Contacts of the strand formed by residues 179 - 184 (chain C) 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 LYS 179 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172C  ILE*     4.9     7.4    -      -       +      -
    176C  ASP*     3.6    47.2    +      -       +      +
    177C  ARG      3.0     2.2    +      -       -      +
    178C  TRP*     1.3    74.2    +      -       -      +
    180C  SER*     1.3    66.5    +      -       -      +
    181C  LEU*     3.8     6.5    +      -       +      +
    193C  GLN*     3.2     6.2    -      -       -      -
    194C  ILE*     2.8    48.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 180 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178C  TRP      4.1     2.5    +      -       -      -
    179C  LYS*     1.3    76.6    -      -       -      +
    181C  LEU*     1.3    70.3    +      -       -      +
    182C  HIS*     4.1    25.1    +      -       -      -
    191C  GLU*     5.6     0.9    -      -       -      -
    192C  LEU      3.6     8.1    -      -       -      -
    193C  GLN*     4.0    18.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 181 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144C  LEU*     4.2     6.7    -      -       +      -
    168C  HIS*     3.9    38.8    -      -       +      +
    179C  LYS*     4.4    11.2    -      -       +      +
    180C  SER*     1.3    83.0    -      -       -      +
    182C  HIS*     1.3    64.0    +      -       -      +
    183C  PHE*     3.5    31.6    +      -       +      -
    190C  LEU      3.9     1.0    -      -       -      +
    191C  GLU*     3.7     6.6    -      -       -      +
    192C  LEU*     2.9    49.2    +      -       +      +
    194C  ILE*     4.0    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 182 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  TYR*     5.9     1.8    -      +       -      -
    180C  SER*     4.1    28.7    +      -       -      -
    181C  LEU*     1.3    74.4    -      -       -      +
    183C  PHE*     1.3    66.4    -      -       -      +
    184C  SER*     4.1     2.3    +      -       -      +
    190C  LEU      3.7     4.5    -      -       -      -
    191C  GLU*     2.7    38.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 183 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144C  LEU*     5.0     4.9    -      -       +      -
    146C  VAL*     5.3     3.6    -      -       +      -
    166C  VAL*     3.8    40.8    -      -       +      -
    167C  SER      3.3    26.9    -      -       -      -
    168C  HIS*     3.9    14.1    -      +       +      -
    181C  LEU*     3.5    44.9    -      -       +      -
    182C  HIS*     1.3    77.3    -      -       -      +
    184C  SER*     1.3    61.9    +      -       -      +
    185C  GLY      3.9     0.7    -      -       -      -
    188C  ALA      4.2     0.2    -      -       -      +
    189C  HIS*     3.2     8.7    -      -       -      +
    190C  LEU*     3.0    43.0    +      -       +      +
    192C  LEU*     3.9    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 184 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166C  VAL*     5.5     1.5    -      -       -      +
    182C  HIS*     4.1     3.1    +      -       -      +
    183C  PHE*     1.3    71.1    -      -       -      +
    185C  GLY*     1.3    61.0    +      -       -      +
    189C  HIS*     2.8    32.1    +      -       -      -
----------------------------------------------------------
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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