Contacts of the strand formed by residues 133 - 139 (chain A) in PDB entry 5FDK


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 ILE 133 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  ARG*     4.5     8.5    -      -       +      -
     97A  TYR      3.1    11.2    +      -       -      +
     98A  ILE*     3.6    23.9    -      -       +      -
     99A  ASP*     3.0    25.6    +      -       -      +
    128A  LYS*     4.1     2.7    -      -       -      +
    131A  ASP*     5.8     0.4    -      -       -      +
    132A  GLY*     1.3    68.8    -      -       -      -
    134A  CYS*     1.3    57.4    +      -       -      +
    135A  PHE*     3.5    17.8    -      -       +      -
    146A  PHE*     5.3     1.8    -      -       +      -
    148A  GLU*     5.7     0.2    -      -       -      +
    193A  ILE*     3.5    37.0    -      -       +      -
    197A  TYR*     4.0    33.0    -      -       +      -
    198A  PHE*     3.7    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  ASP*     3.1    14.1    -      -       +      +
    124A  MET*     3.2    52.5    -      -       -      -
    127A  VAL*     3.9    19.7    -      -       +      -
    128A  LYS*     2.8    43.6    +      -       +      +
    132A  GLY      4.4     0.7    -      -       -      +
    133A  ILE*     1.3    71.8    -      -       -      +
    135A  PHE*     1.3    67.1    +      -       -      +
    148A  GLU*     3.6     0.7    -      -       -      +
    149A  ALA*     3.1    16.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  ILE*     4.0     4.0    -      -       +      -
     99A  ASP      3.0    13.2    +      -       -      -
    100A  PHE*     3.0    54.1    -      +       +      -
    101A  GLU      3.0     4.5    +      -       -      -
    124A  MET*     4.3     3.7    -      -       -      +
    133A  ILE*     3.5    18.4    -      -       +      -
    134A  CYS*     1.3    76.5    -      -       -      +
    136A  VAL*     1.3    78.7    +      -       -      +
    137A  ILE*     3.4    20.4    -      -       +      -
    146A  PHE*     2.5    52.5    -      +       +      -
    147A  LEU      3.8    10.5    -      -       -      +
    148A  GLU*     4.2     7.6    -      -       -      +
    149A  ALA*     4.0     7.0    -      -       -      +
    189A  TYR*     4.1     5.8    -      +       +      -
    193A  ILE*     3.7    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  GLU      3.5     7.9    -      -       -      +
    103A  LYS*     5.0     1.3    -      -       +      +
    116A  PHE*     3.5    28.3    -      -       +      -
    124A  MET*     4.3     6.5    -      -       +      -
    135A  PHE*     1.3    88.2    -      -       -      +
    137A  ILE*     1.3    69.2    +      -       -      +
    138A  ILE*     3.2    26.5    -      -       +      +
    146A  PHE*     3.5     2.6    -      -       -      -
    147A  LEU*     2.9    44.7    +      -       +      +
    149A  ALA*     5.4     0.4    -      -       -      -
    152A  LEU*     3.6    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  LEU*     4.3    18.4    -      -       +      -
    100A  PHE*     3.4    32.1    -      -       +      -
    101A  GLU      2.9     8.5    +      -       -      +
    102A  ALA*     3.2     7.9    -      -       +      +
    103A  LYS      2.9    25.5    +      -       -      -
    135A  PHE*     3.4    24.0    -      -       +      -
    136A  VAL*     1.3    76.1    -      -       -      +
    138A  ILE*     1.3    63.2    +      -       -      +
    139A  SER*     4.2     1.1    +      -       -      +
    144A  VAL*     3.8    26.2    -      -       +      -
    145A  TYR      3.4     4.7    -      -       -      +
    146A  PHE*     4.4     6.3    -      -       +      -
    179A  ILE*     4.2     4.9    -      -       +      -
    187A  ILE*     5.2     3.1    -      -       +      -
    189A  TYR*     4.0    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  LYS      3.1    10.3    -      -       -      +
    111A  PHE*     3.7    40.2    -      -       +      -
    136A  VAL*     3.2    38.1    -      -       +      +
    137A  ILE*     1.3    76.8    -      -       -      +
    139A  SER*     1.3    63.3    +      -       -      +
    140A  ALA*     3.7     9.0    +      -       +      +
    143A  GLN      3.7     1.2    -      -       -      +
    144A  VAL*     3.4     2.1    -      -       -      +
    145A  TYR*     2.8    44.1    +      -       +      +
    147A  LEU*     3.6    28.9    -      -       +      +
    172A  LEU*     4.1    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ARG      3.6     4.5    +      -       -      +
     32A  GLY      2.9    36.3    +      -       -      -
     33A  MET      5.6     0.2    -      -       -      -
    103A  LYS      2.9     9.9    +      -       -      -
    104A  GLU*     3.1    16.0    -      -       -      +
    105A  THR      2.9    24.6    +      -       -      +
    137A  ILE*     4.2     1.5    -      -       -      -
    138A  ILE*     1.3    73.6    -      -       -      +
    140A  ALA*     1.3    59.2    +      -       -      +
    143A  GLN      3.6     8.3    +      -       -      -
    144A  VAL*     4.4    18.3    -      -       -      +
----------------------------------------------------------
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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