Contacts of the strand formed by residues 53 - 59 (chain F) in PDB entry 2ZJQ


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 53 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12F  LEU      3.4    19.5    +      -       -      +
     13F  PRO      3.7     0.6    +      -       -      +
     14F  ALA*     6.5     0.2    -      -       -      -
     41F  PHE*     4.4     5.1    -      -       +      -
     45F  THR*     4.5    17.9    -      -       +      -
     48F  LYS*     3.3    44.4    -      -       +      +
     51F  ALA      3.4    10.4    +      -       -      +
     52F  ILE*     1.3    83.0    -      -       -      +
     54F  PRO*     1.3    75.9    -      -       +      +
     55F  VAL*     3.6    12.7    +      -       +      +
     69F  THR*     4.1    17.0    -      -       +      -
     70F  LYS      3.5    25.1    -      -       -      +
     71F  THR      4.4     1.1    -      -       -      -
     72F  PRO*     3.6    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 54 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10F  LEU      3.7     8.1    -      -       -      +
     11F  GLN*     3.6    26.9    -      -       +      +
     52F  ILE      4.3     0.2    -      -       -      -
     53F  ILE*     1.3    84.1    -      -       +      +
     55F  VAL*     1.3    61.5    +      -       -      +
     70F  LYS*     2.8    41.9    +      -       +      +
     71F  THR      3.2    28.5    -      -       -      +
     73F  PRO*     3.7    20.6    -      -       +      -
    111F  LYS*     5.8     0.2    -      -       -      +
   1071X    U      6.0     1.8    -      -       -      +
   1072X    U      6.3     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 55 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9F  LYS*     4.9     0.2    -      -       -      +
     10F  LEU*     3.1    38.3    +      -       +      +
     11F  GLN*     4.8     0.2    -      -       -      +
     12F  LEU*     5.7     4.0    -      -       +      +
     37F  PHE*     4.7    13.5    -      -       +      -
     41F  PHE*     3.5    32.8    -      -       +      -
     53F  ILE*     3.6     9.6    +      -       +      +
     54F  PRO*     1.3    79.7    -      -       -      +
     56F  GLU*     1.3    65.6    +      -       -      +
     57F  ILE*     5.0     0.4    -      -       +      -
     67F  PHE*     3.5    31.9    -      -       +      -
     68F  ILE      3.7    10.8    -      -       -      +
     69F  THR*     4.5    14.8    -      -       -      +
     70F  LYS*     3.2     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 56 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7F  ILE*     4.9     6.4    -      -       +      +
      8F  VAL      3.8     6.5    -      -       -      +
      9F  LYS*     3.2    39.3    +      -       +      +
     55F  VAL*     1.3    75.8    -      -       -      +
     57F  ILE*     1.3    62.8    +      -       -      +
     58F  THR*     3.9     5.5    +      -       -      +
     66F  THR      3.7     0.2    -      -       -      +
     67F  PHE*     3.4    20.3    +      -       -      -
     68F  ILE*     3.8    16.1    +      -       +      +
     70F  LYS*     3.3    35.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 57 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7F  ILE*     3.7     5.2    -      -       -      +
      8F  VAL*     2.8    50.4    +      -       +      +
     10F  LEU*     3.8    26.5    -      -       +      -
     27F  LEU*     4.6    16.8    -      -       +      -
     37F  PHE*     3.7    39.5    -      -       +      -
     55F  VAL*     4.7     3.1    -      -       +      +
     56F  GLU*     1.3    75.0    -      -       -      +
     58F  THR*     1.3    63.1    +      -       -      +
     59F  ILE*     4.1    12.7    +      -       +      -
     65F  PHE*     3.7    26.0    -      -       +      -
     66F  THR      3.3    13.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 58 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7F  ILE*     4.7    14.1    -      -       +      +
     56F  GLU*     3.9     6.1    +      -       -      +
     57F  ILE*     1.3    75.8    +      -       -      +
     59F  ILE*     1.3    66.8    +      -       -      +
     60F  TYR*     3.9    22.1    +      -       +      +
     64F  SER      3.6     1.7    -      -       -      +
     65F  PHE*     3.2     3.5    -      -       -      -
     66F  THR*     3.0    43.3    +      -       -      +
     68F  ILE*     6.1     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 59 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2F  LYS      5.7     4.0    -      -       -      +
      3F  LYS      4.8     8.5    -      -       -      +
      4F  VAL*     5.5     9.6    -      -       +      +
      8F  VAL*     4.5    16.8    -      -       +      +
     27F  LEU*     4.3    23.8    -      -       +      -
     30F  TYR*     4.8    17.9    -      -       +      -
     57F  ILE*     4.0     8.4    +      -       +      -
     58F  THR*     1.3    78.1    -      -       -      +
     60F  TYR*     1.3    78.9    +      -       -      +
     63F  ARG*     4.6     8.3    -      -       -      -
     64F  SER      3.4    15.0    -      -       -      +
     65F  PHE*     3.6    23.3    -      -       +      +
----------------------------------------------------------
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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