Contacts of the strand formed by residues 135 - 145 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133D  VAL      3.6     1.4    +      -       -      -
    134D  PRO*     1.3    74.8    -      -       -      +
    136D  TYR*     1.3    65.6    +      -       -      -
    137D  TYR*     3.4    10.7    -      -       -      -
    186D  GLN*     3.4     3.4    -      -       -      -
    187D  LEU      2.9    33.9    +      -       -      -
    218D  LEU*     4.3     2.5    -      -       -      -
    220D  PHE      3.3    11.2    -      -       -      -
    221D  PRO*     3.9     0.4    -      -       -      -
    222D  SER*     3.5    17.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 136 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135D  GLY*     1.3    74.5    -      -       -      -
    137D  TYR*     1.3    55.0    +      -       -      +
    184D  VAL*     4.1    18.2    -      -       +      -
    185D  LEU      3.7     1.8    -      -       -      -
    186D  GLN*     3.2    47.3    +      -       +      -
    218D  LEU*     3.5     2.1    -      -       -      +
    219D  ILE*     2.5    42.7    +      -       +      +
    220D  PHE*     2.8    57.0    +      +       +      +
    222D  SER*     4.6     5.6    -      -       -      -
     89F  LYS*     3.6    14.8    +      -       -      -
     93F  VAL*     3.9    11.7    -      -       +      -
    117F  THR*     3.5    22.7    +      -       -      -
    119F  PRO*     3.5    27.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 137 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93D  PRO*     4.0    13.5    -      -       +      +
    129D  PHE*     3.6    30.1    -      +       -      -
    131D  CYS*     4.0    12.2    -      -       -      -
    132D  THR      4.6     1.7    +      -       -      -
    133D  VAL*     2.4    44.5    +      -       -      +
    135D  GLY      3.4    17.9    -      -       -      -
    136D  TYR*     1.3    74.1    -      -       -      +
    138D  TYR*     1.3    59.4    +      -       -      +
    139D  PHE*     3.4    22.9    -      +       +      -
    183D  MET      3.8     0.2    -      -       -      +
    184D  VAL*     3.1     6.6    -      -       -      +
    185D  LEU      2.8    34.0    +      -       -      +
    187D  LEU*     4.0    13.5    -      -       +      -
    217D  PHE*     3.2    19.5    -      -       -      -
    218D  LEU*     3.5    31.1    -      -       +      +
    219D  ILE*     3.8     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 138 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137D  TYR*     1.3    73.5    -      -       -      +
    139D  PHE*     1.3    74.9    +      -       -      +
    140D  THR*     3.9    16.1    +      -       +      -
    182D  GLY*     3.8    14.6    +      -       -      -
    183D  MET*     3.2    32.5    -      -       -      -
    184D  VAL*     3.7    12.3    -      -       +      -
    216D  GLY*     3.0     5.5    -      -       -      -
    217D  PHE*     2.9    70.2    +      +       +      -
    219D  ILE*     3.9     9.7    -      -       +      +
    142E  TYR*     5.2     3.6    -      +       -      -
    139F  TYR*     4.8     8.3    -      +       -      -
    141F  VAL*     3.3    27.8    -      -       +      +
    143F  HIS*     4.0    11.1    +      -       -      -
    210F  SER*     4.0    14.5    +      -       -      -
    212F  PHE*     3.8    10.8    -      +       +      -
----------------------------------------------------------
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Residues in contact with PHE 139 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95D  PHE*     3.9    12.6    -      +       -      -
    129D  PHE*     3.6    48.2    -      +       +      -
    137D  TYR*     3.4    28.0    -      +       +      -
    138D  TYR*     1.3    78.3    -      -       -      +
    140D  THR*     1.3    62.0    -      -       -      +
    153D  ILE*     4.2    20.0    -      -       +      -
    182D  GLY*     2.9    24.1    -      -       -      -
    183D  MET*     2.9    15.7    +      -       +      +
    185D  LEU*     3.8    23.8    -      -       +      -
    187D  LEU*     3.7    13.9    -      -       +      -
    193D  VAL*     4.0    19.1    -      -       +      -
    214D  PHE*     4.3     8.3    -      +       +      -
    215D  SER      3.5     4.3    -      -       -      +
    216D  GLY*     3.8    16.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 140 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138D  TYR*     3.9    16.7    -      -       +      -
    139D  PHE*     1.3    77.4    -      -       -      +
    141D  PHE*     1.3    62.2    +      -       -      +
    142D  GLN*     3.4    17.6    +      -       -      +
    153D  ILE*     4.4     1.7    -      -       -      +
    181D  GLY      2.8    20.6    +      -       -      -
    182D  GLY*     3.9     1.2    -      -       -      -
    214D  PHE*     3.5     5.5    -      -       -      -
    215D  SER*     2.9    50.6    +      -       -      +
    216D  GLY*     6.0     0.2    -      -       -      -
    217D  PHE*     5.9     1.1    -      -       +      -
    142E  TYR*     3.4    27.5    +      -       +      +
    184E  GLY*     5.9     0.2    -      -       -      -
    143F  HIS*     4.1     9.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 141 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111D  PHE*     5.0     0.2    -      -       +      -
    140D  THR*     1.3    74.9    +      -       -      +
    142D  GLN*     1.3    71.0    +      -       -      +
    143D  VAL*     3.9     8.5    -      -       +      -
    151D  LEU*     3.6    46.7    -      -       +      -
    152D  SER      4.8     0.9    -      -       -      -
    153D  ILE*     3.6    41.3    -      -       +      -
    167D  PHE*     3.8    30.3    -      +       +      -
    179D  VAL*     3.8    13.9    -      -       +      -
    180D  SER*     3.2    36.2    -      -       -      -
    181D  GLY      3.0    17.5    +      -       -      +
    195D  VAL*     4.3    12.1    -      -       +      -
    213D  VAL      3.3    12.8    -      -       -      +
    214D  PHE*     4.4    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140D  THR*     3.4    35.4    +      -       -      +
    141D  PHE*     1.3    79.2    +      -       -      +
    143D  VAL*     1.3    60.5    +      -       -      +
    178D  VAL*     3.8    15.3    -      -       +      -
    179D  VAL      3.4     6.3    -      -       -      -
    180D  SER*     4.3     1.7    -      -       -      -
    211D  ASP      4.4     2.8    -      -       -      +
    212D  SER*     3.3     4.7    -      -       -      -
    213D  VAL*     2.9    43.2    +      -       -      +
    215D  SER*     5.4     1.0    +      -       -      -
    142E  TYR*     4.3     4.9    +      -       -      -
    170E  PHE*     4.2     9.6    -      -       +      -
    182E  THR*     3.6    33.6    +      -       +      +
    183E  GLY*     3.9     3.6    -      -       -      -
    184E  GLY*     3.1    34.4    +      -       -      +
    143F  HIS*     5.6     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 143 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109D  VAL*     5.5     0.9    -      -       +      -
    111D  PHE*     4.0    27.6    -      -       +      -
    141D  PHE*     3.9    11.4    -      -       +      -
    142D  GLN*     1.3    78.1    -      -       -      +
    144D  LEU*     1.3    65.6    +      -       -      +
    145D  SER*     3.8     0.5    +      -       -      -
    149D  ILE*     5.0     2.5    -      -       +      -
    151D  LEU*     3.3    36.8    -      -       +      -
    177D  GLN      3.6     0.5    -      -       -      +
    178D  VAL*     3.3     5.5    -      -       -      +
    179D  VAL*     2.9    39.8    +      -       +      +
    195D  VAL*     5.4     0.2    -      -       +      -
    204D  ILE*     3.8    30.7    -      -       +      -
    211D  ASP      5.2     0.2    -      -       -      -
    212D  SER*     3.6    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 144 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142D  GLN      4.3     0.4    +      -       -      -
    143D  VAL*     1.3    73.9    -      -       -      +
    145D  SER*     1.3    60.6    +      -       -      +
    176D  PHE*     3.9    26.5    -      -       +      -
    177D  GLN      3.6    12.3    -      -       -      +
    178D  VAL*     3.8     7.0    -      -       +      +
    204D  ILE*     3.6     9.7    -      -       -      +
    205D  TYR*     2.8    51.8    +      -       +      +
    210D  ALA*     3.2    36.6    -      -       +      -
    211D  ASP      3.9     8.3    -      -       -      +
    212D  SER*     2.8    17.9    +      -       -      +
    171E  CYS      3.0    29.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 145 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143D  VAL      5.0     0.7    -      -       -      -
    144D  LEU*     1.3    74.7    -      -       -      +
    146D  GLN*     1.3    71.4    +      -       -      +
    147D  TRP      3.3    13.7    +      -       -      -
    149D  ILE*     3.4    30.5    -      -       -      +
    169D  ASP*     5.5     0.9    -      -       -      -
    175D  LEU      3.6     0.2    -      -       -      +
    176D  PHE*     3.4     5.7    -      -       -      -
    177D  GLN*     2.8    38.9    +      -       -      +
    203D  HIS*     2.8    31.0    +      -       -      +
    204D  ILE*     4.9     0.2    -      -       -      -
    205D  TYR*     4.2     2.0    -      -       -      +
----------------------------------------------------------
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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