Contacts of the strand formed by residues 79 - 83 (chain G) in PDB entry 2ZJR


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 PHE 79 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39G  GLN*     3.4    28.0    -      -       +      -
     40G  ASN      3.0    13.5    +      -       -      +
     41G  TRP*     3.1    53.5    -      +       +      -
     42G  VAL*     3.6    17.7    +      -       -      +
     78G  ASP*     1.3    72.8    -      -       -      +
     80G  VAL*     1.3    60.7    +      -       -      +
     81G  VAL      4.1     0.2    +      -       -      -
    146G  THR*     5.1     2.2    -      -       +      -
    147G  ARG*     2.9    74.3    -      -       +      +
    149G  LYS*     4.7     2.2    -      -       -      -
      8X    A      3.8    33.9    -      -       -      -
      9X    U      5.9     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 80 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42G  VAL*     4.1     7.4    -      -       +      +
     44G  VAL*     4.1    20.4    -      -       +      +
     58G  ILE*     3.8    30.7    -      -       +      +
     61G  ARG*     4.3    16.6    -      -       +      +
     62G  ILE*     3.5    29.2    -      -       +      -
     78G  ASP*     3.5     6.9    +      -       +      +
     79G  PHE*     1.3    76.0    -      -       -      +
     81G  VAL*     1.3    76.0    +      -       -      +
     82G  VAL*     4.2     3.1    -      -       +      -
    147G  ARG*     3.3     9.4    +      -       -      +
    148G  LEU*     3.5     1.9    -      -       -      +
    149G  LYS*     2.8    27.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 81 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41G  TRP*     3.1    42.0    -      -       +      +
     42G  VAL      3.4    10.8    +      -       -      +
     43G  VAL*     3.6    14.6    -      -       +      +
     44G  VAL      3.2    24.3    +      -       -      -
     80G  VAL*     1.3    78.5    -      -       -      +
     82G  VAL*     1.3    68.2    +      -       -      +
     83G  ILE*     4.9     0.2    -      -       +      -
    149G  LYS*     3.3    16.6    -      -       +      +
    151G  TYR*     4.2    11.7    -      -       +      -
    161G  GLN*     3.9    35.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44G  VAL*     4.3     5.2    -      -       +      +
     45G  ASP      5.4     0.2    -      -       -      -
     46G  ALA*     4.2    18.2    -      -       +      +
     54G  LEU*     5.0     1.1    -      -       +      -
     58G  ILE*     3.3    33.9    -      -       +      -
     80G  VAL*     4.2     7.2    -      -       +      -
     81G  VAL*     1.3    79.9    -      -       -      +
     83G  ILE*     1.3    74.2    +      -       -      +
     85G  ALA*     4.6     1.8    -      -       +      -
    127G  ILE*     5.1     3.8    -      -       +      -
    148G  LEU*     4.2     4.5    -      -       +      -
    149G  LYS      3.0     8.1    +      -       -      -
    150G  VAL*     3.5    35.8    -      -       +      -
    151G  TYR*     2.7    35.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 83 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43G  VAL*     3.9    23.3    -      -       +      -
     44G  VAL      3.8     3.4    +      -       -      -
     45G  ASP*     3.2    29.6    -      -       -      +
     46G  ALA      3.5     7.3    +      -       -      -
     81G  VAL*     4.9     0.7    -      -       +      -
     82G  VAL*     1.3    83.7    -      -       -      +
     84G  ASN*     1.3    75.7    +      -       -      +
     85G  ALA      2.6    18.2    +      -       -      -
    151G  TYR*     3.2     8.7    -      -       -      -
    153G  GLY      4.1     3.8    -      -       -      +
    154G  GLU*     4.5    12.3    -      -       +      +
    157G  PRO*     4.5     4.3    -      -       +      -
    158G  HIS*     3.9    20.9    -      -       +      +
    161G  GLN*     4.5    11.4    -      -       -      +
    167G  LYS*     3.7    22.7    -      -       -      +
----------------------------------------------------------
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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