Contacts of the strand formed by residues 54 - 61 (chain A) in PDB entry 4GDK


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 LYS 54 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  LYS*     1.3    82.6    -      -       -      +
     55A  ILE*     1.3    69.6    +      -       -      +
     74A  ALA*     3.8    34.8    +      -       +      +
     75A  VAL      3.4    16.2    -      -       -      +
     76A  GLU*     3.6    28.9    -      -       -      +
     77A  ARG*     4.0     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  LYS*     1.3    74.0    -      -       -      +
     56A  ASP*     1.3    65.5    +      -       -      +
     57A  ILE*     3.8     7.4    +      -       +      +
     73A  TRP      3.6     0.7    -      -       -      +
     74A  ALA*     3.6     1.5    -      -       -      -
     75A  VAL*     2.9    41.1    +      -       -      +
     77A  ARG*     3.4    41.5    -      -       +      +
    116A  VAL*     3.5    32.3    -      -       +      -
    117A  GLY*     3.7    14.6    -      -       -      +
    120A  TYR*     3.6    44.6    -      -       +      -
    129A  LEU*     5.3     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  ILE*     1.3    78.1    -      -       -      +
     57A  ILE*     1.3    59.0    +      -       -      +
     73A  TRP      3.5     8.2    -      -       -      +
     74A  ALA*     4.5     9.7    -      -       -      +
    120A  TYR*     4.6     0.2    -      -       -      -
    127A  GLY      3.5    24.0    +      -       -      +
    128A  LYS*     3.3    12.5    -      -       +      +
    129A  LEU*     2.8    32.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  ILE*     4.3     4.9    -      -       +      +
     56A  ASP*     1.3    79.4    -      -       -      +
     58A  LEU*     1.3    62.6    +      -       -      +
     59A  LEU*     3.7    28.7    -      -       +      -
     71A  LYS      3.2     5.5    -      -       -      +
     72A  LYS*     3.5     2.6    -      -       -      -
     73A  TRP*     2.9    37.8    +      -       +      +
     75A  VAL*     3.5    31.2    -      -       +      -
     84A  LEU*     3.8    18.8    -      -       +      -
    116A  VAL*     3.5    31.2    -      -       +      -
    128A  LYS*     5.3     0.4    -      -       -      -
    129A  LEU*     3.4    15.0    -      -       +      +
    131A  LEU*     4.0    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  ASP      4.2     0.8    +      -       -      -
     57A  ILE*     1.3    71.9    -      -       -      +
     59A  LEU*     1.3    66.2    +      -       -      +
     60A  LYS*     3.7    32.3    +      -       +      +
     71A  LYS*     3.6    21.8    -      -       +      +
     72A  LYS*     4.0    27.6    -      -       +      +
    128A  LYS*     4.2    32.7    -      -       +      +
    129A  LEU      3.1     8.9    +      -       -      +
    130A  VAL*     3.6    13.6    -      -       +      +
    131A  LEU      3.1    25.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  ILE*     3.7    25.6    -      -       +      -
     58A  LEU*     1.3    72.7    -      -       -      +
     60A  LYS*     1.3    63.3    +      -       -      +
     61A  ALA      4.4     0.2    +      -       -      -
     68A  MET*     3.9    22.0    -      -       +      -
     70A  THR      4.8     0.2    -      -       -      +
     71A  LYS*     3.0    42.6    +      -       -      +
     73A  TRP*     3.9    23.8    -      -       +      +
     84A  LEU*     5.0     5.6    -      -       +      -
     87A  PHE*     5.2     2.5    -      -       +      -
     88A  ILE*     3.8    33.4    -      -       +      -
    102A  ILE*     5.8     0.9    -      -       +      -
    131A  LEU*     3.4    20.0    -      -       +      +
    133A  TYR*     3.8    17.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  LEU*     3.8    27.8    -      -       +      +
     59A  LEU*     1.3    79.5    -      -       -      +
     61A  ALA*     1.3    61.5    +      -       -      +
     71A  LYS*     5.9     0.9    -      -       -      +
    130A  VAL*     4.1    19.2    -      -       +      +
    131A  LEU      3.0     6.6    +      -       -      +
    132A  HIS*     3.2    40.8    +      -       +      +
    133A  TYR*     3.0    29.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  LYS*     1.3    75.7    -      -       -      +
     62A  VAL*     1.3    64.2    +      -       -      +
     63A  GLY      4.0     2.0    +      -       -      +
     65A  THR*     3.9     4.7    -      -       -      +
     67A  ILE*     3.8    28.3    -      -       +      -
     71A  LYS*     6.4     0.2    -      -       -      +
    132A  HIS*     5.0     0.7    +      -       -      -
    133A  TYR*     3.3    34.7    +      -       +      +
----------------------------------------------------------
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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