Contacts of the helix formed by residues 126 - 146 (chain A) in PDB entry 1GWP


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 VAL 126 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  ASP*     5.3     1.6    -      -       -      +
    104A  ILE*     3.1    33.3    -      -       +      +
    109A  SER*     4.9     0.2    -      -       -      +
    114A  GLN*     3.3    61.2    -      -       +      +
    117A  TRP*     4.4     5.4    -      -       +      -
    118A  MET*     3.5    14.6    -      -       +      +
    124A  ILE*     2.7    30.2    +      -       +      +
    125A  PRO*     1.3    73.2    -      -       -      +
    127A  GLY*     1.3    59.8    +      -       -      +
    129A  ILE*     3.4     3.5    -      -       -      +
    130A  TYR*     3.0    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  GLU      5.2     1.1    -      -       -      -
     46A  GLY*     5.3     4.0    -      -       -      -
     47A  ALA      4.1    19.0    -      -       -      +
     48A  THR*     6.0     0.4    -      -       -      -
     52A  LEU*     4.9     0.2    -      -       -      +
    118A  MET*     4.2    16.7    -      -       -      +
    125A  PRO*     2.9     3.0    -      -       -      +
    126A  VAL*     1.3    80.0    -      -       -      +
    128A  GLU*     1.3    65.5    +      -       -      -
    129A  ILE      2.9     0.7    -      -       -      -
    130A  TYR*     2.9     7.9    +      -       -      +
    131A  LYS*     2.8    24.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  GLU*     4.2    25.1    +      -       -      +
     46A  GLY*     5.2     2.0    -      -       -      -
    125A  PRO*     3.3    19.1    +      -       +      +
    127A  GLY*     1.3    72.1    -      -       -      +
    129A  ILE*     1.3    57.3    +      -       +      +
    131A  LYS*     3.3    27.2    +      -       -      +
    132A  ARG*     2.9    28.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  TRP*     3.8    29.8    -      -       +      +
    104A  ILE*     3.1    35.7    -      -       +      -
    124A  ILE*     4.3     3.1    -      -       +      -
    125A  PRO*     2.6    63.5    +      -       +      +
    126A  VAL*     3.4     5.4    -      -       -      +
    128A  GLU*     1.3    73.8    -      -       +      +
    130A  TYR*     1.3    56.6    +      -       -      +
    132A  ARG*     3.0     7.2    +      -       -      +
    133A  TRP*     2.9    62.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  THR      4.8     1.3    -      -       -      -
     49A  PRO*     4.3    30.9    -      -       +      +
     52A  LEU*     3.9    12.8    -      -       +      -
     53A  ASN*     5.7     1.1    -      -       +      -
     73A  ILE*     4.0    20.8    -      -       +      +
    104A  ILE*     2.7    27.8    -      -       -      -
    105A  ALA*     3.2    25.9    +      -       -      -
    106A  GLY*     5.0     1.7    -      -       -      -
    114A  GLN*     4.9     5.4    -      -       -      +
    126A  VAL*     3.0    19.6    +      -       +      +
    127A  GLY*     2.9     5.7    +      -       -      +
    129A  ILE*     1.3    76.4    -      -       -      +
    131A  LYS*     1.3    55.2    +      -       -      +
    133A  TRP*     3.0    13.3    +      +       -      +
    134A  ILE*     2.7    60.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  SER*     3.3    28.7    -      -       -      +
     44A  SER*     2.6    41.5    -      -       -      +
     45A  GLU*     3.4    15.0    +      -       -      +
     47A  ALA      5.7     0.4    -      -       -      +
     52A  LEU*     3.8    11.2    -      -       +      +
    127A  GLY      2.8    15.7    +      -       -      +
    128A  GLU*     3.3    44.6    +      -       -      +
    130A  TYR*     1.3    76.7    -      -       -      +
    132A  ARG*     1.3    67.0    +      -       -      +
    134A  ILE*     4.8     0.7    -      -       -      -
    135A  ILE*     3.0    42.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  GLU*     4.2    14.9    +      -       -      +
     80A  TRP*     6.4     0.9    -      -       -      -
    128A  GLU*     2.9    15.4    +      -       +      +
    129A  ILE*     3.0    11.0    +      -       -      +
    131A  LYS*     1.3    83.7    -      -       -      +
    133A  TRP*     1.3    58.9    +      -       +      +
    135A  ILE*     3.5    10.1    +      -       +      +
    136A  LEU*     2.7    43.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  THR*     3.8     3.1    -      -       -      +
     73A  ILE*     3.8    34.5    -      -       +      +
     76A  GLU*     3.0    46.0    +      -       +      -
     77A  ALA*     4.1    13.2    -      -       +      -
     80A  TRP*     4.0    12.9    -      +       -      -
    101A  GLY*     3.1    35.9    -      -       -      -
    104A  ILE*     3.4    13.7    -      -       +      -
    105A  ALA*     3.4    28.9    -      -       +      -
    129A  ILE*     2.9    49.3    +      -       +      +
    130A  TYR*     3.0    18.6    +      +       -      +
    132A  ARG*     1.3    75.1    -      -       +      +
    134A  ILE*     1.3    60.2    +      -       -      +
    136A  LEU*     2.5    35.8    +      -       -      +
    137A  GLY      2.9     5.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  PHE*     3.7    17.9    -      -       +      -
     52A  LEU*     3.3    48.2    -      -       +      +
     56A  LEU*     3.4    36.3    -      -       +      -
     69A  LEU*     3.1    18.5    -      -       +      +
     73A  ILE*     3.8    21.5    -      -       +      +
    130A  TYR*     2.7    31.4    +      -       +      +
    131A  LYS      4.0     2.5    -      -       -      +
    133A  TRP*     1.3    71.5    -      -       -      +
    135A  ILE*     1.3    64.3    +      -       +      +
    137A  GLY      3.1     3.1    +      -       -      -
    138A  LEU*     3.0    21.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ILE*     4.0    18.9    -      -       +      +
     40A  PHE*     3.8    25.8    -      -       +      +
     41A  SER*     3.3    44.2    -      -       -      +
     52A  LEU*     5.1     2.5    -      -       +      -
    131A  LYS*     3.0    30.2    +      -       +      +
    132A  ARG*     3.7    10.8    -      -       +      +
    134A  ILE*     1.3    78.3    -      -       +      +
    136A  LEU*     1.3    58.5    +      -       -      +
    138A  LEU*     3.2     5.8    +      -       +      +
    139A  ASN*     2.8    36.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  THR*     3.3    21.8    -      -       +      +
     75A  GLU*     6.1     4.0    -      -       +      +
     76A  GLU*     3.2    39.0    -      -       +      +
    132A  ARG*     2.7    26.8    +      -       +      +
    133A  TRP*     2.5    20.0    +      -       -      +
    135A  ILE*     1.3    72.6    -      -       -      +
    137A  GLY*     1.3    53.6    +      -       -      +
    139A  ASN*     3.3     9.0    +      -       +      +
    140A  LYS*     3.0    34.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  MET*     4.9     0.2    -      -       -      +
     69A  LEU*     3.9    14.4    -      -       -      -
     72A  THR*     2.9    30.5    -      -       -      +
    133A  TRP      2.9     5.3    +      -       -      -
    134A  ILE      3.1     3.6    +      -       -      -
    136A  LEU*     1.3    73.7    -      -       -      +
    138A  LEU*     1.3    53.0    -      -       -      +
    140A  LYS*     2.9     4.4    +      -       -      +
    141A  ILE*     2.7    44.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  TRP*     5.5     3.6    -      -       +      -
     32A  PHE*     3.5    40.8    -      -       +      -
     36A  VAL*     5.3     7.9    -      -       +      -
     37A  ILE*     3.6    20.4    -      -       +      -
     40A  PHE*     3.0    47.3    -      -       +      -
     56A  LEU*     5.9     0.2    -      -       +      -
     59A  VAL*     5.6     3.1    -      -       +      -
     66A  MET*     6.5     0.4    -      -       +      -
     69A  LEU*     3.6    11.5    -      -       +      +
    134A  ILE*     3.0    17.5    +      -       +      +
    135A  ILE*     3.2    12.5    +      -       +      +
    137A  GLY*     1.3    74.5    -      -       -      +
    139A  ASN*     1.3    53.8    +      -       -      +
    141A  ILE*     3.1     7.5    +      -       +      +
    142A  VAL*     2.8    37.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ILE*     3.5    23.4    -      -       +      +
    135A  ILE*     2.8    19.9    +      -       +      +
    136A  LEU*     3.4    10.9    +      -       -      +
    138A  LEU*     1.3    77.2    -      -       -      +
    140A  LYS*     1.3    53.6    +      -       -      +
    142A  VAL*     3.2     4.0    +      -       -      +
    143A  ARG*     2.7    50.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  MET*     3.4    24.4    -      -       +      +
     71A  GLU*     6.0     4.6    +      -       -      +
     72A  THR*     2.9    25.2    +      -       -      +
     75A  GLU*     4.3    17.5    +      -       -      +
    136A  LEU*     3.0    18.9    +      -       +      +
    137A  GLY*     2.9     9.2    +      -       -      +
    139A  ASN*     1.3    77.3    -      -       -      +
    141A  ILE*     1.3    57.8    +      -       -      +
    143A  ARG*     3.4    28.5    +      -       -      +
    144A  MET*     2.8    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  PHE*     3.4    36.1    -      -       +      -
     65A  ALA*     3.2    37.2    -      -       +      +
     68A  MET*     3.5    25.4    -      -       +      -
     69A  LEU*     4.0    11.4    -      -       +      -
    137A  GLY      2.7    32.5    +      -       -      +
    138A  LEU*     3.1    13.0    +      -       -      +
    140A  LYS*     1.3    71.1    -      -       -      +
    142A  VAL*     1.3    65.8    +      -       -      +
    144A  MET*     3.3     2.6    +      -       -      +
    145A  TYR*     3.0    47.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  PHE*     3.2    31.0    -      -       +      +
     33A  SER      3.6     4.7    -      -       -      +
     34A  PRO*     3.9    28.0    -      -       +      -
     37A  ILE*     2.9    42.4    -      -       +      -
    138A  LEU*     2.8    12.6    +      -       +      +
    139A  ASN*     3.7     3.8    -      -       -      +
    141A  ILE*     1.3    73.6    -      -       +      +
    143A  ARG*     1.3    63.3    +      -       -      +
    145A  TYR*     3.4     7.9    -      -       +      +
    146A  SER*     3.2    23.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  ASN*     2.7    32.7    +      -       -      +
    140A  LYS*     3.4    32.9    +      -       -      +
    142A  VAL*     1.3    77.0    -      -       -      +
    144A  MET*     1.3    58.4    +      -       -      +
    146A  SER*     2.5    34.8    +      -       -      +
    148A  THR*     4.5     5.7    +      -       -      -
    150A  ILE*     6.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ALA*     5.9     6.7    -      -       +      -
     68A  MET*     3.4    30.3    -      -       +      -
    140A  LYS      2.8    17.6    +      -       -      +
    141A  ILE      3.6     2.7    -      -       -      +
    143A  ARG*     1.3    77.3    -      -       -      +
    145A  TYR*     1.3    85.7    -      -       +      +
    146A  SER      3.3     7.5    -      -       -      +
    147A  PRO*     5.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ALA      4.6    13.2    +      -       -      -
     32A  PHE*     4.8    16.5    -      -       +      +
     62A  HIS*     4.4    16.6    +      -       -      -
     65A  ALA*     5.7     2.3    -      -       +      +
    141A  ILE*     3.0    39.7    +      -       +      +
    142A  VAL*     3.4    13.7    -      -       -      +
    144A  MET*     1.3    97.3    -      -       +      +
    146A  SER*     1.3    59.6    +      -       -      +
    147A  PRO*     3.8     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  VAL*     3.2    14.5    +      -       -      -
    143A  ARG*     2.5    23.5    -      -       -      +
    144A  MET      3.2     6.6    -      -       -      +
    145A  TYR*     1.3    79.6    -      -       -      +
    147A  PRO*     1.4    66.1    -      -       -      +
    148A  THR*     2.7    14.9    +      -       -      -
    149A  SER*     3.6    24.5    +      -       -      -
----------------------------------------------------------
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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