Contacts of the strand formed by residues 214 - 219 (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 VAL 214 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  ARG*     5.1     5.8    -      -       -      +
    103A  GLY*     3.9    22.8    -      -       -      -
    104A  SER*     3.7    26.5    +      -       -      +
    165A  ILE*     4.0     9.6    -      -       +      -
    166A  ASP      4.1     1.3    -      -       -      +
    167A  LEU*     4.2     6.1    -      -       +      -
    168A  PRO*     3.7    21.5    -      -       +      -
    205A  SER*     3.6    21.3    -      -       -      +
    206A  SER      3.1     5.8    -      -       -      +
    207A  TRP*     3.5    27.1    -      -       +      -
    212A  GLY      3.6     2.4    +      -       -      +
    213A  ILE*     1.3    78.2    -      -       -      +
    215A  SER*     1.3    59.7    +      -       -      +
    216A  ASP*     5.4     2.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  ARG*     3.5    24.8    +      -       -      -
    205A  SER*     3.1     3.9    +      -       -      -
    206A  SER*     2.7    42.4    +      -       -      -
    213A  ILE*     3.9    12.7    +      -       -      +
    214A  VAL*     1.3    74.3    -      -       -      +
    216A  ASP*     1.3    65.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  SER*     5.2     5.9    -      -       -      -
    106A  PHE*     5.7     2.5    -      -       -      -
    168A  PRO*     3.8    23.7    -      -       +      +
    169A  ILE*     6.1     0.7    -      -       +      -
    204A  THR      3.4    12.1    -      -       -      +
    205A  SER*     3.9    11.0    -      -       -      +
    214A  VAL*     5.4     2.0    -      -       +      +
    215A  SER*     1.3    78.0    -      -       -      +
    217A  ARG*     1.3    61.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  LEU*     4.8     1.1    -      -       -      -
    204A  THR*     2.8    54.4    +      -       -      +
    216A  ASP*     1.3    76.4    +      -       -      +
    218A  THR*     1.3    69.8    +      -       -      +
    219A  VAL*     3.8     9.6    +      -       +      -
    253A  TYR*     4.1     8.1    -      -       -      -
    258A  ASP*     2.6    58.4    +      -       -      -
    259A  SER*     4.4     5.3    -      -       -      +
    260A  TRP*     4.2    19.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  ILE*     3.3    36.6    -      -       +      -
    202A  THR      3.6     4.3    -      -       -      +
    203A  LEU*     4.1    15.8    -      -       +      +
    217A  ARG*     1.3    80.1    -      -       -      +
    219A  VAL*     1.3    62.7    -      -       -      +
    220A  THR*     3.8    13.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  GLY      3.9     0.3    -      -       -      +
    201A  ILE*     3.4     4.3    -      -       -      -
    202A  THR*     2.7    42.1    +      -       -      +
    204A  THR*     3.7    20.6    -      -       +      -
    217A  ARG*     4.0    13.2    -      -       +      -
    218A  THR*     1.3    75.2    -      -       -      +
    220A  THR*     1.3    64.4    +      -       -      +
    221A  VAL*     4.3     7.9    -      -       +      -
    222A  THR*     4.1    17.8    +      -       -      +
    224A  HIS      4.4     3.4    -      -       -      +
    226A  MET*     5.0     3.6    -      -       +      -
    260A  TRP*     3.4    57.4    -      -       +      +
----------------------------------------------------------
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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