Contacts of the strand formed by residues 179 - 183 (chain E) 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 VAL 179 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114E  VAL*     3.5    26.5    -      -       +      +
    116E  LEU*     3.8    23.8    -      -       +      +
    138E  PHE*     4.7     3.8    -      -       +      -
    174E  LEU*     4.5    15.3    -      -       +      -
    176E  VAL*     4.1     9.2    -      -       +      -
    178E  LYS*     1.3    79.8    -      -       -      +
    180E  ASP*     1.3    67.3    -      -       -      +
    181E  ILE      3.3    27.1    -      -       -      +
    182E  ILE*     4.7     4.3    -      -       +      -
    207E  TRP*     2.8    20.5    +      -       +      +
    208E  LEU*     3.5     3.6    -      -       -      +
    209E  LYS*     3.0    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 180 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112E  ASP      5.0     0.5    -      -       -      +
    113E  LYS*     3.8    31.3    -      -       +      +
    114E  VAL*     3.1    35.3    +      -       -      +
    179E  VAL*     1.3    76.2    -      -       -      +
    181E  ILE*     1.3    62.5    +      -       +      +
    208E  LEU*     4.1     0.9    -      -       -      -
    209E  LYS*     2.9    41.2    +      -       -      +
    212E  GLY*     3.4     9.0    -      -       -      -
    213E  LEU*     3.2    21.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 181 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109E  VAL*     3.5    35.4    -      -       +      +
    110E  PHE*     3.7    34.5    -      -       +      -
    113E  LYS*     4.2    12.6    -      -       +      -
    114E  VAL      3.3     2.2    +      -       -      +
    115E  VAL*     3.4    10.6    -      -       +      +
    116E  LEU      2.9    24.1    +      -       -      -
    179E  VAL*     3.3     5.0    -      -       -      +
    180E  ASP*     1.3    87.7    -      -       +      +
    182E  ILE*     1.3    71.4    +      -       -      +
    183E  ILE*     4.1     3.4    -      -       +      -
    208E  LEU*     4.3     0.9    -      -       -      -
    213E  LEU*     3.3    21.1    -      -       +      +
    215E  PHE*     3.9    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 182 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116E  LEU*     3.4    28.9    -      -       +      +
    118E  VAL*     4.1    15.3    -      -       +      -
    179E  VAL*     4.7     3.1    -      -       +      -
    181E  ILE*     1.3    76.9    -      -       -      +
    183E  ILE*     1.3    68.4    +      -       -      +
    184E  SER*     4.9     1.6    -      -       -      -
    200E  VAL*     4.8     5.2    -      -       +      -
    203E  ALA*     3.9    10.1    -      -       +      +
    204E  ARG*     3.7    34.5    -      -       -      +
    207E  TRP      5.4     0.2    -      -       -      -
    208E  LEU*     4.1    19.7    -      -       +      +
    213E  LEU      2.9     7.5    +      -       -      -
    214E  MET*     3.3    30.4    -      -       +      +
    215E  PHE*     2.9    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 183 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99E  TYR*     5.5     0.9    -      -       +      -
    103E  MET*     3.9    20.4    -      -       +      -
    110E  PHE*     4.4     5.6    -      -       +      -
    115E  VAL*     3.9    24.0    -      -       +      -
    116E  LEU      2.9     8.0    +      -       -      +
    117E  ASP*     3.5    23.6    -      -       +      +
    118E  VAL      3.0    24.4    +      -       -      -
    125E  LEU*     3.6    37.7    -      -       +      +
    126E  SER*     4.2     1.3    -      -       -      +
    129E  ALA*     4.1     6.3    -      -       +      -
    137E  VAL*     5.3     0.2    -      -       +      -
    181E  ILE*     4.1     7.4    -      -       +      -
    182E  ILE*     1.3    79.0    -      -       -      +
    184E  SER*     1.3    62.9    +      -       -      +
    215E  PHE*     3.3    24.7    -      -       +      +
----------------------------------------------------------
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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