Contacts of the strand formed by residues 130 - 138 (chain G) 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 VAL 130 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29G  VAL*     4.1     6.3    -      -       -      -
     75G  ALA      3.6    17.7    -      -       -      +
     76G  GLY      4.9     0.2    -      -       -      -
     77G  LEU      3.9    10.3    -      -       -      +
     80G  ASP*     3.7    22.7    -      -       +      -
     81G  ALA*     3.9    24.5    -      -       +      -
     84G  LEU*     3.9    27.4    -      -       +      +
    128G  TYR*     3.0    14.9    +      -       +      +
    129G  GLY*     1.3    79.2    -      -       -      +
    131G  GLY*     1.3    74.8    +      -       -      +
    132G  LEU*     4.3     4.9    +      -       +      -
    147G  THR*     4.2     4.5    +      -       -      +
    148G  CYS      4.4     1.4    -      -       -      -
    149G  PRO*     3.7    17.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 131 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29G  VAL*     3.7    13.9    -      -       -      +
     74G  ILE*     3.7     1.2    -      -       -      -
     75G  ALA*     2.9    37.7    +      -       -      -
    130G  VAL*     1.3    75.1    -      -       -      +
    132G  LEU*     1.3    68.4    +      -       -      +
    147G  THR      3.2    12.1    -      -       -      -
    148G  CYS*     6.1     0.2    -      -       -      -
    161G  ILE*     3.8    14.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 132 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72G  ILE*     4.3     9.9    -      -       +      -
     73G  SER      3.6     4.7    -      -       -      +
     74G  ILE*     3.5    29.8    -      -       +      -
     81G  ALA*     5.3     2.7    -      -       +      -
     84G  LEU*     3.9    29.4    -      -       +      -
     88G  MET*     4.0    24.9    -      -       -      -
    112G  ILE*     4.5     4.3    -      -       +      -
    130G  VAL*     4.4     7.9    -      -       +      +
    131G  GLY*     1.3    84.8    -      -       -      +
    133G  LEU*     1.3    64.3    +      -       -      +
    134G  ILE*     4.2    22.2    -      -       +      -
    145G  PHE      4.3     0.2    -      -       -      -
    146G  GLN*     3.3     8.3    -      -       -      +
    147G  THR*     2.9    44.6    +      -       -      +
    161G  ILE*     4.0     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 133 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35G  THR*     3.7    43.1    -      -       +      +
     36G  VAL*     4.0    14.8    -      -       -      +
     37G  GLY*     4.0     4.7    -      -       -      +
     46G  LEU*     4.0    14.5    -      -       +      +
     72G  ILE*     3.3     4.2    -      -       -      +
     73G  SER*     2.8    41.5    +      -       -      +
    132G  LEU*     1.3    82.8    -      -       -      +
    134G  ILE*     1.3    61.3    +      -       -      +
    144G  ILE*     4.9     5.4    -      -       +      -
    145G  PHE      3.2     9.9    -      -       -      +
    146G  GLN*     4.1    17.0    -      -       +      -
    159G  MET*     4.1    21.3    -      -       +      +
    160G  SER*     4.4     0.4    -      -       -      -
    161G  ILE*     4.0    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 134 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70G  ILE*     4.0    20.0    -      -       +      -
     71G  GLY      3.6     9.4    -      -       -      +
     72G  ILE*     3.8    15.0    -      -       +      -
     88G  MET*     4.0     6.3    -      -       +      -
    105G  VAL*     4.1    19.2    -      -       +      +
    108G  LEU*     5.3     0.7    -      -       +      -
    109G  VAL*     3.8    22.2    -      -       +      -
    112G  ILE*     3.9    23.8    -      -       +      -
    132G  LEU*     4.2     9.6    -      -       +      -
    133G  LEU*     1.3    78.5    -      -       -      +
    135G  ALA*     1.3    59.9    +      -       -      +
    136G  GLY      4.1     0.2    +      -       -      -
    143G  HIS      3.3     2.3    -      -       -      +
    144G  ILE*     3.2     9.5    -      -       -      +
    145G  PHE*     3.0    37.3    +      -       +      +
    147G  THR*     4.0    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 135 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44G  ALA*     4.0    13.9    -      -       +      +
     46G  LEU*     3.6    30.1    -      -       +      -
     70G  ILE*     3.5     2.3    -      -       -      +
     71G  GLY      2.9    32.3    +      -       -      +
    133G  LEU      4.0     0.8    +      -       -      -
    134G  ILE*     1.3    74.4    -      -       -      +
    136G  GLY*     1.3    58.4    +      -       -      +
    143G  HIS      3.3     4.7    -      -       -      -
    144G  ILE*     3.7    14.1    -      -       +      -
    215G  VAL*     3.9     7.6    -      -       +      +
    221G  PHE*     4.3     8.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 136 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44G  ALA*     4.0     4.2    -      -       -      +
     69G  HIS      3.1    12.1    -      -       -      -
     70G  ILE*     4.2     2.0    -      -       -      -
    105G  VAL*     4.1    18.8    -      -       -      +
    134G  ILE      4.1     0.4    +      -       -      -
    135G  ALA*     1.3    76.8    -      -       -      +
    137G  TYR*     1.3    61.0    +      -       -      +
    141G  GLY      4.5     0.2    -      -       -      -
    142G  PRO*     3.3     4.0    -      -       -      +
    143G  HIS*     2.9    33.1    +      -       -      +
    215G  VAL*     3.8     8.1    -      -       -      +
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Residues in contact with TYR 137 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41G  LYS      4.8     2.0    +      -       -      -
     42G  THR*     3.6    23.7    -      -       -      -
     69G  HIS*     3.2    30.1    +      -       +      +
    105G  VAL*     4.1     2.2    -      -       -      +
    136G  GLY*     1.3    73.9    -      -       -      -
    138G  ASP*     1.3    77.0    +      -       -      +
    141G  GLY*     3.4    21.8    -      -       -      -
    142G  PRO*     3.4    31.2    -      -       +      -
    215G  VAL*     4.4     6.1    -      -       +      -
    216G  GLY*     4.0    22.7    -      -       -      +
    217G  LYS*     3.4    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 138 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69G  HIS*     5.0     3.8    -      -       +      -
    102G  PRO*     6.6     0.4    -      -       +      -
    104G  PRO*     4.0    11.7    -      -       +      +
    105G  VAL*     3.2    33.1    +      -       +      +
    106G  SER*     4.4     2.4    +      -       -      -
    137G  TYR*     1.3    92.3    -      -       -      +
    139G  ASP*     1.3    63.9    +      -       -      +
    140G  MET*     2.6    30.8    +      -       -      +
    141G  GLY      2.9    20.2    +      -       -      -
    143G  HIS*     3.2    22.5    +      -       -      -
     81g  HIS*     3.6    14.0    +      -       -      +
----------------------------------------------------------
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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