Contacts of the strand formed by residues 205 - 210 (chain A) in PDB entry 4GGA


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 SER 205 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  ALA*     3.3     0.9    -      -       -      -
    202A  LEU      2.7    38.8    +      -       -      -
    204A  ASN*     1.3    83.6    +      -       -      +
    206A  VAL*     1.3    57.2    +      -       -      +
    207A  TYR*     3.9    16.3    +      -       -      -
    218A  GLN*     3.0    25.4    +      -       -      -
    220A  LEU      3.4    11.9    -      -       -      -
    221A  GLN*     3.3    19.4    +      -       -      +
    229A  ILE*     3.2    13.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  ALA*     4.5     1.8    -      -       +      -
    200A  VAL      3.5    11.7    -      -       -      +
    201A  ALA*     4.5     1.3    -      -       -      -
    205A  SER*     1.3    77.8    -      -       -      +
    207A  TYR*     1.3    70.2    +      -       -      +
    208A  LEU*     4.1     8.5    -      -       +      -
    218A  GLN*     3.6     4.3    -      -       -      +
    219A  LEU*     2.8    35.9    +      -       +      -
    220A  LEU*     3.3    29.4    +      -       +      +
    229A  ILE*     3.6    21.5    -      -       +      +
    232A  VAL*     4.3    18.8    -      -       +      -
    241A  LEU*     4.0    24.0    -      -       +      -
    243A  VAL*     4.3     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  LEU      3.5     1.0    -      -       -      +
    199A  ALA*     3.4     4.0    -      -       -      -
    200A  VAL*     2.9    41.8    +      -       +      +
    202A  LEU*     3.8    33.4    -      -       +      -
    205A  SER*     3.9    19.8    -      -       -      -
    206A  VAL*     1.3    75.1    -      -       -      +
    208A  LEU*     1.3    64.7    +      -       -      +
    209A  TRP*     4.1     0.9    -      -       +      -
    216A  ILE*     3.8    27.6    -      -       +      -
    217A  LEU      3.2     7.6    -      -       -      -
    218A  GLN*     3.6    35.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  VAL*     3.7    11.9    -      -       +      -
    198A  LEU      3.2     2.5    -      -       -      -
    199A  ALA*     3.8    22.7    -      -       +      -
    206A  VAL*     4.1    11.0    -      -       +      -
    207A  TYR*     1.3    83.5    -      -       -      +
    209A  TRP*     1.3    60.0    +      -       -      +
    210A  SER      4.2     0.4    -      -       -      -
    215A  ASP      3.8     0.7    -      -       -      +
    216A  ILE*     3.2     8.1    -      -       -      +
    217A  LEU*     2.8    54.7    +      -       +      +
    219A  LEU*     4.2    11.4    -      -       +      -
    234A  TRP*     3.9    15.9    -      -       +      -
    241A  LEU*     4.3     4.7    -      -       +      -
    255A  VAL*     3.0    40.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  ARG*     3.7    33.4    -      -       -      -
    176A  LEU*     3.5    45.4    -      -       +      +
    192A  TRP*     4.9     0.4    -      +       -      -
    197A  VAL*     3.4     3.9    -      -       -      +
    198A  LEU*     2.7    57.0    +      -       +      +
    200A  VAL*     5.8     3.6    -      -       +      -
    207A  TYR*     4.1     0.9    -      -       +      -
    208A  LEU*     1.3    74.4    -      -       -      +
    210A  SER*     1.3    69.1    +      -       -      +
    211A  ALA*     3.4    30.5    -      -       +      -
    214A  GLY*     3.7    32.4    +      -       -      -
    215A  ASP      3.5     1.6    -      -       -      -
    216A  ILE*     3.8    17.0    -      -       +      +
    469A  LEU*     3.9    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196A  ASN      3.9     6.3    +      -       -      -
    197A  VAL*     4.2    14.6    -      -       -      +
    208A  LEU      4.2     0.4    -      -       -      -
    209A  TRP*     1.3    76.0    -      -       -      +
    211A  ALA*     1.3    58.0    +      -       -      +
    212A  SER*     3.1    16.3    +      -       -      -
    213A  SER*     3.2    26.1    +      -       -      -
    214A  GLY*     3.0    28.6    +      -       -      -
    215A  ASP*     3.0    16.6    +      -       -      -
----------------------------------------------------------
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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