Contacts of the strand formed by residues 34 - 39 (chain A) in PDB entry 1HDZ


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 34 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ALA*     1.3    86.3    -      -       +      +
     35A  GLU*     1.3    54.0    +      -       -      +
     78A  GLU      2.7    14.5    +      -       -      -
     79A  GLY*     3.6    28.1    -      -       -      -
     80A  VAL*     3.4    14.6    -      -       -      +
    153A  ASP*     3.6     9.5    -      -       -      +
    154A  GLU*     2.8    45.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PRO*     3.8     4.9    -      -       +      -
     32A  LYS*     3.4    28.4    +      -       -      +
     33A  ALA      3.1     7.7    -      -       -      +
     34A  TYR*     1.3    79.6    -      -       -      +
     36A  VAL*     1.3    64.1    +      -       -      +
     77A  GLY      2.8    24.4    +      -       -      -
     80A  VAL*     3.3     6.2    -      -       -      +
    123A  LEU*     3.1    19.4    -      -       +      +
    125A  ASP*     4.2     6.4    -      -       -      +
    129A  ARG*     2.8    43.6    +      -       -      -
    151A  VAL*     3.3     9.3    -      -       +      +
    152A  VAL      3.4    10.8    -      -       -      +
    153A  ASP*     4.0    14.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PRO*     4.3     0.9    -      -       -      -
     35A  GLU*     1.3    80.7    -      -       -      +
     37A  ARG*     1.4    60.8    +      -       -      +
     38A  ILE*     3.6    27.9    +      -       +      +
     73A  VAL*     3.7    24.0    -      -       +      -
     75A  SER      3.6     4.5    -      -       -      -
     76A  VAL*     3.6    17.7    -      -       +      +
     80A  VAL*     3.7     8.1    -      -       +      -
     83A  VAL*     3.7    18.4    -      -       +      -
    150A  THR      3.7     0.7    -      -       -      +
    151A  VAL*     3.2     7.8    -      -       -      +
    152A  VAL*     2.9    34.6    +      -       -      +
    154A  GLU*     4.7     4.0    -      -       -      -
    157A  VAL*     4.4    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  THR      3.3    17.2    +      -       -      -
      4A  GLY      3.7    10.5    -      -       -      +
      5A  LYS      2.9    27.0    +      -       -      -
      7A  ILE*     3.3    18.0    -      -       -      +
     28A  VAL*     3.0    38.8    +      -       -      -
     29A  ALA      3.5    15.7    +      -       -      -
     30A  PRO*     3.6    11.5    -      -       -      +
     31A  PRO*     3.6    10.1    -      -       +      +
     36A  VAL*     1.4    72.7    -      -       -      +
     38A  ILE*     1.3    56.7    +      -       -      +
     73A  VAL*     3.7     3.3    -      -       -      -
     74A  GLU*     2.7    53.3    +      -       -      +
     75A  SER*     2.8    28.4    +      -       -      +
    149A  TYR*     4.2    11.2    -      -       +      -
    150A  THR      3.1    12.6    -      -       -      +
    151A  VAL*     4.1     2.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  VAL*     3.6    19.3    -      -       +      +
     37A  ARG*     1.3    78.0    -      -       -      +
     39A  LYS*     1.3    62.8    +      -       -      +
     40A  MET*     3.5    23.9    +      -       +      +
     71A  GLY*     3.8    18.6    -      -       -      +
     72A  ILE      3.3    13.0    -      -       -      +
     73A  VAL*     4.2     1.8    -      -       +      -
     74A  GLU*     4.6     0.7    -      -       -      -
     89A  VAL*     3.8    13.5    -      -       +      +
     91A  PRO*     4.5     8.7    -      -       +      -
    149A  TYR*     3.1    12.6    -      -       -      -
    150A  THR*     2.9    30.1    +      -       +      +
    152A  VAL*     4.0    26.5    -      -       +      -
    157A  VAL*     3.7    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  ILE*     1.3    71.8    -      -       -      +
     40A  MET*     1.3    87.1    +      -       -      +
     41A  VAL*     3.3    10.8    +      -       +      +
     71A  GLY*     3.2     2.8    -      -       -      -
     72A  ILE*     2.7    41.6    +      -       +      +
     74A  GLU*     4.6     4.7    -      -       +      +
    148A  GLN*     2.9    48.8    +      -       -      +
    149A  TYR*     3.7    32.1    -      -       +      +
    374A  PHE*     3.9    16.4    -      -       -      +
----------------------------------------------------------
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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