Contacts of the strand formed by residues 213 - 221 (chain D) 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 VAL 213 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96D  SER*     4.4     1.6    -      -       -      -
     97D  ALA      3.3    10.1    -      -       -      +
     98D  ILE*     4.1     8.5    -      -       +      -
    111D  PHE*     3.6     5.0    -      -       -      -
    141D  PHE*     3.3     7.3    -      -       -      +
    142D  GLN*     2.9    42.3    +      -       -      +
    211D  ASP*     4.8     0.7    -      -       +      -
    212D  SER*     1.3    81.3    -      -       -      +
    214D  PHE*     1.3    64.3    +      -       -      +
    215D  SER*     3.7    21.3    -      -       -      +
    168E  VAL*     4.7     3.8    -      -       +      -
    170E  PHE*     3.5    34.8    -      -       +      -
    184E  GLY      3.9     9.4    -      -       -      +
    185E  MET*     3.9    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 214 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95D  PHE*     3.3    30.2    -      +       +      -
     96D  SER*     3.3     0.3    -      -       -      -
     97D  ALA      2.8    30.8    +      -       -      -
    109D  VAL      5.4     0.2    -      -       -      -
    111D  PHE*     3.4    41.9    -      +       +      -
    122D  TYR*     4.0    17.3    -      +       -      -
    127D  GLY      4.2     9.6    -      -       -      -
    129D  PHE*     5.1     0.2    -      -       +      -
    139D  PHE*     4.3    20.4    -      +       +      -
    140D  THR      3.5    12.1    -      -       -      -
    141D  PHE*     4.4     0.7    -      -       +      -
    153D  ILE*     5.0     4.9    -      -       +      -
    193D  VAL*     4.3    10.8    -      -       +      -
    194D  TRP*     4.3    14.8    -      -       -      -
    195D  VAL*     3.7    23.6    -      -       +      -
    213D  VAL*     1.3    72.8    -      -       -      +
    215D  SER*     1.3    75.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 215 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95D  PHE*     3.4    12.8    -      -       -      -
     96D  SER*     2.4    30.1    +      -       -      -
    139D  PHE*     3.5     2.3    -      -       -      -
    140D  THR*     2.9    49.8    +      -       -      +
    142D  GLN*     5.4     0.8    +      -       -      -
    213D  VAL*     3.7    10.5    -      -       -      +
    214D  PHE*     1.3    78.0    -      -       -      +
    216D  GLY*     1.3    59.4    +      -       -      +
    217D  PHE*     5.6     0.7    -      -       -      -
    142E  TYR*     4.5     6.5    -      -       -      -
    184E  GLY      4.4     1.8    +      -       -      -
    185E  MET*     4.2     4.0    -      -       -      -
    186E  VAL*     4.1    10.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 216 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94D  ALA*     3.5     1.0    -      -       -      +
     95D  PHE*     2.9    49.6    +      -       -      +
    129D  PHE*     5.7     1.1    -      -       -      -
    137D  TYR*     5.6     0.4    -      -       -      -
    138D  TYR      3.0    13.7    -      -       -      -
    139D  PHE*     3.8     7.4    -      -       -      -
    215D  SER*     1.3    77.4    -      -       -      +
    217D  PHE*     1.3    68.7    +      -       -      +
    186E  VAL*     4.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 217 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93D  PRO      3.6     6.7    -      -       -      +
     94D  ALA*     4.0     8.7    -      -       +      -
    129D  PHE*     6.2     0.4    -      -       -      -
    137D  TYR*     3.2    11.4    -      -       -      -
    138D  TYR*     2.9    68.5    +      +       +      -
    140D  THR*     5.9     1.8    -      -       +      -
    215D  SER      5.6     0.2    -      -       -      -
    216D  GLY*     1.3    79.6    -      -       -      +
    218D  LEU*     1.3    71.8    +      -       -      +
    219D  ILE*     4.3     3.8    -      -       +      -
    142E  TYR*     3.9    27.6    -      +       +      -
    186E  VAL*     4.2     9.0    -      -       +      -
    218E  PHE*     3.9    17.9    -      +       -      -
    220E  LEU*     3.5    42.8    -      -       +      -
    221E  PHE*     5.0     1.1    -      -       +      -
    212F  PHE*     4.0    18.8    -      +       -      -
    214F  LEU*     5.2     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 218 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91D  PRO*     4.1    26.5    -      -       +      +
     93D  PRO*     3.1    40.6    +      -       +      +
    133D  VAL*     4.2     9.0    -      -       +      +
    135D  GLY*     4.3     1.1    -      -       -      -
    136D  TYR      3.5    17.7    -      -       -      +
    137D  TYR*     3.5    36.2    -      -       +      +
    217D  PHE*     1.3    79.6    -      -       -      +
    219D  ILE*     1.3    61.4    +      -       -      +
    220D  PHE*     3.5    23.8    -      -       -      +
    221D  PRO*     3.8    13.7    -      -       +      -
    220E  LEU*     4.8     2.4    -      -       -      +
    221E  PHE*     3.6    21.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 219 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  TYR*     2.5    17.8    +      -       +      +
    137D  TYR      3.8    12.6    -      -       -      -
    138D  TYR*     3.9    15.7    -      -       +      +
    184D  VAL*     3.7    37.2    -      -       +      -
    217D  PHE*     4.3     6.1    -      -       +      -
    218D  LEU*     1.3    76.7    -      -       -      +
    220D  PHE*     1.3    78.7    +      -       +      +
    221E  PHE*     5.8     1.9    -      -       -      -
     91F  GLN*     5.2     0.2    -      -       -      +
     92F  SER      5.5     0.4    -      -       -      +
     93F  VAL*     4.0     4.3    -      -       +      -
    212F  PHE*     3.8    39.7    -      -       +      -
    213F  LEU      4.4    10.4    -      -       -      +
    214F  LEU*     5.4     6.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 220 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135D  GLY*     3.3     0.2    -      -       -      -
    136D  TYR*     2.8    71.6    +      +       +      -
    218D  LEU*     3.5     5.8    -      -       -      -
    219D  ILE*     1.3    95.6    -      -       +      +
    221D  PRO*     1.3    84.2    -      -       +      +
    222D  SER*     5.1     2.9    -      -       -      -
     89F  LYS*     4.2    15.7    -      -       +      -
     91F  GLN*     3.4    60.1    -      -       +      +
     92F  SER      4.7     1.3    -      -       -      -
     93F  VAL*     4.2    17.7    -      -       +      -
    120F  GLN*     4.3     4.7    -      -       -      -
    213F  LEU      5.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 221 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91D  PRO*     4.5    14.4    -      -       +      -
    133D  VAL*     4.0    18.4    -      -       +      -
    134D  PRO      3.3    13.5    -      -       -      +
    135D  GLY*     3.9     0.7    -      -       -      -
    218D  LEU*     3.8    10.5    -      -       +      -
    220D  PHE*     1.3   102.7    -      -       +      +
    222D  SER*     1.3    64.4    +      -       -      +
     91F  GLN*     6.0     0.2    -      -       -      +
----------------------------------------------------------
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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