Contacts of the strand formed by residues 164 - 171 (chain F) in PDB entry 5MWF


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 164 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45F  LEU*     4.9    12.4    -      -       -      +
    146F  VAL      4.3     0.3    -      -       -      +
    147F  GLU*     3.5     0.9    -      -       -      -
    148F  ALA*     2.8    32.0    +      -       +      +
    162F  LEU*     3.3     8.6    -      -       -      +
    163F  ILE*     1.3    81.4    -      -       -      +
    165F  ARG*     1.3    78.2    +      -       -      +
    166F  VAL*     4.1    19.1    -      -       +      -
    185F  GLY*     3.6     6.8    -      -       -      -
    186F  HIS*     3.1    19.1    +      -       -      +
    187F  VAL*     3.0    32.2    +      -       -      +
    188F  ALA*     3.4    30.4    +      -       +      +
    190F  LEU*     4.4     5.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 165 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45F  LEU*     5.8     1.4    -      -       +      +
     84F  PRO*     3.7    36.2    +      -       -      +
    145F  ILE*     4.2    15.5    -      -       +      -
    146F  VAL      3.7     3.4    -      -       -      -
    147F  GLU*     2.6    38.9    +      -       +      -
    149F  TRP*     4.4     4.9    -      -       -      -
    159F  GLU*     3.6    30.5    +      -       -      -
    162F  LEU*     3.8    24.7    -      -       +      +
    164F  GLU*     1.3    88.9    +      -       -      +
    166F  VAL*     1.3    65.7    +      -       -      +
    167F  SER*     6.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 166 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145F  ILE*     3.4    12.0    -      -       -      +
    146F  VAL*     3.0    54.6    +      -       +      +
    164F  GLU*     4.1    10.3    -      -       +      -
    165F  ARG*     1.3    79.2    -      -       -      +
    167F  SER*     1.3    62.4    +      -       -      +
    183F  PHE*     3.5    52.0    -      -       +      -
    185F  GLY*     5.8     3.6    -      -       -      +
    190F  LEU*     4.1    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 167 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82F  VAL*     3.6    39.3    -      -       -      +
    144F  LEU      3.3     9.4    -      -       -      -
    145F  ILE*     4.3     5.6    -      -       -      +
    165F  ARG*     6.2     0.2    -      -       -      -
    166F  VAL*     1.3    78.5    -      -       -      +
    168F  HIS*     1.3    65.1    +      -       -      +
    183F  PHE*     3.3    13.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 168 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82F  VAL*     5.2     2.0    -      -       -      -
    142F  PHE*     4.3    20.0    -      +       -      -
    143F  THR*     3.6     2.7    -      -       -      -
    144F  LEU*     2.7    44.4    +      -       +      +
    167F  SER*     1.3    77.6    +      -       -      +
    169F  ALA*     1.3    79.7    +      -       -      +
    170F  GLY*     4.1     7.7    +      -       -      -
    181F  LEU*     4.0    37.4    -      -       +      +
    183F  PHE*     3.8    19.2    -      -       +      -
    194F  ILE*     5.1     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 169 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78F  TYR*     3.6    25.5    +      -       +      +
     79F  GLN      4.0    12.3    -      -       -      +
     82F  VAL*     4.6     9.0    -      -       +      +
    142F  PHE      3.6     4.3    -      -       -      -
    143F  THR*     3.7    21.1    -      -       +      +
    168F  HIS*     1.3    88.6    +      -       -      +
    170F  GLY*     1.3    57.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 170 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78F  TYR*     3.8     9.9    -      -       -      -
    141F  SER*     3.4     3.5    -      -       -      -
    142F  PHE*     3.0    40.3    +      -       -      +
    168F  HIS*     4.1    13.8    +      -       -      -
    169F  ALA*     1.3    75.0    -      -       -      +
    171F  MET*     1.3    64.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 171 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78F  TYR*     5.8     5.2    -      -       +      -
    140F  ARG*     3.3    58.3    -      -       +      +
    141F  SER*     4.0    17.7    -      -       -      -
    142F  PHE*     3.7     3.9    -      -       -      -
    170F  GLY*     1.3    80.3    -      -       -      +
    172F  ILE*     1.3    64.4    +      -       -      +
    176F  ASP*     4.5     2.8    -      -       -      +
    179F  LYS*     5.8     3.1    -      -       -      +
----------------------------------------------------------
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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