Contacts of the strand formed by residues 135 - 141 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133D  ASP      3.4     3.6    +      -       -      +
    134D  VAL*     1.3    76.6    +      -       -      +
    136D  TYR*     1.3    84.9    +      -       -      +
    159D  GLY      2.9    27.5    +      -       -      -
    160D  THR*     3.6     7.1    -      -       -      +
    161D  ARG*     2.7    47.4    +      -       -      +
    185D  GLY*     3.6     3.8    -      -       -      -
    186D  ARG*     3.1    68.5    +      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
    106D  GLY*     3.3    20.1    +      -       -      -
    107D  ALA*     3.4    28.9    -      -       +      -
    124D  TRP*     3.7    15.9    -      +       +      +
    126D  VAL*     3.5    29.6    -      -       +      +
    127D  GLY      3.1    23.3    +      -       -      -
    130D  ALA*     4.2     1.2    -      -       -      +
    134D  VAL*     3.8    20.2    -      -       +      +
    135D  GLN*     1.3    86.4    +      -       -      +
    137D  ASP*     1.3    65.7    +      -       -      +
    153D  TYR*     4.1     1.1    -      -       -      -
    160D  THR*     3.9    12.1    -      -       +      -
    161D  ARG*     2.8    54.6    +      -       -      +
    183D  VAL*     3.9    11.4    -      -       +      -
    184D  ARG      3.4    16.6    -      -       -      +
    185D  GLY*     3.9     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 137 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124D  TRP*     5.8     0.4    -      -       -      -
    136D  TYR*     1.3    75.7    -      -       -      +
    138D  LEU*     1.3    60.6    +      -       -      +
    139D  TYR*     3.2    34.9    +      -       +      +
    149D  GLU*     4.0     5.6    -      -       -      +
    153D  TYR*     3.4     9.6    -      -       -      +
    161D  ARG*     2.9    27.2    +      -       -      -
    182D  LEU      3.5     1.0    -      -       -      +
    183D  VAL*     3.3     5.9    -      -       -      -
    184D  ARG*     3.0    36.6    +      -       +      +
    185D  GLY      6.1     0.2    -      -       -      -
    186D  ARG*     3.1    34.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 138 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110D  LEU*     4.8     0.4    -      -       +      -
    122D  CYS*     3.9    16.4    -      -       +      -
    124D  TRP*     3.6    34.1    -      -       +      -
    137D  ASP*     1.3    74.5    -      -       -      +
    139D  TYR*     1.3    71.5    +      -       -      +
    140D  LEU*     5.1     0.9    -      -       +      -
    149D  GLU*     3.4     5.2    -      -       -      +
    150D  CYS*     2.9    28.9    +      -       +      -
    153D  TYR*     3.0    15.0    +      -       +      -
    164D  CYS*     3.9     8.3    -      -       +      -
    166D  PHE*     3.6    34.1    -      -       +      -
    181D  ILE*     3.8    22.0    -      -       +      -
    182D  LEU      3.1     8.5    -      -       -      +
    183D  VAL*     3.7    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 139 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137D  ASP*     3.2    45.4    +      -       +      +
    138D  LEU*     1.3    76.9    -      -       -      +
    140D  LEU*     1.3    62.0    +      -       -      +
    141D  ASN*     4.1     1.1    -      -       -      -
    147D  GLN*     3.5    41.1    -      -       +      +
    148D  TYR      3.5     3.6    -      -       -      +
    149D  GLU*     3.9    37.2    +      -       +      -
    180D  HIS      3.9     0.9    -      -       -      +
    181D  ILE*     3.5     7.1    -      -       -      +
    182D  LEU*     2.9    51.6    +      -       +      +
    184D  ARG*     3.8    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 140 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120D  LEU*     3.6    31.4    -      -       +      -
    138D  LEU*     5.1     0.2    -      -       +      -
    139D  TYR*     1.3    75.4    -      -       -      +
    141D  ASN*     1.3    60.4    +      -       -      +
    142D  VAL*     3.5    29.3    +      -       +      -
    146D  GLN      3.7     2.3    -      -       -      +
    147D  GLN      3.5     2.3    -      -       -      -
    148D  TYR*     2.9    50.4    +      -       +      +
    166D  PHE*     4.0    24.2    -      -       +      -
    169D  ILE*     4.8     7.0    -      -       +      -
    172D  LEU*     5.0    11.0    -      -       +      -
    179D  SER*     3.8    12.1    -      -       -      +
    180D  HIS      3.7     2.7    -      -       -      -
    181D  ILE*     3.6    12.8    -      -       +      -
    201D  PHE*     5.1     3.1    -      -       +      -
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Residues in contact with ASN 141 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75D  LEU*     5.9     2.0    -      -       -      +
    139D  TYR*     4.9     1.3    -      -       -      +
    140D  LEU*     1.3    75.0    +      -       -      +
    142D  VAL*     1.3    60.7    +      -       -      +
    143D  ALA      4.3     2.5    -      -       -      +
    145D  ARG*     3.4    26.4    +      -       -      +
    146D  GLN      4.0     4.3    -      -       -      -
    147D  GLN*     3.1    40.9    +      -       -      +
    179D  SER*     3.1     8.8    -      -       -      -
    180D  HIS*     2.8    71.2    +      -       +      +
    182D  LEU*     5.4     3.8    -      -       -      +
----------------------------------------------------------
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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