Contacts of the strand formed by residues 135 - 142 (chain C) in PDB entry 4JZJ


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 GLN 135 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133C  ASP      4.7     2.7    -      -       -      +
    134C  VAL*     1.3    82.8    +      -       -      +
    136C  TYR*     1.3    68.6    +      -       -      +
    159C  GLY      3.2    22.8    +      -       -      -
    160C  THR*     3.8     0.6    -      -       -      +
    161C  ARG*     2.8    50.5    +      -       -      +
    185C  GLY*     3.3     3.6    -      -       -      -
    186C  ARG*     2.8    74.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 136 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105C  ALA      2.8    24.8    +      -       -      -
    106C  GLY*     3.4    10.9    +      -       -      -
    107C  ALA*     3.7    19.7    -      -       +      -
    124C  TRP*     3.5    24.2    -      +       +      +
    126C  VAL*     3.6    18.7    -      -       +      +
    127C  GLY      3.4    10.6    +      -       -      -
    130C  ALA*     3.9     2.4    -      -       -      +
    134C  VAL*     3.9    13.0    -      -       +      -
    135C  GLN*     1.3    79.6    +      -       -      +
    137C  ASP*     1.3    64.6    +      -       -      +
    138C  LEU      4.3     0.2    -      -       -      -
    153C  TYR*     4.2     1.7    -      -       -      -
    160C  THR*     3.8    21.1    -      -       +      -
    161C  ARG*     3.1    46.0    +      -       -      +
    183C  VAL*     3.8    15.0    -      -       +      -
    184C  ARG      3.2    15.0    -      -       -      +
    185C  GLY*     3.6    15.5    -      -       -      -
    192C  ILE*     4.3     0.2    -      -       +      -
    193C  PRO      5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 137 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136C  TYR*     1.3    75.1    -      -       -      +
    138C  LEU*     1.3    60.6    +      -       -      +
    139C  TYR*     3.6    27.9    +      -       +      +
    149C  GLU*     3.8    18.1    -      -       -      +
    153C  TYR*     3.6     4.3    -      -       -      -
    161C  ARG*     3.0    27.2    +      -       -      -
    183C  VAL*     3.4     5.2    -      -       -      -
    184C  ARG*     2.9    37.3    +      -       +      +
    185C  GLY      5.9     0.2    -      -       -      -
    186C  ARG*     3.1    35.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122C  CYS*     4.0    24.9    -      -       +      -
    124C  TRP*     4.0    10.0    -      -       +      -
    137C  ASP*     1.3    71.1    -      -       -      +
    139C  TYR*     1.3    65.6    +      -       -      +
    149C  GLU*     3.7     4.0    -      -       -      +
    150C  CYS*     3.2    30.9    +      -       +      -
    153C  TYR*     3.3    17.2    +      -       +      -
    164C  CYS*     3.5    25.4    -      -       +      +
    166C  PHE*     3.4    31.4    -      -       +      -
    181C  ILE*     3.5    29.4    -      -       +      -
    182C  LEU      3.5     1.8    -      -       -      -
    183C  VAL*     3.6    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 139 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137C  ASP*     3.6    37.1    +      -       +      +
    138C  LEU*     1.3    76.8    -      -       -      +
    140C  LEU*     1.3    60.1    +      -       -      +
    141C  ASN      4.0     0.4    -      -       -      +
    147C  GLN*     3.4    39.9    -      -       +      +
    148C  TYR      3.5     1.3    -      -       -      -
    149C  GLU*     3.5    42.9    +      -       +      -
    166C  PHE*     4.1     5.2    -      -       -      -
    180C  HIS      3.7     0.5    -      -       -      +
    181C  ILE*     3.4     7.8    -      -       -      +
    182C  LEU*     2.6    54.0    +      -       +      +
    184C  ARG*     4.0    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 140 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120C  LEU*     4.1    10.3    -      -       +      -
    139C  TYR*     1.3    72.4    -      -       -      +
    141C  ASN*     1.3    59.8    +      -       -      +
    142C  VAL*     4.1    22.4    -      -       +      -
    146C  GLN      4.0     0.5    -      -       -      +
    147C  GLN*     3.3     2.6    -      -       -      +
    148C  TYR*     2.7    45.2    +      -       +      +
    166C  PHE*     3.6    18.2    -      -       +      -
    169C  ILE*     3.8    23.6    -      -       +      -
    172C  LEU*     4.3    18.6    -      -       +      -
    173C  SER*     4.5     7.2    -      -       -      -
    179C  SER*     3.5    25.6    -      -       -      +
    180C  HIS      3.8     1.3    -      -       -      +
    181C  ILE*     3.6    24.2    -      -       +      -
    201C  PHE*     4.6     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 141 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139C  TYR      4.0     1.1    +      -       -      +
    140C  LEU*     1.3    74.1    -      -       -      +
    142C  VAL*     1.3    61.0    +      -       -      +
    143C  ALA      3.7     1.4    +      -       -      -
    144C  LYS*     3.2    33.7    +      -       -      +
    145C  ARG      5.8     0.2    -      -       -      -
    146C  GLN      3.5     6.7    +      -       -      +
    147C  GLN*     3.5    31.8    +      -       -      +
    179C  SER*     3.6     3.5    -      -       -      -
    180C  HIS*     2.9    55.8    +      -       +      +
    182C  LEU*     5.7     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140C  LEU*     4.1    11.7    -      -       +      -
    141C  ASN*     1.3    72.3    -      -       -      +
    143C  ALA*     1.3    75.9    +      -       +      +
    144C  LYS      3.1     2.3    +      -       -      -
    145C  ARG*     3.2    12.6    +      -       -      +
    146C  GLN*     2.8    21.0    +      -       +      +
    148C  TYR*     3.9    28.5    -      -       +      -
    172C  LEU      4.0     0.4    -      -       -      +
    173C  SER*     3.6    31.9    -      -       -      +
    174C  SER*     5.0     5.2    -      -       -      -
    176C  SER*     3.5    24.9    -      -       -      +
    179C  SER*     4.6     5.4    -      -       -      -
----------------------------------------------------------
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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