Contacts of the strand formed by residues 233 - 237 (chain I) in PDB entry 5G04


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 TYR 233 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218I  SER*     3.4    28.9    +      -       -      -
    219I  VAL      3.4     9.2    -      -       -      -
    220I  VAL*     4.6     4.5    -      -       +      +
    232I  SER*     1.3    74.9    -      -       -      +
    234I  PHE*     1.3    59.2    +      -       -      +
    235I  GLN*     2.8    36.8    +      -       +      -
    552I  ILE      4.2     4.3    -      -       -      -
    553I  CYS*     3.5    11.8    -      -       -      -
    554I  ILE*     3.1    63.7    +      -       +      +
    556I  LEU*     4.5     7.4    -      -       +      -
    575I  LEU*     4.2    13.9    -      -       +      -
    584I  HIS*     4.6     5.5    -      -       -      +
    586I  LEU*     3.6    28.9    -      -       +      -
    601I  LEU*     4.4     9.8    -      -       +      +
    603I  ARG*     3.9    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 234 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200I  GLY      4.7    10.8    -      -       -      -
    201I  ILE*     4.2    20.4    -      -       +      -
    202I  ALA*     5.6     6.7    -      -       +      -
    218I  SER*     3.3     1.4    -      -       -      -
    219I  VAL*     2.4    54.8    +      -       +      +
    221I  THR*     3.3    32.5    -      -       +      -
    232I  SER*     4.3     7.4    -      -       -      -
    233I  TYR*     1.3    75.8    -      -       -      +
    235I  GLN*     1.3    57.2    +      -       -      +
    236I  LEU*     3.6    12.0    -      -       +      +
    551I  ALA*     4.3    20.0    -      -       +      -
    552I  ILE      3.9     2.7    -      -       -      -
    553I  CYS*     4.0    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 235 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216I  SER*     3.7    20.1    +      -       -      -
    218I  SER*     3.7    12.7    -      -       -      +
    233I  TYR*     2.8    38.7    +      -       +      +
    234I  PHE*     1.3    69.3    -      -       -      +
    236I  LEU*     1.3    63.4    +      -       -      +
    551I  ALA*     3.1     2.9    -      -       -      -
    552I  ILE*     2.8    44.6    +      -       +      +
    584I  HIS*     5.1     3.5    -      -       -      +
    603I  ARG*     3.5    28.5    -      -       -      +
    604I  HIS      3.6    19.0    +      -       -      +
    607I  ILE*     3.6    34.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 236 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185I  ILE*     4.1    17.3    -      -       +      -
    198I  VAL*     3.8    29.6    -      -       +      -
    201I  ILE*     4.7     5.6    -      -       +      -
    216I  SER*     3.2     9.1    -      -       -      -
    217I  LEU*     2.8    54.3    +      -       +      +
    219I  VAL*     4.6     4.0    -      -       +      -
    234I  PHE*     3.6    34.5    -      -       +      +
    235I  GLN*     1.3    76.7    -      -       -      +
    237I  GLU*     1.3    61.1    +      -       -      +
    238I  THR*     5.1     0.7    -      -       +      -
    548I  MET*     4.6    14.8    -      -       +      +
    550I  GLN      3.4    10.8    -      -       -      +
    551I  ALA*     4.2     8.5    -      -       +      -
    607I  ILE*     4.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 237 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215I  LYS      4.4     0.2    -      -       -      +
    235I  GLN      4.1     0.4    +      -       -      -
    236I  LEU*     1.3    72.4    -      -       -      +
    238I  THR*     1.3    59.6    +      -       -      +
    239I  ASN*     3.5    26.1    +      -       +      +
    547I  SER      4.4     0.9    -      -       -      +
    548I  MET*     3.7    21.3    -      -       -      +
    549I  ASN      5.0     0.2    +      -       -      -
    550I  GLN*     3.2    33.4    +      -       +      +
    552I  ILE*     5.6     0.9    -      -       -      +
    606I  ASP*     5.7     0.5    -      -       -      +
    607I  ILE*     3.3    47.3    +      -       +      +
    608I  SER*     5.3     5.1    +      -       -      -
----------------------------------------------------------
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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