Contacts of the strand formed by residues 128 - 134 (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 128 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  ASP*     3.3    22.7    -      -       +      +
     57A  ILE      4.8     0.7    -      -       -      +
     58A  LEU*     4.2    32.1    -      -       +      +
     72A  LYS*     6.2     5.2    -      -       +      +
    120A  TYR*     3.6     8.6    -      -       -      -
    124A  GLY*     3.5     0.3    -      -       -      -
    125A  SER*     2.8    40.4    +      -       -      +
    126A  ASP*     4.0    18.5    +      -       -      +
    127A  GLY*     1.3    82.3    -      -       -      +
    129A  LEU*     1.3    60.5    +      -       -      +
    130A  VAL*     3.9    15.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  ILE*     5.3     0.2    -      -       +      -
     56A  ASP      2.8    14.1    +      -       -      +
     57A  ILE*     3.4    11.3    -      -       +      +
     58A  LEU      3.1    20.6    +      -       -      -
    104A  VAL*     4.6     6.3    -      -       +      -
    116A  VAL*     3.6    33.0    -      -       +      +
    119A  LEU*     3.8    34.8    -      -       +      +
    120A  TYR*     3.9    15.0    -      -       +      +
    123A  PHE*     3.9    22.4    -      -       +      +
    124A  GLY*     4.5     0.4    -      -       -      -
    128A  LYS*     1.3    73.1    -      -       -      +
    130A  VAL*     1.3    67.0    +      -       -      +
    131A  LEU*     3.6    32.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  LEU*     3.6    23.1    -      -       +      +
     60A  LYS*     4.1    22.4    -      -       +      +
    103A  TYR      4.1     3.5    -      -       -      +
    104A  VAL*     4.5     6.2    -      -       -      +
    105A  ASN      4.5     5.4    +      -       -      -
    123A  PHE      5.3     1.8    +      -       -      -
    125A  SER*     5.6     7.0    -      -       -      +
    128A  LYS*     3.9    21.7    +      -       +      +
    129A  LEU*     1.3    78.8    -      -       -      +
    131A  LEU*     1.3    70.3    +      -       -      +
    132A  HIS*     3.8    27.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  ILE*     4.0    11.2    -      -       +      -
     58A  LEU      3.1     7.1    +      -       -      -
     59A  LEU*     3.4    19.3    -      -       +      +
     60A  LYS      3.0    23.6    +      -       -      +
     81A  ILE*     4.6     7.6    -      -       +      -
     84A  LEU*     3.6    31.6    -      -       +      -
    102A  ILE*     4.2    20.2    -      -       +      -
    103A  TYR      3.5    13.5    -      -       -      +
    104A  VAL*     3.6    21.1    -      -       +      -
    116A  VAL*     5.1     0.9    -      -       +      -
    129A  LEU*     3.6    30.9    +      -       +      +
    130A  VAL*     1.3    83.8    -      -       -      +
    132A  HIS*     1.3    64.7    +      -       -      +
    133A  TYR      4.0     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  LYS*     3.2    38.2    +      -       +      +
     61A  ALA      5.0     1.0    +      -       -      -
     62A  VAL*     4.0    25.1    -      -       +      +
    101A  PHE      3.7     0.5    -      -       -      +
    102A  ILE*     3.4     4.5    -      -       -      -
    103A  TYR*     2.9    36.2    +      -       +      +
    105A  ASN      5.6     0.9    -      -       -      -
    106A  GLN*     3.3    51.6    +      -       +      +
    130A  VAL*     3.8    21.5    -      -       +      +
    131A  LEU*     1.3    77.4    -      -       -      +
    133A  TYR*     1.3    59.1    +      -       -      +
    139A  TRP*     4.3    12.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  LEU*     3.8    32.6    +      -       +      -
     60A  LYS      3.0    36.4    +      -       -      -
     61A  ALA*     3.3    18.0    +      -       +      +
     62A  VAL*     3.1    25.9    +      -       -      +
     65A  THR*     3.5    14.4    +      -       -      -
     66A  PRO      3.4    20.0    -      -       -      -
     67A  ILE*     3.5     4.3    -      -       -      +
     68A  MET*     3.0    36.9    +      -       +      +
     71A  LYS*     5.5     0.9    -      -       -      -
     88A  ILE*     4.7    12.8    -      -       +      -
     92A  LEU*     3.7    19.7    -      -       +      -
    100A  LEU*     4.4    10.8    -      -       +      -
    101A  PHE      3.3     8.1    -      -       -      +
    102A  ILE*     4.6    10.8    -      -       +      +
    131A  LEU      4.6     0.9    -      -       -      -
    132A  HIS*     1.3    73.6    -      -       -      +
    134A  CYS*     1.3    63.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  VAL*     3.4    32.8    -      -       +      +
     63A  GLY      4.2     7.2    -      -       -      -
     65A  THR*     3.6     8.7    -      -       -      -
    100A  LEU*     3.6     5.0    -      -       -      +
    101A  PHE*     2.7    39.8    +      -       -      +
    103A  TYR*     4.8     6.3    -      -       +      -
    132A  HIS      5.5     0.2    -      -       -      -
    133A  TYR*     1.3    78.1    -      -       -      +
    135A  LYS*     1.3    62.0    +      -       -      +
    136A  SER*     3.2    37.9    +      -       -      +
    138A  ALA*     4.4    12.3    -      -       +      -
----------------------------------------------------------
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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