Contacts of the strand formed by residues 202 - 207 (chain A) in PDB entry 1GOG


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 THR 202 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  TRP*     3.7    20.9    -      -       +      -
    187A  SER      4.4     1.3    -      -       -      +
    188A  SER*     3.3    10.1    -      -       -      +
    201A  ILE*     1.4    75.9    -      -       -      +
    203A  LEU*     1.3    78.0    +      -       -      +
    204A  THR*     3.7     2.4    +      -       +      -
    218A  THR*     3.6     0.5    -      -       -      -
    219A  VAL*     2.7    40.7    +      -       -      +
    224A  HIS      2.6    24.3    +      -       -      -
    225A  ASP*     3.2     1.6    -      -       -      -
    226A  MET*     2.7    46.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  PHE*     4.3    15.7    -      -       +      -
    169A  ILE*     4.0    11.2    -      -       +      +
    186A  TRP*     3.3     3.6    -      -       -      +
    187A  SER*     3.0    32.8    +      -       -      +
    188A  SER      2.8    14.3    +      -       -      +
    189A  TYR      3.6    19.5    -      -       -      +
    190A  ARG*     3.7     1.8    -      -       -      -
    191A  ASN*     3.3    39.7    -      -       +      +
    201A  ILE*     4.5    11.9    -      -       +      -
    202A  THR*     1.3    73.0    -      -       -      +
    204A  THR*     1.3    63.5    +      -       -      +
    217A  ARG      4.0     3.8    -      -       -      +
    218A  THR*     4.1    18.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  ILE*     4.4     2.4    -      -       -      +
    184A  LEU*     3.9    15.1    -      -       +      +
    185A  MET      3.2    10.1    -      -       -      -
    186A  TRP*     3.7    14.8    -      -       +      -
    202A  THR*     4.0     9.0    -      -       +      +
    203A  LEU*     1.3    81.8    -      -       -      +
    205A  SER*     1.3    64.4    +      -       -      +
    216A  ASP*     3.4     4.3    -      -       -      +
    217A  ARG*     2.8    52.1    +      -       -      +
    219A  VAL*     3.7    23.8    -      -       +      +
    226A  MET*     4.3     6.7    -      -       +      -
    260A  TRP*     4.4    10.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  LEU*     4.4     6.1    -      -       -      +
    168A  PRO*     3.5    28.9    -      -       -      +
    169A  ILE*     3.8    19.7    -      -       -      -
    184A  LEU*     3.8     3.5    -      -       -      +
    185A  MET*     2.8    38.0    +      -       -      +
    204A  THR*     1.3    78.8    +      -       -      +
    206A  SER*     1.3    58.0    +      -       -      +
    214A  VAL*     3.6    12.8    -      -       -      +
    215A  SER      3.1    12.7    +      -       -      -
    216A  ASP*     3.9     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  GLU*     2.9    26.0    +      -       -      -
    182A  ARG*     3.7    31.6    +      -       -      -
    183A  VAL      3.2     7.2    +      -       -      -
    184A  LEU*     4.1     6.8    -      -       -      +
    185A  MET*     4.2     2.5    -      -       -      -
    205A  SER*     1.3    72.4    +      -       -      +
    207A  TRP*     1.3    61.2    +      -       -      +
    208A  ASP      4.1     0.2    -      -       -      -
    213A  ILE      3.5     1.8    -      -       -      +
    214A  VAL*     3.1     6.3    -      -       -      +
    215A  SER*     2.7    43.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  SER*     5.8     1.4    +      -       -      -
    163A  PRO*     6.2     0.2    -      -       +      -
    165A  ILE*     3.7    33.9    -      -       +      +
    182A  ARG*     3.4     4.6    -      -       -      -
    183A  VAL*     2.8    45.6    +      -       +      +
    185A  MET*     3.8    17.2    -      -       +      +
    206A  SER*     1.3    76.7    -      -       -      +
    208A  ASP*     1.3    61.9    +      -       -      +
    209A  PRO*     3.3    44.8    -      -       +      +
    212A  GLY*     3.6    26.9    +      -       -      -
    213A  ILE      3.5     0.9    -      -       -      -
    214A  VAL*     3.5    26.9    -      -       +      -
    502A  LEU*     4.1     6.5    -      -       +      -
    506A  ARG*     4.5     7.9    -      -       -      -
    508A  PHE*     3.6    31.6    -      +       +      -
    527A  ILE*     3.7    20.0    -      -       +      -
----------------------------------------------------------
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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