14.5    -      -       +      +
    253I  GLY      3.9     4.0    -      -       -      -
    254I  SER      3.6    25.1    -      -       -      +
    255I  VAL*     3.8     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 136 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106I  ALA*     3.6     5.0    -      -       -      +
    107I  GLU*     2.9    37.5    +      -       +      +
    109I  ALA*     4.1    10.3    -      -       +      -
    135I  PRO*     1.3    76.2    -      -       -      +
    137I  LEU*     1.3    62.6    +      -       -      +
    164I  TYR*     5.6     0.4    -      -       +      -
    165I  VAL      3.1    13.2    -      -       -      +
    166I  ILE*     4.4     5.4    -      -       +      -
    229I  LEU*     3.9    28.3    -      -       +      -
    249I  ILE*     4.7     0.3    -      -       -      +
    255I  VAL*     3.7    11.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 137 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104I  ILE*     4.2    13.5    -      -       +      -
    105I  GLU      3.4     9.4    -      -       -      +
    106I  ALA*     4.2     0.9    -      -       -      -
    136I  ALA*     1.3    79.1    -      -       -      +
    138I  GLU*     1.3    60.0    +      -       -      +
    139I  VAL      4.1     0.4    -      -       -      -
    164I  TYR*     3.3     6.2    -      -       -      +
    165I  VAL*     2.8    42.9    +      -       +      +
    185I  MET*     3.9    19.5    -      -       -      -
    245I  PHE*     4.5    11.4    -      -       +      +
    246I  GLU      5.3     0.2    -      -       -      -
    247I  ALA*     3.8    29.2    -      -       +      +
    255I  VAL*     3.8    23.8    -      -       +      +
    256I  ALA*     4.0     1.6    -      -       -      -
    257I  ALA*     3.9    35.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 138 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60I  LYS*     3.0    49.6    +      -       -      +
     82I  LEU*     5.1     1.2    -      -       +      +
     86I  MET*     5.7     0.5    -      -       -      +
    104I  ILE*     3.2     3.4    -      -       -      -
    105I  GLU*     2.8    42.2    +      -       +      +
    107I  GLU*     3.1    33.3    -      -       -      +
    137I  LEU*     1.3    73.6    -      -       -      +
    139I  VAL*     1.3    64.0    +      -       -      +
    140I  VAL*     3.5    15.8    +      -       -      +
    161I  CYS*     3.7    15.6    -      -       -      -
    162I  GLY      4.7     1.4    +      -       -      -
    163I  VAL      3.8    10.1    -      -       -      +
    164I  TYR*     4.2     1.8    -      -       +      -
    229I  LEU*     3.8    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 139 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94I  ILE*     4.3     8.3    -      -       +      -
     99I  VAL*     4.1    14.8    -      -       +      -
    102I  PRO*     4.0    23.3    -      -       +      -
    103I  ARG      3.3    11.4    -      -       -      +
    104I  ILE*     3.5    18.4    -      -       +      -
    138I  GLU*     1.3    70.7    -      -       -      +
    140I  VAL*     1.3    60.2    +      -       -      +
    162I  GLY*     3.2     8.1    +      -       -      -
    163I  VAL*     2.9    52.9    +      -       +      +
    165I  VAL*     4.7     8.3    -      -       +      -
    239I  VAL*     4.9     0.2    -      -       +      -
    259I  PHE*     3.9    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 140 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60I  LYS*     4.0     1.3    -      -       -      +
     99I  VAL*     3.7     2.2    -      -       -      +
    102I  PRO*     3.4     5.2    -      -       -      +
    103I  ARG*     2.7    56.2    +      -       +      +
    105I  GLU*     3.7    15.5    -      -       -      +
    138I  GLU*     3.5    20.1    +      -       +      +
    139I  VAL*     1.3    75.5    -      -       -      +
    141I  GLY*     1.3    58.3    +      -       -      +
    147I  TRP*     3.7    21.8    -      -       +      -
    160I  SER*     3.2    17.7    -      -       -      +
    162I  GLY      4.2     0.4    -      -       -      +
    236I  MET*     3.9    13.2    -      -       +      -
   1262I  PO4      3.3    24.9    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il