Contacts of the strand formed by residues 196 - 207 (chain A) in PDB entry 5E67


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 PHE 196 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  LEU*     4.2    11.0    -      -       +      -
    187A  LYS      3.3    24.9    -      -       -      +
    188A  LYS*     3.7    40.6    -      -       +      -
    189A  SER*     4.2     1.1    -      -       -      -
    192A  ILE*     3.5    21.7    -      -       -      +
    194A  VAL*     3.3    20.4    -      -       -      +
    195A  GLY*     1.3    80.1    -      -       -      +
    197A  GLN*     1.3    63.4    +      -       -      +
    198A  SER      4.1     1.2    +      -       -      -
    281A  HIS      5.0     1.9    -      -       -      +
    282A  LEU*     5.6     0.5    -      -       -      +
    287A  LEU*     4.0    26.0    -      -       +      +
    291A  ARG*     3.9    30.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  ILE      3.4     2.3    -      -       -      +
    186A  LEU*     3.3     7.4    -      -       -      -
    187A  LYS*     2.9    50.2    +      -       +      +
    189A  SER*     4.0     4.8    -      -       -      -
    192A  ILE*     3.5    21.6    -      -       +      +
    196A  PHE*     1.3    72.1    -      -       -      +
    198A  SER*     1.3    63.9    +      -       -      +
    199A  ILE*     3.5    26.6    +      -       +      +
    287A  LEU*     5.8     0.2    -      -       -      -
      3B    T      3.4    35.7    +      -       +      +
      4B    A      3.0    48.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  SER*     5.2     1.4    +      -       -      -
    185A  ILE      3.4     5.9    +      -       -      -
    186A  LEU*     3.8    16.4    -      -       -      +
    196A  PHE      4.1     2.0    +      -       -      -
    197A  GLN*     1.3    77.3    +      -       -      +
    199A  ILE*     1.3    63.9    +      -       -      +
    200A  LEU*     5.4     0.2    -      -       -      +
    272A  ILE*     4.2     2.9    -      -       -      +
    276A  MET*     3.1    38.7    -      -       -      +
    281A  HIS*     4.2    19.0    -      -       -      -
    287A  LEU*     5.3     3.1    -      -       -      +
    290A  ILE*     3.7    24.8    -      -       -      +
      3B    T      4.9     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  LYS      3.8     0.2    -      -       -      +
    184A  SER*     3.6     3.6    +      -       -      -
    185A  ILE*     2.8    48.9    +      -       +      +
    187A  LYS*     3.7    19.7    -      -       +      -
    197A  GLN*     3.5    43.3    -      -       +      +
    198A  SER*     1.3    78.5    +      -       -      +
    200A  LEU*     1.3    69.2    +      -       -      +
    201A  VAL*     3.8    20.5    +      -       +      -
    240A  THR*     5.0    14.4    -      -       +      +
    276A  MET*     4.8     0.7    -      -       -      -
      4B    A      4.5     4.0    -      -       +      +
      5B    C      4.2    17.5    -      -       -      +
     20C    T      5.1     3.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  LYS      3.4     3.8    -      -       -      +
    184A  SER*     4.4     5.8    -      -       -      -
    198A  SER      4.3     0.8    +      -       -      -
    199A  ILE*     1.3    81.9    -      -       -      +
    201A  VAL*     1.3    63.8    +      -       -      +
    202A  PHE      4.2     0.2    -      -       -      -
    239A  VAL      3.8     7.1    -      -       -      +
    240A  THR*     4.1     8.8    -      -       -      +
    242A  PHE*     4.2    14.7    -      -       +      -
    245A  ILE*     4.2    22.7    -      -       +      +
    269A  TRP*     3.7    39.5    -      -       +      +
    272A  ILE*     3.4    26.7    -      -       +      -
    273A  ALA*     3.6    39.0    -      -       +      +
    276A  MET*     4.0    12.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  SER      3.7     1.0    -      -       -      +
    183A  LYS*     2.8    66.3    +      -       +      +
    185A  ILE*     4.5    13.7    -      -       +      -
    199A  ILE*     3.8    18.6    -      -       +      -
    200A  LEU*     1.3    80.0    -      -       -      +
    202A  PHE*     1.3    72.2    +      -       -      +
    203A  GLN*     4.7     2.2    -      -       +      +
    238A  THR*     3.9    18.6    -      -       +      -
    239A  VAL      3.4     7.9    -      -       -      +
    240A  THR*     4.1    10.5    -      -       +      -
    269A  TRP*     3.8     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  VAL*     3.7    21.3    -      -       +      -
    181A  SER      3.7     6.3    -      -       -      -
    182A  PHE*     3.5    40.4    -      +       -      -
    201A  VAL*     1.3    75.1    -      -       -      +
    203A  GLN*     1.3    69.5    +      -       -      +
    204A  ILE*     3.9    13.5    -      -       +      -
    221A  LEU*     4.3     7.2    -      -       +      -
    237A  TYR*     3.9    25.1    -      +       -      -
    238A  THR*     3.4     4.0    -      -       -      -
    239A  VAL*     2.8    36.4    +      -       +      +
    245A  ILE*     4.0    19.7    -      -       +      +
    249A  ILE*     3.7    22.7    -      -       +      -
    253A  PHE*     3.5    28.9    -      +       -      -
    269A  TRP*     4.1     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  ASP      4.7     0.2    -      -       -      -
    180A  GLY*     3.1     4.7    -      -       -      -
    181A  SER*     2.7    46.3    +      -       -      +
    183A  LYS*     2.8    38.5    +      -       -      -
    201A  VAL*     4.7     3.8    -      -       +      +
    202A  PHE*     1.3    79.9    -      -       -      +
    204A  ILE*     1.3    72.9    +      -       -      +
    205A  THR*     3.0    22.4    +      -       -      +
    236A  TYR*     3.5    25.2    -      -       +      -
    237A  TYR      3.2    10.8    -      -       -      +
    238A  THR*     4.6     4.9    +      -       -      +
     17C    A      3.2    25.0    +      -       -      +
     18C    G      4.9     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  LEU*     4.2    11.9    -      -       +      -
    175A  PHE*     3.7    27.6    -      -       +      -
    176A  VAL*     3.6    26.0    -      -       +      -
    179A  ASP      3.5     9.6    -      -       -      +
    180A  GLY*     4.3     1.8    -      -       -      -
    202A  PHE*     3.9    22.2    -      -       +      -
    203A  GLN*     1.3    78.4    -      -       -      +
    205A  THR*     1.3    64.1    +      -       -      +
    214A  MET*     3.3    18.3    -      -       +      +
    217A  LEU*     3.9    19.7    -      -       +      -
    221A  LEU*     5.0     1.3    -      -       +      -
    236A  TYR*     3.5     1.4    -      -       -      -
    237A  TYR*     2.9    44.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  ASP*     3.0    23.6    +      -       -      +
    181A  SER*     5.2     0.5    +      -       -      -
    203A  GLN*     3.0    26.9    +      -       -      +
    204A  ILE*     1.3    72.5    -      -       -      +
    206A  GLN*     1.3    81.0    +      -       -      +
    214A  MET*     4.2     0.2    -      -       -      -
    234A  TRP*     5.4     0.7    -      -       +      -
    235A  LEU      3.5     4.9    -      -       -      +
    236A  TYR*     3.6    20.9    -      -       +      -
     15C    T      3.7    32.5    -      -       +      -
     16C    C      3.3    28.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  ASP      4.8     3.2    +      -       -      -
    101A  THR*     4.3    10.6    +      -       +      +
    175A  PHE*     3.6    23.2    -      -       +      -
    179A  ASP*     2.3    31.5    -      -       -      +
    205A  THR*     1.3    80.7    -      -       -      +
    207A  HIS*     1.3    73.1    +      -       -      +
    209A  ARG*     5.6     3.6    -      -       -      +
    210A  ASP*     3.9    23.9    +      -       +      +
    213A  LEU*     5.4     1.1    -      -       +      -
    214A  MET*     3.7    28.1    -      -       +      +
    234A  TRP*     3.6     3.1    -      -       -      +
    235A  LEU*     2.9    34.3    +      -       -      +
     15C    T      4.5     9.1    +      -       -      -
     16C    C      4.8     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206A  GLN*     1.3    91.1    -      -       -      +
    208A  ALA*     1.3    74.9    +      -       -      +
    209A  ARG*     3.3    63.3    +      -       +      +
    210A  ASP*     3.1    22.6    +      -       -      +
    233A  PRO*     3.4    39.5    +      -       +      +
    234A  TRP*     4.5     0.4    -      -       -      -
    235A  LEU*     4.5     1.8    -      -       -      +
     15C    T      3.1    36.3    +      -       -      +
----------------------------------------------------------
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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