Contacts of the strand formed by residues 186 - 191 (chain B) in PDB entry 4PKO


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 GLU 186 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161B  LEU*     4.3     3.8    -      -       -      +
    184B  GLN      3.7     4.7    +      -       -      +
    185B  ASP*     1.3    75.6    -      -       -      +
    187B  LEU*     1.3    64.1    +      -       -      +
    188B  ASP*     2.9    32.2    +      -       -      +
    379B  ILE*     3.6     3.3    -      -       -      +
    380B  LYS*     2.7    64.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161B  LEU*     3.8    28.9    -      -       +      +
    164B  GLU*     3.8    37.9    -      -       +      +
    165B  ALA*     3.9    19.5    -      -       +      +
    168B  LYS*     5.6     3.1    -      -       +      -
    186B  GLU*     1.3    74.6    -      -       -      +
    188B  ASP*     1.3    75.8    +      -       -      +
    189B  VAL*     4.1    17.8    +      -       +      +
    377B  ALA*     4.8     3.1    -      -       +      -
    378B  VAL      3.8     5.2    -      -       -      +
    379B  ILE*     3.8    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 188 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  GLU*     2.9    25.8    -      -       -      +
    187B  LEU*     1.3    80.4    -      -       -      +
    189B  VAL*     1.3    67.0    +      -       -      +
    190B  VAL*     5.8     2.9    -      -       +      -
    376B  VAL      4.6     0.2    -      -       -      +
    377B  ALA*     3.8     0.7    -      -       -      -
    378B  VAL*     3.0    44.0    +      -       +      +
    380B  LYS*     3.4    33.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 189 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  ALA*     5.5     1.3    -      -       -      -
    168B  LYS*     3.7    46.0    -      -       +      +
    169B  VAL*     3.8    26.0    -      -       +      -
    187B  LEU*     4.1    23.3    +      -       +      +
    188B  ASP*     1.3    81.0    -      -       -      +
    190B  VAL*     1.3    68.1    +      -       -      +
    191B  GLU*     4.2    16.3    +      -       +      +
    376B  VAL      4.1     1.8    -      -       -      -
    377B  ALA*     4.7     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169B  VAL*     4.2     0.7    -      -       -      +
    188B  ASP*     5.8     2.5    -      -       +      -
    189B  VAL*     1.3    77.2    -      -       -      +
    191B  GLU*     1.3    73.1    +      -       -      +
    192B  GLY      4.6     2.8    -      -       -      +
    194B  GLN*     3.0    55.4    -      -       +      +
    331B  THR*     5.5     1.3    -      -       +      -
    375B  GLY*     3.4     3.5    -      -       -      -
    376B  VAL*     3.0    43.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168B  LYS*     3.3    30.6    -      -       -      +
    169B  VAL*     4.4     4.4    -      -       -      +
    189B  VAL*     4.2    16.3    +      -       +      +
    190B  VAL*     1.3    82.6    -      -       -      +
    192B  GLY*     1.3    64.7    +      -       -      +
    193B  MET      4.1     0.3    +      -       -      -
    331B  THR*     4.9     8.8    -      -       -      +
    332B  ILE      5.0     0.5    -      -       -      +
    333B  ILE*     5.7     1.7    -      -       -      -
    374B  GLY*     4.4     2.1    -      -       -      -
    375B  GLY*     3.9    16.1    +      -       -      -
----------------------------------------------------------
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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