Contacts of the strand formed by residues 229 - 233 (chain A) in PDB entry 4HXG


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 ILE 229 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  HIS*     3.5    32.8    -      -       +      +
    184A  VAL*     3.6    30.3    -      -       +      -
    202A  ILE*     6.4     0.2    -      -       +      -
    204A  LEU*     4.9     1.8    -      -       +      -
    213A  LEU*     4.6    12.6    -      -       +      -
    221A  ALA*     3.8    28.5    -      -       +      -
    223A  ASP      3.7     8.7    -      -       -      +
    224A  SER*     4.9     0.4    -      -       -      -
    228A  ARG*     1.3    73.4    -      -       -      +
    230A  LEU*     1.3    63.0    +      -       -      +
    231A  LEU*     3.8    13.2    +      -       +      -
    247A  TYR      3.4     2.6    -      -       -      +
    248A  ILE*     3.7     2.0    -      -       -      -
    249A  TYR*     2.9    56.2    +      -       +      +
    269A  ILE*     5.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 230 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  ALA*     3.5     3.6    -      -       -      -
    222A  ILE*     3.0    41.2    +      -       +      +
    223A  ASP*     3.0    21.3    +      -       +      +
    228A  ARG      4.1     0.8    +      -       -      -
    229A  ILE*     1.3    71.1    -      -       -      +
    231A  LEU*     1.3    62.2    +      -       -      +
    246A  ILE*     4.1     9.9    -      -       +      -
    247A  TYR      3.4    27.1    -      -       -      +
    248A  ILE*     4.5     6.1    -      -       +      +
    256A  ILE*     4.9     0.4    -      -       +      -
    267A  ALA*     3.8    28.5    -      -       +      -
    268A  LYS*     4.0    24.5    -      -       -      +
    269A  ILE*     4.0    14.8    -      -       +      +
    274A  VAL*     4.2    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  ILE*     4.3    12.1    -      -       +      -
    214A  PHE*     4.1    19.7    -      -       +      -
    219A  PHE*     3.5    46.7    -      -       +      -
    220A  TYR      3.5     5.8    -      -       -      -
    221A  ALA*     3.8    24.5    -      -       +      +
    229A  ILE*     3.9    18.6    -      -       +      +
    230A  LEU*     1.3    74.5    -      -       -      +
    232A  TYR*     1.3    60.9    +      -       -      +
    233A  GLY      4.1     0.2    -      -       -      -
    245A  LYS      3.7     0.2    -      -       -      +
    246A  ILE*     3.1     9.4    -      -       -      +
    247A  TYR*     2.7    49.2    +      -       +      +
    249A  TYR*     4.2    12.8    -      -       +      -
    253A  VAL*     4.8     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  SER      4.4     0.2    -      -       -      +
    219A  PHE*     3.3     3.5    -      -       -      -
    220A  TYR*     2.8    54.0    +      +       +      +
    222A  ILE*     3.4    39.3    -      -       +      -
    230A  LEU      4.1     0.2    +      -       -      -
    231A  LEU*     1.3    72.7    -      -       -      +
    233A  GLY*     1.3    59.4    +      -       -      +
    244A  ASP*     3.4    37.0    +      -       +      +
    245A  LYS      3.5     3.8    -      -       -      -
    246A  ILE*     4.2    11.7    -      -       +      -
    263A  GLU*     4.5     2.9    +      -       -      +
    264A  VAL*     2.7    40.0    +      -       +      -
    265A  ALA*     4.3    11.0    +      -       -      -
    266A  GLN*     5.0     1.3    -      -       -      -
    267A  ALA*     5.2     1.6    -      -       +      -
    279A  PHE*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  SER      3.6     7.2    -      -       -      -
    219A  PHE*     3.4     9.5    -      -       -      +
    231A  LEU      4.1     0.6    -      -       -      -
    232A  TYR*     1.3    75.9    -      -       -      +
    234A  LYS*     1.3    63.1    +      -       -      +
    244A  ASP*     3.9    19.1    -      -       -      -
    245A  LYS*     2.8    25.0    +      -       -      +
    247A  TYR*     2.9    17.7    -      -       -      -
----------------------------------------------------------
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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