Contacts of the strand formed by residues 66 - 72 (chain A) in PDB entry 1GII


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 LEU 66 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  ILE*     4.1    16.2    -      -       +      +
     55A  LEU*     4.2    17.1    +      -       +      +
     56A  LYS*     3.9    47.0    +      -       +      +
     58A  LEU      5.7     1.4    +      -       -      -
     59A  ASN*     5.7     0.4    -      -       -      +
     64A  VAL      3.5     4.0    +      -       -      +
     65A  LYS*     1.3    79.4    -      -       -      +
     67A  LEU*     1.3    61.9    +      -       -      +
     68A  ASP      3.6    16.2    -      -       -      +
     69A  VAL*     4.1    14.8    -      -       +      -
     78A  LEU*     4.0    14.1    -      -       +      -
     79A  VAL      3.4    22.2    -      -       -      +
     80A  PHE*     3.7    27.6    -      -       +      -
    146A  PHE*     5.9     2.7    -      -       +      -
    148A  LEU*     6.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  GLU*     5.6     5.6    -      -       +      -
     30A  VAL*     3.5    19.1    -      -       +      -
     56A  LYS*     4.8     7.4    -      -       -      +
     65A  LYS*     3.4    42.9    +      -       +      +
     66A  LEU*     1.3    74.0    -      -       -      +
     68A  ASP*     1.3    71.0    +      -       +      +
     79A  VAL*     2.7    18.2    +      -       +      +
     80A  PHE      3.4     9.0    -      -       -      +
     81A  GLU*     3.4    31.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  PHE*     6.3     0.4    -      -       +      -
     56A  LYS*     4.9     7.1    -      -       -      +
     66A  LEU*     3.6     6.3    -      -       -      +
     67A  LEU*     1.3    88.1    -      -       +      +
     69A  VAL*     1.3    73.4    +      -       -      +
     70A  ILE*     4.2     4.9    -      -       +      +
     78A  LEU      3.7     0.2    -      -       -      -
     79A  VAL*     2.8    46.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ILE*     5.4     6.7    -      -       +      +
     52A  ILE*     3.6    35.9    -      -       +      -
     53A  SER*     5.3     3.1    -      -       -      +
     56A  LYS*     4.1    22.3    -      -       +      +
     66A  LEU*     4.1    11.7    -      -       +      -
     68A  ASP*     1.3    85.0    +      -       -      +
     70A  ILE*     1.3    65.8    +      -       -      +
     71A  HIS*     3.9     4.3    +      -       +      +
     76A  LEU*     3.7    23.1    -      -       +      -
     77A  TYR      3.6     3.1    -      -       -      -
     78A  LEU*     4.1     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     4.5    25.6    -      -       +      -
      4A  PHE*     3.5    33.4    -      -       +      -
     32A  LEU*     5.3     0.7    -      -       +      -
     68A  ASP*     5.1     5.6    -      -       +      -
     69A  VAL*     1.3    75.8    -      -       -      +
     71A  HIS*     1.3    58.2    +      -       -      +
     72A  THR*     3.6    24.6    +      -       +      +
     75A  LYS      3.5     1.6    -      -       -      +
     76A  LEU*     3.5     5.4    -      -       -      -
     77A  TYR*     2.9    53.3    +      -       +      +
     79A  VAL*     4.0    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  VAL*     3.4    39.5    +      -       +      +
     49A  ILE*     3.8    25.4    -      -       +      +
     69A  VAL*     3.9     5.2    +      -       +      -
     70A  ILE*     1.3    70.8    -      -       -      +
     72A  THR*     1.3    63.5    +      -       -      +
     74A  ASN*     4.2    16.1    +      -       -      -
     75A  LYS      3.2    19.3    -      -       -      -
     76A  LEU*     3.9     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     4.4    21.9    -      -       +      +
      2A  GLU*     6.0     0.2    -      -       -      +
     70A  ILE*     3.6    22.1    +      -       +      +
     71A  HIS*     1.3    78.5    +      -       -      +
     73A  GLU*     1.3    83.3    +      -       +      +
     74A  ASN      3.0     2.0    -      -       -      -
     75A  LYS*     2.8    37.2    +      -       -      +
     77A  TYR*     5.0     8.7    -      -       +      -
----------------------------------------------------------
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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