Contacts of the helix formed by residues 494 - 508 (chain Z) in PDB entry 5GJQ


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 ARG 494 (chain Z).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489Z  TYR*     4.2     8.7    -      -       +      +
    492Z  SER      4.0     6.3    -      -       -      +
    493Z  ASN*     1.3    75.7    -      -       -      +
    495Z  GLU*     1.3    63.5    +      -       -      +
    496Z  ASP*     3.5    16.7    +      -       +      +
    497Z  VAL*     3.9    14.1    +      -       +      +
    498Z  LEU*     4.0     7.1    +      -       -      +
    525Z  ILE*     4.9     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 495 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494Z  ARG*     1.3    71.5    -      -       -      +
    496Z  ASP*     1.3    53.0    +      -       -      +
    498Z  LEU*     3.0    12.4    +      -       +      +
    499Z  THR*     2.4    38.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 496 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494Z  ARG*     3.2    10.6    -      -       +      +
    495Z  GLU*     1.3    75.3    -      -       -      +
    497Z  VAL*     1.3    50.7    -      -       -      +
    499Z  THR*     2.7    11.8    +      -       -      -
    500Z  LEU*     2.2    41.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 497 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    485Z  LEU*     4.7    22.2    -      -       +      +
    489Z  TYR*     5.5     6.1    -      -       +      -
    494Z  ARG*     3.9    14.0    +      -       +      +
    495Z  GLU      3.4     0.4    -      -       -      -
    496Z  ASP*     1.3    75.9    -      -       -      +
    498Z  LEU*     1.3    51.4    +      -       -      +
    500Z  LEU*     3.2     9.1    -      -       -      +
    501Z  LEU*     2.3    41.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 498 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494Z  ARG      4.0     3.6    +      -       -      +
    495Z  GLU*     3.0    19.5    +      -       +      +
    497Z  VAL*     1.3    76.3    -      -       -      +
    499Z  THR*     1.3    56.1    +      -       -      +
    501Z  LEU*     2.5    11.4    +      -       -      -
    502Z  LEU*     2.2    44.6    +      -       +      +
    522Z  CYS*     5.7    11.8    -      -       +      +
    534Z  VAL*     6.5     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 499 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    495Z  GLU*     2.4    24.3    +      -       -      -
    496Z  ASP*     2.7    14.5    +      -       -      -
    498Z  LEU*     1.3    71.4    -      -       -      +
    500Z  LEU*     1.3    58.4    +      -       -      +
    502Z  LEU*     4.2     8.2    -      -       -      +
    503Z  PRO*     4.5    11.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 500 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    470Z  VAL*     6.5     1.3    -      -       +      -
    471Z  LEU*     6.3     2.9    -      -       -      -
    496Z  ASP      2.2    26.6    +      -       -      +
    497Z  VAL*     3.2    14.6    -      -       -      +
    498Z  LEU      2.8     2.2    +      -       -      -
    499Z  THR*     1.3    70.4    -      -       -      +
    501Z  LEU*     1.3    59.7    +      -       +      +
    503Z  PRO*     4.0     2.6    -      -       -      +
    504Z  VAL*     3.5    17.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 501 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497Z  VAL      2.3    32.4    +      -       -      +
    498Z  LEU*     2.5     4.1    +      -       -      +
    500Z  LEU*     1.3    68.0    -      -       +      +
    502Z  LEU*     1.3    51.4    +      -       -      +
    504Z  VAL*     2.9    10.0    +      -       +      -
    505Z  MET*     2.1    42.9    +      -       +      +
    518Z  THR*     4.1    26.0    -      -       -      -
    522Z  CYS*     5.8     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 502 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    498Z  LEU*     2.2    42.9    +      -       +      +
    499Z  THR*     4.2     5.6    -      -       -      +
    501Z  LEU*     1.3    65.2    -      -       -      +
    503Z  PRO*     1.3    51.2    -      -       -      +
    505Z  MET*     3.0    10.5    -      -       -      +
    506Z  GLY*     2.4    32.4    +      -       -      -
    537Z  THR*     5.3    14.4    -      -       -      -
    541Z  THR*     5.6     1.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 503 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    498Z  LEU      4.3     0.4    -      -       -      -
    499Z  THR      4.5     8.8    -      -       -      +
    500Z  LEU      4.0     6.3    -      -       -      +
    501Z  LEU      3.3     0.2    -      -       -      -
    502Z  LEU*     1.3    74.8    -      -       -      +
    504Z  VAL*     1.3    57.2    +      -       -      +
    506Z  GLY*     3.0     4.4    +      -       -      +
    507Z  ASP*     2.3    36.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 504 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    473Z  ASN*     5.0    13.7    -      -       +      -
    500Z  LEU      3.5    14.6    +      -       -      +
    501Z  LEU*     2.9    12.9    +      -       +      +
    503Z  PRO*     1.3    77.1    -      -       -      +
    505Z  MET*     1.3    51.7    +      -       -      +
    507Z  ASP*     3.0    12.5    +      -       -      +
    508Z  SER      2.6    29.6    +      -       -      -
    513Z  GLU*     3.9    16.1    -      -       +      +
    515Z  ALA*     3.1    17.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 505 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    501Z  LEU*     2.1    28.7    +      -       +      +
    502Z  LEU*     3.0    18.8    -      -       -      +
    504Z  VAL*     1.3    65.7    -      -       -      +
    506Z  GLY*     1.3    58.3    +      -       -      +
    508Z  SER*     2.8    26.9    +      -       -      -
    515Z  ALA*     3.4    17.2    -      -       +      +
    518Z  THR*     6.2     0.2    -      -       -      -
    519Z  ALA*     6.0     5.6    -      -       +      +
    541Z  THR*     5.2    12.3    -      -       -      -
    546Z  SER*     3.9     3.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 506 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    502Z  LEU      2.4    23.3    +      -       -      -
    503Z  PRO*     3.1     6.7    -      -       -      -
    505Z  MET*     1.3    67.0    -      -       -      +
    507Z  ASP*     1.3    60.7    +      -       -      +
    541Z  THR*     5.1     4.3    -      -       -      -
    546Z  SER*     3.3    26.4    -      -       -      -
    547Z  GLU*     3.5     8.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 507 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    473Z  ASN*     6.2     2.7    -      -       +      -
    503Z  PRO      2.3    26.5    +      -       -      +
    504Z  VAL*     3.1    18.6    -      -       -      +
    506Z  GLY*     1.3    71.1    -      -       -      +
    508Z  SER*     1.3    65.8    +      -       -      +
    509Z  LYS*     3.6     4.7    -      -       +      +
    513Z  GLU*     4.3     9.6    -      -       +      -
    547Z  GLU*     3.0    12.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 508 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    504Z  VAL      2.6    16.2    +      -       -      -
    505Z  MET*     2.8    18.7    +      -       -      +
    506Z  GLY      3.9     0.2    -      -       -      -
    507Z  ASP*     1.3    77.0    -      -       -      +
    509Z  LYS*     1.3    58.1    +      -       -      +
    510Z  SER      4.3     0.4    -      -       -      -
    515Z  ALA*     4.7     2.5    -      -       -      -
    516Z  GLY      5.9     1.1    -      -       -      +
    546Z  SER*     3.2    28.9    -      -       -      -
    547Z  GLU*     3.5     4.0    -      -       -      -
    548Z  THR*     3.5    24.0    +      -       -      -
    549Z  GLU      5.0     1.6    -      -       -      -
    554Z  TYR*     5.6     8.7    -      -       -      -
----------------------------------------------------------
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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