Contacts of the strand formed by residues 133 - 143 (chain D) 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 TYR 133 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  THR      4.6     0.2    +      -       -      -
    150B  PRO*     3.6    30.6    -      -       -      +
    151B  THR*     3.8    38.2    +      -       +      +
    140C  ARG*     3.6     3.5    -      -       -      +
    141C  LYS*     3.2    39.4    +      -       +      +
    126D  GLU*     3.9    30.7    -      -       +      +
    127D  ARG*     3.3    11.9    -      -       -      -
    128D  GLN*     3.2    49.8    +      -       +      -
    132D  GLY*     1.3    73.9    -      -       -      -
    134D  ILE*     1.3    61.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 134 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138C  PHE*     4.2    19.3    -      -       +      -
    139C  THR      3.3    15.3    -      -       -      +
    140C  ARG*     3.2    32.8    -      -       +      +
    124D  HIS*     3.3     9.7    -      -       +      -
    126D  GLU*     4.1     3.8    -      -       -      +
    127D  ARG      2.8    37.8    +      -       -      +
    129D  ASP*     3.6    26.5    -      -       +      +
    133D  TYR*     1.3    76.7    -      -       -      +
    135D  SER*     1.3    71.1    +      -       -      +
    136D  ARG*     3.7    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 135 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138C  PHE*     3.2     8.4    -      -       -      +
    139C  THR*     3.0    45.2    +      -       -      -
    124D  HIS*     3.5    17.9    -      -       -      -
    125D  GLU*     3.9     1.6    -      -       -      -
    126D  GLU*     3.8    22.9    +      -       -      +
    134D  ILE*     1.3    74.5    -      -       -      +
    136D  ARG*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 136 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137C  CYS*     3.5     7.9    -      -       -      +
    138C  PHE*     4.4     6.3    -      -       +      +
    140C  ARG*     3.7    11.1    -      -       -      +
    103D  HIS*     3.4    50.2    +      -       -      +
    104D  PHE*     3.9    16.4    -      -       +      -
    123D  LYS*     3.5     3.1    -      -       -      +
    124D  HIS*     3.2    59.3    +      -       -      +
    129D  ASP*     3.0    26.7    +      -       -      +
    130D  GLU*     5.2     0.4    +      -       -      -
    134D  ILE*     3.7    26.0    -      -       +      +
    135D  SER*     1.3    80.0    -      -       -      +
    137D  CYS*     1.3    64.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 137 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135C  SER      6.2     0.2    -      -       -      -
    136C  ARG*     3.5     2.2    -      -       -      +
    137C  CYS*     2.0    77.6    +      -       -      +
    104D  PHE*     4.8     0.7    -      -       -      -
    122D  GLY      3.3    12.1    -      -       -      +
    123D  LYS*     4.4    14.6    -      -       +      -
    136D  ARG*     1.3    76.8    -      -       -      +
    138D  PHE*     1.3    67.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 138 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134C  ILE*     4.3    14.1    -      -       +      -
    135C  SER*     3.1    15.0    -      -       -      +
    136C  ARG*     4.4     7.0    -      -       +      +
     99D  LEU*     4.2    19.1    -      -       +      -
    101D  VAL*     3.8    24.0    -      -       +      -
    104D  PHE*     3.6    37.0    -      +       -      -
    109D  LEU*     4.3     7.4    -      -       +      -
    120D  ILE*     3.8    20.0    -      -       +      -
    121D  THR*     3.4     3.8    -      -       -      -
    122D  GLY*     3.1    49.0    +      -       -      +
    137D  CYS*     1.3    79.5    -      -       -      +
    139D  THR*     1.3    76.0    +      -       -      +
    140D  ARG*     4.3     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 139 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126C  GLU*     5.3     4.1    -      -       -      +
    133C  TYR      4.4     0.3    -      -       -      -
    134C  ILE*     3.3     6.1    -      -       -      +
    135C  SER*     2.9    44.6    +      -       -      -
    119D  GLU*     3.9    32.5    -      -       +      +
    120D  ILE      3.3     5.2    -      -       -      -
    121D  THR*     3.5    14.8    -      -       +      +
    138D  PHE*     1.3    79.1    +      -       -      +
    140D  ARG*     1.3    64.5    +      -       -      +
    141D  LYS*     4.7    11.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 140 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129C  ASP*     3.2    38.4    +      -       -      -
    131C  HIS*     3.9    16.3    -      -       -      +
    132C  GLY      4.0     4.4    -      -       -      +
    133C  TYR      3.2    10.0    +      -       -      +
    134C  ILE*     3.6    32.9    -      -       +      +
    136C  ARG*     4.0    10.9    -      -       -      +
     86D  SER*     3.4    10.3    +      -       -      -
     99D  LEU*     4.1    18.0    -      -       +      +
    118D  VAL      3.8     0.3    -      -       -      +
    119D  GLU*     3.5     3.5    -      -       -      +
    120D  ILE*     2.8    41.5    +      -       +      +
    138D  PHE*     4.1     9.4    -      -       +      -
    139D  THR*     1.3    75.4    -      -       -      +
    141D  LYS*     1.3    67.1    +      -       -      +
    142D  TYR*     3.2    35.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 141 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126C  GLU*     2.8    35.5    +      -       -      +
    132C  GLY*     3.5     8.0    -      -       -      -
    133C  TYR*     3.1    39.6    +      -       +      +
    117D  VAL*     3.9    17.0    -      -       +      -
    118D  VAL      3.2     9.6    -      -       -      +
    119D  GLU*     4.2    27.8    +      -       +      -
    139D  THR*     4.7     6.7    -      -       +      +
    140D  ARG*     1.3    80.0    -      -       -      +
    142D  TYR*     1.3    65.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 142 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131C  HIS*     3.9    31.4    -      -       +      -
    132C  GLY*     5.3     2.0    -      -       -      -
     86D  SER*     2.3    39.9    +      -       -      -
     88D  ILE*     5.1     2.9    -      -       +      -
     95D  TRP*     4.0    23.6    -      +       +      -
     97D  VAL*     4.2    32.7    -      -       +      +
     99D  LEU*     4.3     6.8    -      -       -      +
    117D  VAL*     3.3     8.1    -      -       -      +
    118D  VAL*     3.0    40.9    +      -       +      +
    120D  ILE*     3.8    28.9    -      -       +      -
    140D  ARG*     3.2    20.4    -      -       +      -
    141D  LYS*     1.3    77.2    -      -       -      +
    143D  THR*     1.3    61.2    +      -       -      +
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Residues in contact with THR 143 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133C  TYR*     5.9     3.3    -      -       -      -
     95D  TRP*     4.2    14.1    +      -       -      -
    116D  GLY      3.8    10.8    -      -       -      +
    117D  VAL*     4.7     7.3    -      -       +      +
    142D  TYR*     1.3    72.9    -      -       -      +
    144D  LEU*     1.3    74.8    +      -       -      +
    145D  PRO*     4.0     0.9    -      -       -      +
----------------------------------------------------------
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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