Contacts of the strand formed by residues 6 - 13 (chain B) 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 VAL 6 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  LYS*     1.3   111.1    +      -       -      +
      7B  ILE*     1.3    62.3    +      -       -      +
      8B  LYS*     3.9     2.0    +      -       +      +
     27B  GLU*     3.6    33.7    -      -       +      -
     28B  VAL      3.6     5.8    -      -       -      +
     29B  ALA*     4.1     9.4    -      -       +      -
     30B  PRO*     3.9    18.3    -      -       +      +
     37B  ARG*     4.2     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 7 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  THR*     3.7    32.5    -      -       +      +
      5B  LYS      3.3     1.5    +      -       -      +
      6B  VAL*     1.3    76.7    -      -       -      +
      8B  LYS*     1.3    76.8    +      -       -      +
      9B  CYS*     4.2     4.0    -      -       +      -
     27B  GLU*     3.1     6.2    -      -       -      -
     28B  VAL*     2.9    40.3    +      -       +      +
     37B  ARG*     3.6    16.6    -      -       -      +
     74B  GLU*     3.1    27.8    -      -       -      +
    149B  TYR*     3.7    37.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 8 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  LYS*     6.2     1.6    -      -       -      +
      6B  VAL*     3.9     2.1    +      -       +      +
      7B  ILE*     1.3    79.0    -      -       -      +
      9B  CYS*     1.3    72.0    +      -       -      +
     25B  ASP*     3.9    27.5    -      -       +      +
     26B  VAL      3.3     9.9    -      -       -      +
     27B  GLU*     4.6    19.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 9 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  ILE*     4.2     2.0    -      -       +      -
      8B  LYS*     1.3    79.1    -      -       -      +
     10B  LYS*     1.3    64.2    +      -       -      +
     25B  ASP*     3.0    12.4    -      -       -      +
     26B  VAL*     2.8    35.4    +      -       -      -
     28B  VAL*     3.8    28.9    -      -       -      -
    147B  SER*     4.1    13.7    -      -       -      -
    148B  GLN*     3.0    19.5    -      -       +      +
    149B  TYR*     4.2    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 10 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  CYS*     1.3    75.8    -      -       -      +
     11B  ALA*     1.3    60.8    +      -       -      +
     23B  ILE*     4.1    19.3    +      -       +      +
     24B  GLU*     3.0    20.1    -      -       -      +
     25B  ASP*     3.1    36.9    +      -       -      +
    147B  SER*     3.5     2.7    +      -       -      -
    148B  GLN*     2.7    58.5    +      -       -      +
    352B  PHE*     4.1    13.8    -      -       +      -
    353B  GLU*     5.9     2.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 11 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  LYS*     1.3    76.2    -      -       -      +
     12B  ALA*     1.3    60.7    +      -       -      +
     13B  VAL*     3.3     8.7    +      -       +      +
     23B  ILE*     4.3     0.4    -      -       -      -
     24B  GLU      2.8    30.2    +      -       -      +
     26B  VAL*     3.5    20.0    -      -       +      -
     64B  ILE*     3.8    15.7    -      -       +      -
    146B  PHE      3.4    10.5    -      -       -      +
    147B  SER*     3.3    20.6    -      -       -      +
    352B  PHE*     3.9     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  ALA*     1.3    68.4    -      -       -      +
     13B  VAL*     1.3    61.4    +      -       -      +
     14B  LEU      4.2     0.2    +      -       -      -
     21B  PHE*     4.1    13.8    -      -       +      -
     22B  SER      3.2     8.1    -      -       -      -
     23B  ILE*     4.2     4.9    -      -       +      +
     64B  ILE*     3.8    17.0    -      -       -      +
     65B  LEU      4.5     1.0    +      -       -      -
    146B  PHE*     3.0    17.9    +      -       +      +
    352B  PHE*     3.5    12.7    -      -       +      -
    355B  ILE*     3.7    42.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  ALA      3.4    15.7    -      -       -      +
     12B  ALA*     1.3    75.0    -      -       -      +
     14B  LEU*     1.3    59.8    +      -       -      +
     15B  TRP*     3.5    43.5    -      -       +      +
     21B  PHE*     3.8     3.1    -      -       -      -
     22B  SER*     2.8    29.8    +      -       -      +
     24B  GLU*     4.3     8.3    -      -       +      -
     26B  VAL*     4.0    22.0    -      -       +      -
     62B  PRO*     4.1     7.6    -      -       +      -
     63B  VAL      3.7     9.4    -      -       -      +
     64B  ILE*     4.0    13.5    -      -       +      -
    137B  ILE*     3.9    19.3    -      -       +      -
----------------------------------------------------------
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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