Contacts of the strand formed by residues 2085 - 2092 (chain A) in PDB entry 4ZWJ


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 TYR2085 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239A  GLU*     4.0    15.9    -      -       -      -
   2062A  LEU*     5.2     7.6    -      -       +      -
   2064A  CYS*     2.3    52.9    +      -       +      +
   2083A  ASP      3.4     2.4    -      -       -      -
   2084A  LEU*     1.3    80.9    -      -       -      +
   2086A  PHE*     1.3    69.5    +      -       -      +
   2087A  SER*     3.4    30.3    -      -       -      -
   2122A  THR      4.9     6.4    +      -       -      -
   2124A  PRO*     4.1    20.5    -      -       +      +
   2126A  TYR*     3.2    32.8    -      +       -      -
   2127A  LEU*     3.6    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE2086 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239A  GLU*     5.2     2.7    +      -       -      +
    240A  SER*     5.6    11.4    -      -       -      +
    242A  THR*     5.8     2.5    -      -       -      -
   2061A  THR*     4.3     7.4    -      -       -      -
   2062A  LEU      3.8     7.6    -      -       -      -
   2063A  THR*     3.3    32.5    -      -       +      -
   2064A  CYS      4.2     0.2    -      -       -      +
   2083A  ASP*     4.9    12.1    -      -       +      +
   2085A  TYR*     1.3    89.1    -      -       -      +
   2087A  SER*     1.3    66.3    +      -       -      +
   2088A  ARG*     3.5    46.2    -      -       +      -
   2162A  GLU*     3.3    47.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER2087 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2062A  LEU*     2.5    62.9    +      -       -      +
   2085A  TYR*     3.4    28.3    -      -       -      -
   2086A  PHE*     1.3    78.9    -      -       -      +
   2088A  ARG*     1.3    58.5    +      -       -      +
   2089A  VAL*     5.6     1.1    -      -       -      -
   2121A  LEU*     4.1     6.4    -      -       -      +
   2122A  THR      5.0     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG2088 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2059A  TYR*     5.2     6.1    -      -       +      -
   2061A  THR*     3.7    21.5    -      -       +      +
   2086A  PHE*     3.5    38.2    -      -       +      -
   2087A  SER*     1.3    72.3    -      -       -      +
   2089A  VAL*     1.3    72.2    +      -       -      +
   2153A  PHE*     5.8     0.2    -      -       +      -
   2159A  ASP*     2.6    58.9    +      -       -      +
   2160A  PRO*     5.0     6.6    -      -       -      +
   2162A  GLU*     4.3    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL2089 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2059A  TYR*     3.3     7.8    -      -       -      +
   2060A  VAL*     2.4    58.4    +      -       +      +
   2087A  SER*     4.7     2.5    -      -       -      +
   2088A  ARG*     1.3    84.9    -      -       -      +
   2090A  GLN*     1.3    72.6    +      -       +      +
   2119A  PHE*     5.6     4.3    -      -       +      -
   2120A  LEU      5.4     5.4    -      -       -      +
   2121A  LEU*     3.3    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN2090 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2057A  LYS*     2.9    36.9    +      -       -      +
   2058A  VAL      4.0     0.2    -      -       -      -
   2059A  TYR*     3.6    19.6    -      -       +      -
   2060A  VAL*     4.1     0.2    -      -       -      +
   2089A  VAL*     1.3    91.4    -      -       +      +
   2091A  VAL*     1.3    70.0    +      -       -      +
   2093A  PRO      4.3     0.2    -      -       -      +
   2094A  PRO*     5.0     3.1    -      -       +      +
   2095A  VAL*     3.2    41.2    -      -       +      +
   2119A  PHE*     5.5     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL2091 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2046A  VAL*     3.5    22.2    -      -       +      -
   2048A  VAL*     5.5     0.4    -      -       +      -
   2058A  VAL*     3.0    18.6    +      -       +      +
   2059A  TYR      4.3     0.7    -      -       -      -
   2060A  VAL*     3.4    37.9    -      -       +      +
   2090A  GLN*     1.3    82.1    -      -       -      +
   2092A  TYR*     1.3    64.4    +      -       +      +
   2093A  PRO      3.8     0.7    -      -       -      -
   2094A  PRO*     2.9    37.0    -      -       -      +
   2117A  TYR*     3.4    35.3    -      -       +      +
   2118A  PRO      4.8     4.3    -      -       -      +
   2119A  PHE*     4.7     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR2092 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2048A  VAL*     4.3     9.6    -      -       +      -
   2049A  ASP      5.7     0.2    -      -       -      -
   2050A  PRO*     4.9    10.0    +      -       +      +
   2053A  VAL*     3.7    44.5    +      -       +      -
   2054A  LYS*     5.6     1.1    -      -       -      -
   2055A  GLY      6.2     0.4    -      -       -      -
   2056A  LYS      3.8     6.5    -      -       -      +
   2057A  LYS*     3.5     9.2    -      -       -      +
   2058A  VAL*     3.2    40.1    +      -       +      -
   2091A  VAL*     1.3    84.9    -      -       +      +
   2093A  PRO*     1.4    76.3    -      -       +      +
   2094A  PRO*     5.5     0.2    -      -       +      -
   2117A  TYR*     3.4    45.5    -      +       +      -
----------------------------------------------------------
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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