Contacts of the strand formed by residues 132 - 143 (chain E) in PDB entry 6GJH


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 132 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128E  GLN*     3.2    11.4    -      -       -      +
    129E  ASP*     2.8    40.8    +      -       -      +
    131E  HIS*     1.3    80.4    -      -       -      +
    133E  TYR*     1.3    67.8    +      -       -      -
    140F  ARG*     4.1     0.9    -      -       -      +
    141F  LYS      3.6     8.5    -      -       -      -
    142F  TYR*     5.3     0.9    -      -       -      -
    143F  THR      6.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 133 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126E  GLU*     3.5    32.5    -      -       +      +
    127E  ARG*     3.2    16.6    -      -       -      +
    128E  GLN*     4.0    33.0    +      -       +      -
    132E  GLY*     1.3    79.1    -      -       -      -
    134E  ILE*     1.3    62.3    +      -       -      +
    139F  THR      4.4     0.7    -      -       -      -
    140F  ARG*     3.2     9.3    -      -       -      +
    141F  LYS*     2.8    51.3    +      -       +      -
    143F  THR*     4.7    15.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 134 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124E  HIS*     3.6     5.2    -      -       +      -
    126E  GLU*     3.3     4.0    -      -       -      +
    127E  ARG*     2.9    47.0    +      -       +      +
    129E  ASP*     4.1    13.9    -      -       +      +
    133E  TYR*     1.3    76.6    -      -       -      +
    135E  SER*     1.3    74.2    +      -       -      +
    136E  ARG*     3.7    43.3    -      -       +      +
    138F  PHE*     4.1    11.7    -      -       +      -
    139F  THR      3.3    14.4    -      -       -      +
    140F  ARG*     3.5    41.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 135 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124E  HIS*     3.6    17.5    -      -       -      -
    125E  GLU*     4.6     0.9    -      -       -      -
    126E  GLU*     3.8    19.7    +      -       -      +
    134E  ILE*     1.3    76.5    -      -       -      +
    136E  ARG*     1.3    64.7    +      -       -      +
    137F  CYS*     6.2     0.2    -      -       -      -
    138F  PHE*     3.1     8.5    -      -       -      +
    139F  THR*     2.9    50.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 136 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103E  HIS*     3.4    55.3    +      -       -      +
    104E  PHE*     3.7    15.8    -      -       +      -
    123E  LYS*     3.4     2.6    +      -       -      +
    124E  HIS*     3.2    48.4    +      -       -      +
    127E  ARG*     4.0    12.1    -      -       -      +
    129E  ASP*     5.1     4.4    +      -       -      +
    134E  ILE*     3.7    39.8    -      -       +      +
    135E  SER*     1.3    80.6    -      -       -      +
    137E  CYS*     1.3    65.1    +      -       -      +
     84F  GLY*     5.2    10.3    +      -       -      -
    137F  CYS*     3.5     6.5    -      -       -      +
    138F  PHE*     4.5     7.0    -      -       +      -
    140F  ARG*     4.2    10.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 137 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104E  PHE*     4.6     0.9    -      -       -      -
    122E  GLY      3.2    11.9    -      -       -      +
    123E  LYS*     4.2    22.2    -      -       +      +
    136E  ARG*     1.3    76.8    -      -       -      +
    138E  PHE*     1.3    68.0    +      -       -      +
    136F  ARG*     3.5     2.8    -      -       -      +
    137F  CYS*     2.0    78.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 138 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99E  LEU*     4.2    16.2    -      -       +      -
    101E  VAL*     3.9    24.5    -      -       +      -
    104E  PHE*     3.8    33.0    -      +       -      -
    109E  LEU*     4.4     2.2    -      -       +      -
    120E  ILE*     3.7    26.7    -      -       +      -
    121E  THR*     3.4     2.6    -      -       -      +
    122E  GLY*     2.9    51.4    +      -       -      +
    137E  CYS*     1.3    79.2    -      -       -      +
    139E  THR*     1.3    73.8    +      -       -      +
    140E  ARG*     3.9     8.7    -      -       +      -
    134F  ILE*     4.3    13.5    -      -       +      -
    135F  SER*     3.2    16.4    -      -       -      +
    136F  ARG*     4.4     9.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 139 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119E  GLU*     3.7    33.4    -      -       +      +
    120E  ILE      3.2     5.4    -      -       -      +
    121E  THR*     3.4    18.4    +      -       -      +
    138E  PHE*     1.3    80.2    +      -       -      +
    140E  ARG*     1.3    63.2    +      -       -      +
    141E  LYS*     4.7    11.2    -      -       -      +
    126F  GLU*     5.4     3.6    -      -       -      +
    133F  TYR      4.1     0.5    -      -       -      +
    134F  ILE*     3.2     4.3    -      -       -      -
    135F  SER*     3.0    41.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 140 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99E  LEU*     4.1    23.2    -      -       +      +
    118E  VAL      3.8     0.5    -      -       -      +
    119E  GLU*     3.5     3.3    -      -       -      +
    120E  ILE*     2.8    36.3    +      -       +      +
    138E  PHE*     3.9    13.4    -      -       +      -
    139E  THR*     1.3    74.0    -      -       -      +
    141E  LYS*     1.3    68.0    +      -       -      +
    142E  TYR*     3.0    38.6    -      -       +      -
    129F  ASP*     2.7    42.0    +      -       -      -
    131F  HIS*     3.5    24.9    -      -       -      +
    132F  GLY      3.6    12.7    +      -       -      +
    133F  TYR      3.4     7.0    -      -       -      +
    134F  ILE*     3.3    29.9    -      -       +      +
    136F  ARG*     3.7     5.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 141 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117E  VAL*     3.9    19.3    -      -       +      -
    118E  VAL      3.2     9.9    -      -       -      +
    119E  GLU*     4.0    28.0    -      -       +      -
    139E  THR*     4.7     8.7    -      -       +      +
    140E  ARG*     1.3    80.4    -      -       -      +
    142E  TYR*     1.3    72.1    +      -       -      +
    126F  GLU*     2.7    35.7    +      -       -      +
    132F  GLY*     4.6     4.2    -      -       -      -
    133F  TYR*     3.1    33.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 142 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95E  TRP*     4.3    19.5    -      +       +      -
     97E  VAL*     3.9    40.2    -      -       +      -
     98E  SER      4.3     6.8    +      -       -      -
     99E  LEU*     4.3    18.7    -      -       +      +
    117E  VAL*     3.3     5.8    -      -       -      -
    118E  VAL*     2.8    38.1    +      -       +      +
    120E  ILE*     3.7    30.3    -      -       +      -
    140E  ARG*     3.0    34.3    +      -       +      -
    141E  LYS*     1.3    77.9    -      -       -      +
    143E  THR*     1.3    62.8    +      -       -      +
    144E  LEU      3.7     0.3    +      -       -      -
    131F  HIS*     4.2    25.3    -      -       +      +
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Residues in contact with THR 143 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95E  TRP*     4.7     7.4    +      -       -      -
    116E  GLY      3.9     9.4    -      -       -      +
    117E  VAL*     4.3    13.2    -      -       +      +
    142E  TYR*     1.3    71.6    -      -       -      +
    144E  LEU*     1.3    75.3    +      -       -      +
    145E  PRO*     4.3     2.1    -      -       -      +
----------------------------------------------------------
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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