Contacts of the strand formed by residues 179 - 184 (chain F) in PDB entry 2HU4


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 179 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134F  LEU*     3.7     3.2    -      -       -      +
    177F  ALA*     3.4     3.2    -      -       -      +
    178F  TRP*     1.3   102.0    -      -       -      +
    180F  ALA*     1.3    63.1    +      -       -      +
    192F  ILE      3.8     0.2    -      -       -      +
    194F  ILE*     2.9    35.8    +      -       -      +
    224F  ARG*     4.0     2.0    -      -       -      +
    225F  THR*     3.1    28.6    +      -       -      +
    227F  GLU*     3.1    23.8    +      -       -      -
    805F  G39      4.3     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 180 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121F  PHE*     4.7     4.9    -      -       +      -
    134F  LEU*     4.1     9.1    -      -       +      +
    158F  LEU*     3.7    35.7    -      -       +      -
    179F  SER*     1.3    76.2    +      -       -      +
    181F  SER*     1.3    63.1    +      -       -      +
    192F  ILE      2.9    16.6    -      -       -      +
    193F  GLY*     4.2     1.8    -      -       -      -
    225F  THR*     3.1    11.6    -      -       -      +
    227F  GLU*     3.0    38.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 181 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121F  PHE*     4.1     6.5    -      -       -      -
    158F  LEU*     4.9     0.7    -      -       -      +
    180F  ALA*     1.3    81.6    -      -       -      +
    182F  ALA*     1.3    63.0    +      -       -      +
    191F  THR*     3.5     0.5    -      -       -      -
    192F  ILE*     2.6    44.2    +      -       -      +
    225F  THR*     4.2    11.0    -      -       -      -
    226F  GLN*     3.3    22.8    +      -       -      -
    228F  SER      3.3    16.2    +      -       -      -
    230F  CYS*     3.6    13.0    -      -       -      +
    239F  THR*     3.8    10.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 182 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121F  PHE*     3.8    14.8    -      -       +      -
    123F  SER*     3.8     2.5    +      -       -      -
    132F  PHE*     3.9    33.7    -      -       +      -
    158F  LEU*     5.4     1.3    -      -       +      -
    181F  SER*     1.3    79.7    +      -       -      +
    183F  CYS*     1.3    62.5    +      -       -      +
    189F  TRP*     4.7     0.2    -      -       +      -
    190F  LEU      3.1    14.1    -      -       -      +
    191F  THR*     3.9     7.0    -      -       +      -
    229F  GLU*     3.0    13.2    -      -       -      +
    230F  CYS*     3.0    23.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 183 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123F  SER*     3.7    12.6    -      -       -      +
    182F  ALA*     1.3    76.3    -      -       -      +
    184F  HIS*     1.3    57.8    +      -       -      +
    185F  ASP      4.3     0.3    +      -       -      -
    188F  SER      4.2     0.2    -      -       -      +
    189F  TRP*     3.3     8.4    -      -       -      -
    190F  LEU*     2.8    42.5    +      -       -      +
    229F  GLU*     5.1     0.4    -      -       -      +
    230F  CYS*     2.0    57.9    -      -       -      +
    232F  CYS*     3.4    28.7    -      -       -      -
    237F  CYS*     4.0     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 184 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85F  LEU*     3.4    17.9    -      -       +      +
    123F  SER*     4.4     0.2    +      -       -      -
    124F  CYS      3.6    22.0    +      -       -      +
    125F  SER*     3.2    27.0    -      -       -      -
    126F  HIS*     3.8     9.4    +      +       -      -
    183F  CYS*     1.3    76.8    -      -       -      +
    185F  ASP*     1.3    58.2    +      -       -      +
    186F  GLY*     3.1    47.3    +      -       -      -
    187F  THR      3.5     8.4    +      -       -      -
    188F  SER*     3.5    25.1    -      -       -      -
    189F  TRP*     3.3    36.5    +      +       +      -
    232F  CYS*     3.7     9.7    -      -       -      +
----------------------------------------------------------
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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