Contacts of the strand formed by residues 135 - 145 (chain A) in PDB entry 2JG8


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 GLY 135 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  VAL      3.7     1.8    +      -       -      -
    134A  PRO*     1.3    75.6    -      -       -      +
    136A  TYR*     1.3    64.5    +      -       -      -
    137A  TYR*     3.4    10.6    -      -       -      -
    186A  GLN*     3.5     3.4    -      -       -      -
    187A  LEU      2.9    33.0    +      -       -      -
    218A  LEU*     4.2     3.1    -      -       -      -
    220A  PHE      3.5    10.5    -      -       -      -
    221A  PRO*     3.9     0.9    -      -       -      -
    222A  SER*     3.4    17.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  GLY*     1.3    75.0    -      -       -      -
    137A  TYR*     1.3    53.8    +      -       -      +
    184A  VAL*     4.1    15.3    -      -       +      -
    185A  LEU      3.7     2.9    -      -       -      -
    186A  GLN*     3.6    44.9    +      -       +      -
    218A  LEU*     3.4     3.5    -      -       -      +
    219A  ILE*     2.7    34.3    +      -       +      +
    220A  PHE*     2.9    60.5    +      +       +      +
    222A  SER*     4.5    10.3    -      -       -      -
     88C  GLN*     4.6     7.8    +      -       +      +
     93C  VAL*     3.9    11.9    -      -       +      -
    117C  THR*     3.5    22.7    -      -       -      -
    119C  PRO*     3.7    27.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  PRO*     4.0    12.0    -      -       +      +
    129A  PHE*     3.7    28.2    -      +       -      -
    131A  CYS*     3.8    15.2    -      -       -      -
    132A  THR      4.6     1.4    +      -       -      -
    133A  VAL*     2.3    48.0    +      -       -      +
    135A  GLY      3.4    18.4    -      -       -      -
    136A  TYR*     1.3    75.0    -      -       -      +
    138A  TYR*     1.3    60.0    +      -       -      +
    139A  PHE*     3.4    22.5    +      +       +      -
    183A  MET      3.7     0.3    -      -       -      +
    184A  VAL*     3.1     5.4    -      -       -      -
    185A  LEU      2.8    33.1    +      -       -      +
    187A  LEU*     3.9    14.1    -      -       +      -
    217A  PHE*     3.3     8.1    -      -       -      +
    218A  LEU*     3.5    43.3    -      -       +      +
    219A  ILE*     3.9     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  TYR*     1.3    73.3    -      -       -      +
    139A  PHE*     1.3    67.7    -      -       -      +
    140A  THR*     3.8    21.3    -      -       +      -
    182A  GLY*     3.7    15.6    +      -       -      -
    183A  MET*     3.1    32.5    -      -       -      -
    184A  VAL*     3.8     6.1    -      -       +      -
    216A  GLY*     3.1     4.5    -      -       -      -
    217A  PHE*     2.8    74.6    +      +       +      -
    219A  ILE*     3.7    10.3    -      -       +      +
    142B  TYR*     5.1     3.6    -      +       -      -
    139C  TYR*     4.7     8.1    -      +       -      -
    141C  VAL*     3.2    28.6    -      -       +      +
    143C  HIS*     4.1     9.4    +      -       -      -
    210C  SER*     4.1    14.9    +      -       -      -
    212C  PHE*     3.8    15.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with PHE 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  PHE*     4.1    10.8    -      +       -      -
    129A  PHE*     3.6    48.0    -      +       +      -
    137A  TYR*     3.4    28.9    -      +       +      -
    138A  TYR*     1.3    76.4    -      -       -      +
    140A  THR*     1.3    61.8    +      -       -      +
    153A  ILE*     3.9    18.5    -      -       +      +
    182A  GLY*     2.9     3.6    -      -       -      -
    183A  MET*     2.9    36.4    +      -       +      +
    185A  LEU*     3.9    26.7    -      -       +      -
    187A  LEU*     3.8    12.3    -      -       +      -
    193A  VAL*     3.8    19.3    -      -       +      -
    214A  PHE*     4.3     8.7    -      +       +      -
    215A  SER      3.5     6.3    -      -       -      +
    216A  GLY*     3.8    16.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  TYR*     3.8    18.5    -      -       +      -
    139A  PHE*     1.3    76.7    -      -       -      +
    141A  PHE*     1.3    61.4    +      -       -      +
    142A  GLN*     3.0    21.1    +      -       -      +
    153A  ILE*     4.6     1.3    -      -       -      -
    181A  GLY      3.1    15.2    +      -       -      -
    182A  GLY*     3.9     1.5    -      -       -      -
    213A  VAL      4.9     0.2    -      -       -      -
    214A  PHE*     3.4     6.1    -      -       -      -
    215A  SER*     3.0    45.0    +      -       -      +
    217A  PHE*     5.6     1.3    -      -       +      -
    142B  TYR*     3.4    31.7    +      -       +      +
    143C  HIS*     4.3     8.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  THR*     1.3    76.4    +      -       -      +
    142A  GLN*     1.3    68.3    +      -       -      +
    143A  VAL*     3.9    10.1    -      -       +      -
    151A  LEU*     3.7    44.0    -      -       +      -
    153A  ILE*     3.7    41.5    -      -       +      -
    167A  PHE*     3.8    23.1    -      +       +      -
    179A  VAL*     4.0     7.6    -      -       +      -
    180A  SER*     3.2    26.9    -      -       -      -
    181A  GLY*     2.9    31.8    +      -       -      +
    195A  VAL*     4.6    12.6    -      -       +      -
    213A  VAL      3.3    12.6    -      -       -      +
    214A  PHE*     4.3     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  THR*     3.0    36.9    +      -       -      +
    141A  PHE*     1.3    79.0    +      -       -      +
    143A  VAL*     1.3    61.7    +      -       -      +
    144A  LEU      4.2     0.2    +      -       -      -
    178A  VAL*     3.9    15.3    -      -       +      -
    179A  VAL      3.4     5.4    -      -       -      -
    180A  SER*     4.1     1.7    -      -       -      -
    211A  ASP      4.4     2.1    -      -       -      +
    212A  SER*     3.3     5.0    -      -       -      -
    213A  VAL*     2.9    40.9    +      -       -      +
    215A  SER*     5.4     1.2    +      -       -      -
    142B  TYR*     4.2     4.9    +      -       -      -
    170B  PHE*     4.6     8.3    -      -       +      -
    182B  THR*     3.9    33.8    +      -       +      +
    183B  GLY*     3.9     5.8    -      -       -      -
    184B  GLY*     3.1    33.8    +      -       -      +
    143C  HIS*     5.5     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  VAL*     5.5     0.7    -      -       +      -
    111A  PHE*     4.0    30.5    -      -       +      -
    141A  PHE*     3.9    12.1    -      -       +      -
    142A  GLN*     1.3    76.9    -      -       -      +
    144A  LEU*     1.3    68.7    -      -       -      +
    145A  SER      3.7     0.7    +      -       -      -
    149A  ILE*     3.5    23.8    -      -       +      -
    151A  LEU*     3.5    26.9    -      -       +      -
    178A  VAL*     3.6     3.7    -      -       -      +
    179A  VAL*     2.8    39.6    +      -       +      +
    195A  VAL*     5.4     0.2    -      -       +      -
    204A  ILE*     4.0    16.8    -      -       +      -
    212A  SER*     3.7    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  GLN      4.2     0.6    +      -       -      -
    143A  VAL*     1.3    74.3    -      -       -      +
    145A  SER*     1.3    61.6    +      -       -      +
    176A  PHE*     3.6    35.0    -      -       +      -
    177A  GLN      3.4    18.2    -      -       -      +
    178A  VAL*     4.1     5.6    -      -       +      +
    204A  ILE*     3.5     7.3    -      -       -      -
    205A  TYR*     2.9    44.8    +      -       +      -
    210A  ALA*     3.4    37.5    -      -       +      -
    211A  ASP      4.2     8.0    +      -       -      +
    212A  SER*     2.8    20.2    +      -       -      +
    171B  CYS      3.5    22.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  VAL      3.7     0.4    +      -       -      -
    144A  LEU*     1.3    75.5    -      -       -      +
    146A  GLN*     1.3    69.6    +      -       -      +
    147A  TRP      3.4    12.2    +      -       -      -
    148A  GLU      4.0     2.4    -      -       -      -
    149A  ILE*     3.5    29.4    -      -       -      +
    169A  ASP*     5.6     1.3    -      -       -      -
    175A  LEU      3.6     0.2    -      -       -      +
    176A  PHE*     3.5     4.5    -      -       -      -
    177A  GLN*     2.8    39.3    +      -       -      -
    203A  HIS*     2.6    32.3    +      -       -      +
    205A  TYR*     4.2     1.8    -      -       -      +
----------------------------------------------------------
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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