Contacts of the helix formed by residues 178 - 185 (chain I) in PDB entry 2GLJ


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 178 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176I  ASP      3.4     2.5    +      -       -      -
    177I  ILE*     1.3    88.0    -      -       +      +
    179I  VAL*     1.3    66.5    +      -       -      +
    180I  HIS*     3.5    35.7    -      -       +      +
    181I  LEU*     3.0    20.9    +      -       +      +
    182I  ALA*     3.0    17.0    +      -       -      +
    137L  LYS*     5.4     0.2    -      -       -      -
    345L  ALA*     3.4    34.3    -      -       +      -
    346L  ALA      6.1     0.2    -      -       -      +
    355L  MET*     5.6     5.6    -      -       +      -
    408L  LEU*     4.4     5.8    -      -       +      -
    439L  ASN*     4.7     3.6    -      -       -      +
    440L  MSE      3.8    43.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 179 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177I  ILE      3.7     0.6    +      -       -      -
    178I  LEU*     1.3    72.6    -      -       -      +
    180I  HIS*     1.3    81.5    +      -       +      +
    181I  LEU      3.1     1.0    +      -       -      -
    182I  ALA*     3.2    19.7    +      -       -      +
    183I  SER*     4.2     3.6    +      -       -      -
    134L  GLY      4.0    16.4    -      -       -      +
    135L  ILE*     3.3    27.1    -      -       -      +
    136L  LYS*     3.6    17.1    -      -       +      +
    137L  LYS*     3.4    25.4    -      -       +      +
    440L  MSE      4.7     3.4    +      -       -      +
    441L  HIS*     4.3    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 180 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178I  LEU*     3.0    27.8    +      -       +      -
    179I  VAL*     1.3    87.2    -      -       +      +
    181I  LEU*     1.3    71.4    +      -       +      +
    183I  SER*     5.1     4.0    +      -       -      -
    296L  GLU*     5.2     0.2    -      -       -      -
    408L  LEU*     4.4    12.8    -      -       +      -
    414L  GLY*     3.1    23.0    -      -       -      -
    415L  GLY      3.9    11.7    +      -       -      +
    440L  MSE      3.0    32.0    -      -       +      +
    441L  HIS*     3.4    26.3    +      +       -      -
   6023L   MN      4.5     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 181 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177I  ILE*     4.3     6.8    -      -       +      +
    178I  LEU*     3.0    23.6    +      -       +      -
    180I  HIS*     1.3    95.7    -      -       +      +
    182I  ALA*     1.3    56.4    +      -       -      +
    183I  SER*     3.1     9.7    +      -       -      +
    184I  GLU*     4.4     4.3    +      -       -      +
    345L  ALA*     5.6     0.2    -      -       +      -
    354L  VAL*     3.5    47.2    -      -       +      +
    355L  MET*     4.1     7.4    -      -       +      -
    408L  LEU*     3.7    26.9    -      -       +      +
    409L  GLY*     3.6    27.1    -      -       -      +
    413L  GLN*     3.9    11.7    +      -       +      +
    414L  GLY*     3.9    17.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 182 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177I  ILE*     4.4     5.4    -      -       +      +
    178I  LEU      3.0    10.6    +      -       -      +
    179I  VAL*     3.2    11.8    +      -       -      +
    181I  LEU*     1.3    76.4    -      -       -      +
    183I  SER*     1.3    63.1    +      -       -      +
    184I  GLU      3.3     2.5    -      -       -      -
    185I  GLN*     2.9    32.3    +      -       -      +
    137L  LYS*     3.2    39.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 183 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179I  VAL      4.2     3.4    +      -       -      -
    180I  HIS      5.3     2.9    -      -       -      -
    181I  LEU*     3.1     6.3    -      -       -      +
    182I  ALA*     1.3    77.9    -      -       -      +
    184I  GLU*     1.3    63.5    +      -       -      +
    185I  GLN      3.1     1.2    +      -       -      -
    186I  LEU*     3.9    21.0    -      -       -      +
    413L  GLN*     5.1    14.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 184 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181I  LEU      4.4     5.4    +      -       -      +
    182I  ALA      3.3     0.8    -      -       -      -
    183I  SER*     1.3    78.8    +      -       -      +
    185I  GLN*     1.3    55.7    +      -       -      +
    186I  LEU*     3.3    15.5    +      -       -      +
    187I  GLU*     4.7     1.0    +      -       -      +
    192I  LYS*     5.1     4.5    -      -       -      +
    353L  ASN*     5.5     3.1    -      -       -      +
    354L  VAL*     6.1     1.0    -      -       +      -
    413L  GLN*     3.8    25.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 185 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176I  ASP*     3.7     7.7    +      -       -      -
    177I  ILE*     3.3    25.3    -      -       +      +
    182I  ALA*     2.9    17.6    +      -       -      +
    184I  GLU*     1.3    75.5    -      -       -      +
    186I  LEU*     1.3    58.0    +      -       -      +
    192I  LYS*     2.9    49.8    +      -       +      +
    193I  VAL*     3.4    18.8    -      -       -      +
    137L  LYS*     2.6    35.7    +      -       -      -
    189L  LYS*     4.1    14.2    -      -       +      +
    190L  ALA*     4.8     3.8    +      -       -      -
    351L  TYR*     4.4     4.2    +      -       -      -
----------------------------------------------------------
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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