Contacts of the strand formed by residues 207 - 216 (chain F) in PDB entry 2JG8


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 SER 207 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97F  THR*     2.8    25.0    +      -       -      -
     98F  ARG*     3.1    25.9    +      -       -      -
    112F  PHE*     3.9     3.1    -      -       -      -
    143F  HIS      3.3     4.0    -      -       -      -
    144F  ALA*     3.4     5.6    -      -       -      -
    145F  SER*     2.9    28.9    +      -       -      -
    199F  MET*     3.4    33.6    +      -       -      +
    206F  ASP*     1.3    74.8    +      -       -      +
    208F  VAL*     1.3    59.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 208 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165D  LEU*     3.8    25.8    -      -       +      -
    167D  PHE*     4.0     7.9    -      -       +      -
    182D  GLY      3.4    23.8    -      -       -      +
    183D  MET*     4.9     0.2    -      -       +      -
     95F  THR*     3.3    26.9    -      -       +      -
     96F  VAL      3.2    18.2    -      -       -      +
    112F  PHE*     4.0     5.1    -      -       -      -
    116F  LEU*     4.5     0.7    -      -       +      -
    141F  VAL      5.7     0.2    -      -       -      +
    142F  TYR*     3.2     7.3    -      -       -      +
    143F  HIS*     2.8    55.3    +      -       +      +
    144F  ALA*     4.8     0.7    -      -       -      +
    207F  SER*     1.3    75.3    -      -       -      +
    209F  PHE*     1.3    58.8    +      -       -      +
    210F  SER*     4.9     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 209 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94F  PHE*     3.5    19.3    -      +       -      -
     95F  THR*     3.4     0.9    -      -       -      -
     96F  VAL*     2.8    44.1    +      -       +      +
    112F  PHE*     3.9    22.4    -      +       +      -
    123F  TYR*     3.9    30.5    -      +       -      -
    130F  PHE*     5.4     0.7    -      -       +      -
    140F  PHE*     4.2    22.9    -      +       +      -
    141F  VAL      3.4    11.4    -      -       -      -
    142F  TYR*     4.1     1.1    -      +       +      -
    154F  LEU*     4.6     0.7    -      -       +      -
    189F  VAL*     4.4    14.1    -      -       +      -
    190F  TRP*     4.8     4.3    -      -       -      -
    191F  LEU*     3.7    47.3    -      -       +      -
    208F  VAL*     1.3    74.5    -      -       -      +
    210F  SER*     1.3    75.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 210 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138D  TYR*     4.0    25.0    +      -       -      -
    182D  GLY      4.5     3.3    +      -       -      -
    183D  MET*     4.1     3.1    -      -       -      -
    184D  VAL*     4.5     3.1    -      -       -      -
     94F  PHE*     3.3    11.2    -      -       -      -
     95F  THR*     2.6    31.2    +      -       -      +
    140F  PHE*     3.5     2.6    -      -       -      -
    141F  VAL*     2.9    41.6    +      -       -      +
    208F  VAL*     4.3     2.8    -      -       -      +
    209F  PHE*     1.3    79.1    -      -       -      +
    211F  GLY*     1.3    58.6    +      -       -      +
    212F  PHE*     5.0     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 211 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92F  SER      5.3     0.2    -      -       -      -
     93F  VAL*     3.3     1.7    -      -       -      -
     94F  PHE*     2.9    53.2    +      -       -      +
    130F  PHE*     6.1     0.2    -      -       -      -
    138F  TYR*     5.1     2.0    -      -       -      -
    139F  TYR      3.0    13.0    -      -       -      -
    140F  PHE*     4.0     7.0    -      -       -      -
    210F  SER*     1.3    76.0    -      -       -      +
    212F  PHE*     1.3    66.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 212 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138D  TYR*     3.8    30.5    -      +       +      -
    184D  VAL*     4.0     7.4    -      -       +      -
    217D  PHE*     4.0    29.2    -      +       -      -
    219D  ILE*     3.8    27.4    -      -       +      -
    218E  PHE*     4.6     1.1    -      +       -      -
     92F  SER      3.2    12.3    -      -       -      +
     93F  VAL*     3.7    11.4    -      -       +      -
    138F  TYR*     3.4     9.6    -      -       -      -
    139F  TYR*     3.0    65.3    +      +       +      -
    141F  VAL*     5.1     0.9    -      -       +      -
    210F  SER*     5.0     1.8    -      -       -      -
    211F  GLY*     1.3    81.6    -      -       -      +
    213F  LEU*     1.3    63.5    +      -       -      +
    214F  LEU*     3.6    27.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 213 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219D  ILE*     4.4    14.0    -      -       -      +
    220D  PHE*     5.8     0.3    -      -       -      -
     90F  PHE      4.0    13.9    -      -       -      +
     91F  GLN*     4.3    17.8    -      -       -      +
     92F  SER*     2.8    19.9    +      -       -      +
    134F  VAL*     3.7    34.1    -      -       +      -
    135F  PRO      4.3     0.4    -      -       -      +
    136F  GLY*     4.0     4.5    -      -       -      -
    137F  LEU      3.4    20.9    -      -       -      +
    138F  TYR*     3.6    33.0    -      -       +      +
    212F  PHE*     1.3    71.4    -      -       -      +
    214F  LEU*     1.3    65.3    +      -       -      +
    215F  PHE      3.7    20.2    -      -       -      +
    216F  PRO*     3.9    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 214 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217D  PHE*     5.2     1.3    -      -       +      -
    219D  ILE*     5.4     6.7    -      -       +      +
    218E  PHE*     3.5    48.7    -      -       +      -
    219E  LEU      5.3     2.2    -      -       -      +
    220E  LEU*     4.9     5.8    -      -       +      -
    137F  LEU*     2.8    25.2    +      -       +      +
    139F  TYR*     4.0    10.5    -      -       +      +
    180F  LEU*     3.9    21.8    -      -       +      -
    212F  PHE*     3.9    24.5    -      -       +      +
    213F  LEU*     1.3    76.8    -      -       -      +
    215F  PHE*     1.3    77.4    +      -       +      +
    216F  PRO*     4.0     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 215 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93E  GLN      4.4     5.8    -      -       -      -
     94E  LYS*     3.8    41.6    +      -       +      +
     95E  ILE      3.5    35.2    -      -       -      -
     96E  ALA*     4.0     0.9    -      -       +      -
    122E  MET*     4.8     1.5    -      -       +      +
    218E  PHE*     4.7     2.0    -      -       +      -
    219E  LEU*     3.3    34.5    -      -       +      -
    220E  LEU      5.6     1.6    -      -       -      -
    136F  GLY*     3.2     1.0    -      -       -      -
    137F  LEU*     2.9    63.6    +      -       +      -
    213F  LEU*     3.7     3.4    -      -       -      -
    214F  LEU*     1.3   100.6    -      -       +      +
    216F  PRO*     1.3    69.0    -      -       +      +
    217F  ASP*     4.8     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 216 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94E  LYS*     2.5    30.4    +      -       -      -
     90F  PHE      4.8     6.7    -      -       -      +
     91F  GLN*     5.7     5.6    -      -       -      +
    134F  VAL*     4.7     7.0    -      -       +      -
    135F  PRO      3.7     9.0    -      -       -      +
    213F  LEU*     3.9    21.3    -      -       +      -
    214F  LEU      4.0     6.1    -      -       -      +
    215F  PHE*     1.3    86.2    -      -       +      +
    217F  ASP*     1.3    59.1    +      -       -      +
----------------------------------------------------------
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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