Contacts of the strand formed by residues 162 - 166 (chain J) in PDB entry 5DST


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 162 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126J  SER*     3.5    37.2    -      -       -      +
    127J  MET*     3.8    22.9    -      -       +      -
    130J  ALA*     3.9    17.5    -      -       +      -
    137J  VAL*     3.3    17.3    -      -       +      +
    139J  GLY      5.1     0.7    -      -       -      +
    153J  ILE*     3.6    29.6    -      -       +      +
    158J  LEU*     2.9    25.3    +      -       +      +
    159J  ASP*     2.9    22.0    -      -       -      +
    161J  ILE*     1.3    73.3    -      -       -      +
    163J  THR*     1.3    68.4    +      -       -      +
    164J  ILE*     3.9    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 163 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136J  LYS*     3.5    21.8    +      -       -      -
    137J  VAL      2.9     5.7    +      -       -      -
    138J  PHE*     3.4    19.5    -      -       -      -
    139J  GLY      3.0    22.5    +      -       -      +
    159J  ASP      4.8     1.0    +      -       -      -
    162J  ILE*     1.3    78.3    +      -       -      +
    164J  ILE*     1.3    70.3    +      -       -      +
    165J  PHE*     4.0    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 164 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120J  SER*     3.8    22.4    -      -       -      +
    123J  GLY*     5.4     0.7    -      -       -      -
    126J  SER*     4.9     3.1    -      -       -      +
    139J  GLY*     3.3    16.8    -      -       -      +
    141J  GLU*     5.0     1.1    -      -       +      -
    146J  SER*     4.2    17.5    -      -       -      -
    149J  SER*     3.6    23.3    -      -       -      +
    150J  GLU*     4.0    31.0    +      -       +      +
    153J  ILE*     3.8    29.2    -      -       +      -
    162J  ILE*     3.9    11.7    -      -       +      -
    163J  THR*     1.3    78.9    -      -       -      +
    165J  PHE*     1.3    75.1    +      -       -      +
    166J  LYS*     3.9     2.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 165 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138J  PHE*     3.8    24.0    -      +       +      -
    139J  GLY      2.6    17.4    +      -       -      +
    140J  ILE*     3.5     5.9    -      -       +      +
    141J  GLU      3.3    19.2    +      -       -      -
    163J  THR*     4.0    25.4    -      -       +      -
    164J  ILE*     1.3    76.6    -      -       -      +
    166J  LYS*     1.3    61.0    +      -       -      +
    167J  GLY      3.1     7.6    +      -       -      -
    172J  VAL*     4.3    22.2    -      -       +      -
    173J  GLU      4.3    13.2    -      -       -      -
    174J  LEU*     3.7    25.4    -      -       +      -
    175J  PRO*     3.5    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 166 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141J  GLU      3.5     4.0    -      -       -      +
    142J  CYS      4.6     6.9    +      -       -      +
    143J  SER      4.2     5.3    -      -       -      +
    144J  SER*     3.8    23.1    -      -       -      +
    146J  SER*     2.9    30.3    -      -       -      +
    147J  ASP*     3.2    29.6    +      -       -      +
    150J  GLU*     6.1     2.9    -      -       -      +
    164J  ILE*     3.9     4.2    +      -       +      +
    165J  PHE*     1.3    68.4    -      -       -      +
    167J  GLY*     1.3    59.2    +      -       -      +
    172J  VAL*     4.4     4.4    -      -       -      +
----------------------------------------------------------
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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