Contacts of the strand formed by residues 341 - 346 (chain A) in PDB entry 4ZSQ


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 PHE 341 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  LEU      4.0     4.2    -      -       -      +
    153A  GLN*     4.6     5.2    -      -       -      -
    154A  LEU      4.7     0.7    +      -       -      -
    298A  ILE*     3.6    31.6    -      -       +      -
    299A  THR      3.6     9.4    -      -       -      -
    300A  ILE*     3.4    31.0    -      -       +      -
    337A  ILE*     3.1    30.1    -      -       +      -
    338A  MET*     2.7    22.2    +      -       -      +
    339A  GLU      3.4     0.6    -      -       -      -
    340A  GLY*     1.3    87.9    -      -       -      +
    342A  TYR*     1.3    66.0    +      -       -      +
    343A  VAL*     3.8    12.2    +      -       +      +
    354A  PHE*     4.2    12.1    -      +       +      -
    355A  ALA      3.0    19.3    -      -       -      +
    356A  VAL*     4.2     1.6    -      -       -      -
    357A  SER*     3.5    11.5    +      -       -      -
    368A  ALA*     4.4     6.1    -      -       +      -
    369A  ALA      3.8    11.2    -      -       -      -
    370A  VAL*     3.6    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  SER*     2.7    37.5    +      -       -      -
    152A  LEU      3.3    22.9    -      -       -      -
    153A  GLN*     3.9     9.6    -      -       +      +
    175A  ILE*     3.7     5.4    -      -       -      +
    179A  ILE*     3.5    14.1    -      -       +      -
    180A  ASP      2.9    34.3    +      -       -      -
    183A  LEU*     3.6    29.4    -      -       +      +
    184A  TYR*     3.3    42.2    -      +       +      -
    188A  LEU*     4.5     4.1    -      -       +      +
    341A  PHE*     1.3    73.9    -      -       -      +
    343A  VAL*     1.3    59.4    +      -       -      +
    344A  VAL*     4.1    11.0    -      -       +      -
    353A  GLY      3.5     1.6    -      -       -      +
    354A  PHE*     3.5     5.0    -      -       -      -
    355A  ALA*     2.8    28.2    +      -       +      +
    357A  SER*     3.8     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  SER*     3.3     2.1    -      -       -      -
    152A  LEU      2.9    37.4    +      -       -      +
    227A  VAL*     4.4     4.9    -      -       +      -
    338A  MET*     4.1    27.1    -      -       +      +
    341A  PHE*     4.0    20.2    -      -       +      +
    342A  TYR*     1.3    77.4    -      -       -      +
    344A  VAL*     1.3    62.6    +      -       -      +
    345A  PHE*     3.6    31.9    -      -       +      -
    352A  ILE*     3.6    22.4    -      -       +      -
    353A  GLY      3.4     3.4    -      -       -      +
    354A  PHE*     4.2    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  LEU*     4.4    11.4    -      -       +      -
    150A  PHE      3.9     7.2    -      -       -      +
    151A  SER*     3.9    13.9    -      -       -      -
    179A  ILE*     3.9    31.2    -      -       +      -
    188A  LEU*     3.7    26.7    -      -       +      -
    190A  TYR*     4.3     6.3    -      -       +      +
    342A  TYR*     4.1    15.0    -      -       +      -
    343A  VAL*     1.3    73.6    -      -       -      +
    345A  PHE*     1.3    62.5    +      -       -      +
    346A  ASP*     3.2    12.5    +      -       +      +
    352A  ILE*     3.1     9.7    -      -       -      +
    353A  GLY*     2.7    42.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  THR*     3.7    21.5    -      -       +      -
    149A  LEU*     3.5     1.3    -      -       -      -
    150A  PHE*     2.7    66.9    +      +       +      +
    152A  LEU*     3.8    20.2    -      -       +      -
    199A  TYR*     3.7    39.9    -      +       +      -
    227A  VAL*     3.7    26.5    -      -       +      -
    338A  MET*     4.1     5.2    -      -       +      -
    343A  VAL*     3.6    39.7    -      -       +      -
    344A  VAL*     1.3    69.6    -      -       -      +
    346A  ASP*     1.3    59.5    +      -       -      +
    347A  ARG*     3.1    11.5    +      -       -      +
    351A  ARG      3.9     1.8    -      -       -      -
    352A  ILE*     4.3     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  LEU*     3.5    28.7    -      -       +      +
    190A  TYR*     4.4     8.5    +      -       +      -
    193A  ILE*     4.9     1.3    -      -       -      -
    344A  VAL*     3.2     5.8    +      -       +      +
    345A  PHE*     1.3    69.8    -      -       -      +
    347A  ARG*     1.3    58.6    +      -       -      +
    348A  ALA*     3.6     7.8    +      -       -      +
    349A  ARG*     3.1    25.8    +      -       -      +
    350A  LYS      3.0     8.3    +      -       -      -
    351A  ARG*     2.8    78.8    +      -       +      +
----------------------------------------------------------
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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