Contacts of the strand formed by residues 139 - 143 (chain E) in PDB entry 2ZUQ


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 THR 139 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137E  ALA      4.2     5.0    +      -       -      -
    138E  PRO*     1.3    68.8    -      -       -      +
    140E  VAL*     1.3    62.1    +      -       -      +
    141E  SER*     3.9     1.7    +      -       -      -
    160E  PHE      3.0    13.0    -      -       -      +
    162E  ASN*     2.7    35.2    +      -       -      +
    163E  ASN*     4.6     6.9    +      -       -      +
    143F  THR*     5.1    16.1    -      -       +      +
    188F  THR*     5.3     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 140 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138E  PRO      3.3    11.2    +      -       -      +
    139E  THR*     1.3    75.1    -      -       -      +
    141E  SER*     1.3    66.4    +      -       -      +
    160E  PHE      3.3     6.5    -      -       -      +
    161E  LEU*     4.1    20.4    -      -       +      -
    219E  CYS*     3.9    27.8    -      -       -      +
    221E  ALA*     4.3    10.5    -      -       +      +
    230E  ILE*     3.4    43.0    -      -       +      +
    232E  LYS*     3.9    26.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 141 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139E  THR      4.7     1.5    +      -       -      -
    140E  VAL*     1.3    78.4    -      -       -      +
    142E  ILE*     1.3    58.7    +      -       -      +
    143E  PHE*     3.2    24.2    -      -       -      -
    159E  CYS*     3.1     4.9    -      -       -      -
    160E  PHE*     2.9    36.8    +      -       -      +
    162E  ASN*     4.9     0.7    +      -       -      -
    232E  LYS*     3.7    14.4    -      -       -      +
    143F  THR*     3.4    31.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 142 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141E  SER*     1.3    70.1    -      -       -      +
    143E  PHE*     1.3    76.6    +      -       -      +
    144E  PRO*     4.2     3.8    -      -       -      +
    157E  VAL*     4.3     2.2    -      -       +      -
    158E  VAL      3.7     7.6    -      -       -      +
    159E  CYS*     3.4    10.3    -      -       +      -
    173E  TRP*     3.8    20.2    -      -       +      -
    218E  THR*     3.8     9.6    -      -       -      +
    219E  CYS*     3.7    28.3    -      -       -      +
    232E  LYS*     3.1    53.1    +      -       +      +
    233E  SER      4.2    10.8    -      -       -      +
    234E  PHE*     3.8    32.5    -      -       +      +
    132F  PRO*     4.9     2.8    -      -       -      +
    133F  VAL*     4.7     6.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 143 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141E  SER*     3.2    37.0    -      -       -      -
    142E  ILE*     1.3    92.6    -      -       -      +
    144E  PRO*     1.3    68.3    -      -       +      +
    156E  SER      4.5     0.2    -      -       -      +
    157E  VAL*     3.4     5.9    -      -       -      +
    158E  VAL*     2.8    51.3    +      -       +      +
    160E  PHE*     4.0    15.3    -      +       -      -
    232E  LYS*     5.4     0.2    -      -       -      -
    130F  LEU*     3.4    43.5    -      -       +      -
    131F  ALA      3.8     8.5    -      -       -      +
    132F  PRO*     3.8    18.8    -      -       +      -
    143F  THR*     3.2    26.7    -      -       -      -
    144F  LEU*     3.9     7.9    -      -       -      -
    145F  GLY      3.8     9.2    -      -       -      -
----------------------------------------------------------
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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