Contacts of the strand formed by residues 153 - 158 (chain B) in PDB entry 4WGK


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 153 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  PHE      3.5     1.4    -      -       -      +
    143B  ILE*     3.4     6.1    -      -       -      +
    144B  MET*     2.9    37.8    +      -       -      +
    151B  ASN      4.2     0.9    -      -       -      +
    152B  ARG*     1.3    80.5    -      -       -      +
    154B  VAL*     1.3    64.3    +      -       -      +
    155B  PHE      4.2     0.4    -      -       -      -
    187B  ASN*     3.5     8.5    -      -       +      -
    423B  LEU*     4.1    18.4    -      -       +      +
    424B  ALA      4.2    14.1    -      -       -      +
    425B  SER*     4.9     0.2    -      -       -      -
    527B  ILE*     3.7    33.7    -      -       +      -
    529B  LEU*     3.2    21.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 154 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141B  ALA*     4.7     2.0    -      -       +      -
    142B  PHE      3.4     7.2    -      -       -      +
    143B  ILE*     4.1    15.5    -      -       +      -
    153B  THR*     1.3    79.1    -      -       -      +
    155B  PHE*     1.3    62.1    +      -       -      +
    156B  VAL*     3.6    24.7    -      -       +      -
    183B  TYR*     3.5    37.7    -      -       +      -
    187B  ASN      2.8    13.4    +      -       -      +
    188B  VAL*     3.5    17.6    -      -       +      -
    189B  ILE*     2.8    27.9    +      -       -      +
    231B  ILE*     4.4    17.3    -      -       +      -
    527B  ILE*     3.9     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 155 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141B  ALA*     3.5     1.0    -      -       -      -
    142B  PHE*     2.8    43.3    +      +       +      +
    144B  MET*     5.0     7.1    -      -       +      +
    153B  THR      4.2     0.4    -      -       -      -
    154B  VAL*     1.3    73.4    -      -       -      +
    156B  VAL*     1.3    63.4    +      -       -      +
    157B  SER*     4.1    16.8    -      -       -      -
    189B  ILE*     3.8    17.9    -      -       +      -
    191B  SER*     4.2    16.6    -      -       -      -
    297B  ILE*     3.8    42.2    -      -       +      -
    299B  TRP*     3.9    14.8    -      +       -      -
    346B  ALA*     3.6    24.5    -      -       +      -
    527B  ILE*     6.0     2.0    -      -       +      -
    534B  ILE*     4.5    18.8    -      -       +      -
    570B  SER*     3.5    24.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 156 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139B  SER*     3.3    26.9    -      -       -      +
    140B  ARG      3.3    10.8    -      -       -      +
    141B  ALA*     3.9    11.4    -      -       +      -
    154B  VAL*     3.6    22.4    -      -       +      -
    155B  PHE*     1.3    82.1    -      -       -      +
    157B  SER*     1.3    57.5    +      -       -      +
    158B  ILE*     3.6    14.1    -      -       +      -
    189B  ILE      2.9    14.0    +      -       -      +
    190B  LEU*     3.8    20.4    -      -       +      -
    191B  SER*     2.7    35.2    +      -       -      +
    227B  ILE*     4.4     6.1    -      -       +      -
    231B  ILE*     4.2     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 157 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138B  TYR      3.9     1.9    -      -       -      +
    139B  SER*     3.8     0.7    -      -       -      -
    140B  ARG*     2.9    38.0    +      -       -      +
    155B  PHE*     4.1    18.6    -      -       -      -
    156B  VAL*     1.3    71.5    -      -       -      +
    158B  ILE*     1.3    62.7    +      -       -      +
    159B  ASP*     5.6     0.2    -      -       -      +
    191B  SER*     3.4     6.4    +      -       -      -
    192B  GLY      5.4     0.2    -      -       -      -
    193B  THR*     3.6    10.0    +      -       -      +
    344B  ALA*     3.8    25.0    -      -       -      +
    345B  PHE      2.9    24.7    +      -       -      -
    346B  ALA*     3.9     4.9    -      -       -      -
    347B  SER      5.0     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 158 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  CYS*     3.9    23.1    -      -       -      -
    138B  TYR      3.7     2.5    -      -       -      +
    139B  SER*     4.0     5.4    -      -       -      +
    156B  VAL*     3.6    21.5    -      -       +      +
    157B  SER*     1.3    77.6    +      -       -      +
    159B  ASP*     1.3    55.8    +      -       -      +
    160B  ILE*     2.7    36.9    +      -       +      -
    163B  VAL*     3.9    24.2    -      -       +      -
    167B  LEU*     5.1     1.3    -      -       +      -
    190B  LEU*     4.1    14.8    -      -       +      -
    191B  SER      2.6    14.1    +      -       -      +
    192B  GLY*     3.4     1.9    -      -       -      -
    193B  THR*     2.9    25.2    +      -       -      +
    223B  MET*     6.1     0.7    -      -       +      -
    227B  ILE*     3.7    33.4    -      -       +      -
----------------------------------------------------------
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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