Contacts of the strand formed by residues 166 - 171 (chain B) in PDB entry 5WN0


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 166 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159B  VAL*     3.8    26.2    -      -       +      -
    160B  ALA      3.6    11.7    -      -       -      +
    161B  GLU*     3.9    15.3    -      -       +      +
    165B  PHE*     1.3    77.6    -      -       -      +
    167B  LEU*     1.3    63.2    +      -       -      +
    199B  LEU*     4.4    19.5    -      -       +      +
    202B  ARG*     5.6     2.5    -      -       -      +
    203B  LYS*     4.0    20.6    -      -       +      +
    204B  PRO      2.9    13.2    +      -       -      +
    205B  LEU*     3.4    19.0    -      -       +      +
    206B  VAL      2.9    24.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  ILE*     4.2    12.1    -      -       +      -
     91B  ILE*     3.9    40.6    -      -       +      -
     93B  CYS*     4.2    11.2    -      -       -      -
    133B  LEU*     4.2    10.8    -      -       +      +
    158B  ILE      3.7     1.0    -      -       -      +
    159B  VAL*     3.6     1.7    -      -       -      +
    160B  ALA*     2.8    46.1    +      -       +      +
    162B  PHE*     4.3     4.7    -      -       +      -
    165B  PHE*     3.7    13.2    -      -       +      -
    166B  VAL*     1.3    73.4    -      -       -      +
    168B  VAL*     1.3    72.0    +      -       -      +
    169B  THR*     4.6     0.4    -      -       -      +
    206B  VAL*     3.2    37.2    -      -       +      +
    208B  CYS*     4.4    12.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157B  VAL*     4.0    14.8    -      -       +      -
    158B  ILE      3.3     6.5    -      -       -      +
    159B  VAL*     4.0    12.3    -      -       +      -
    167B  LEU*     1.3    79.7    -      -       -      +
    169B  THR*     1.3    75.1    +      -       -      +
    192B  PHE*     4.1    13.5    -      -       +      -
    195B  PHE*     5.0     0.4    -      -       +      -
    196B  LEU*     4.0     7.4    -      -       +      -
    199B  LEU*     3.5    31.9    -      -       +      -
    205B  LEU*     3.9    11.0    -      -       +      -
    206B  VAL      2.8     9.4    +      -       -      +
    207B  LEU*     3.3    21.7    -      -       +      -
    208B  CYS      3.0    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  CYS*     2.8    39.0    -      -       +      -
     94B  LEU      4.6     4.3    -      -       -      +
     95B  GLN*     2.6    38.8    -      -       +      +
    131B  VAL*     5.0     5.5    -      -       +      +
    132B  GLY      5.3     2.7    -      -       -      +
    133B  LEU*     4.5     8.4    -      -       -      +
    156B  ARG      3.5     0.6    -      -       -      +
    157B  VAL*     3.2     6.6    -      -       -      -
    158B  ILE*     3.0    37.3    +      -       -      +
    167B  LEU*     4.6     0.7    -      -       -      +
    168B  VAL*     1.3    75.0    -      -       -      +
    170B  ALA*     1.3    62.9    +      -       -      +
    208B  CYS*     3.1    12.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  GLN*     3.0    19.0    -      -       -      +
    156B  ARG      3.2     6.5    -      -       -      -
    157B  VAL*     4.1     7.4    -      -       +      -
    169B  THR*     1.3    76.7    -      -       -      +
    171B  TYR*     1.3    60.6    +      -       -      +
    172B  VAL*     3.8    13.5    -      -       +      +
    188B  TRP*     4.5     1.3    -      -       +      -
    192B  PHE*     3.7    33.2    -      -       +      -
    207B  LEU*     4.1     8.1    -      -       +      -
    208B  CYS      3.0     6.0    +      -       -      +
    209B  GLY*     3.3     1.7    -      -       -      -
    210B  ASP      3.2    14.8    +      -       -      -
    211B  LEU*     4.9     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  ASN*     3.5    15.3    -      -       -      -
     95B  GLN*     3.6    17.3    -      -       +      -
     96B  GLU*     2.9    46.6    +      -       +      +
    128B  TYR*     5.3     7.8    +      +       -      -
    129B  SER*     3.5    23.8    -      -       -      -
    130B  GLY      4.8     0.4    -      -       -      -
    131B  VAL*     3.8    10.3    -      -       +      -
    156B  ARG*     2.5    75.9    +      -       -      +
    170B  ALA*     1.3    72.9    -      -       -      +
    172B  VAL*     1.3    53.5    +      -       -      +
    174B  ASN*     5.5     6.7    +      -       -      +
    188B  TRP*     5.2     0.2    -      -       -      -
    210B  ASP*     3.5    32.1    -      -       +      -
    212B  ASN*     3.9    13.4    +      -       -      -
----------------------------------------------------------
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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