Contacts of the strand formed by residues 164 - 172 (chain B) 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 ALA 164 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158B  MET*     3.9    18.3    -      -       +      +
    159B  ARG      3.5    15.7    -      -       -      +
    160B  GLY*     4.0     2.7    -      -       -      +
    161B  ARG      5.3     0.9    -      -       -      +
    162B  GLU      4.2     0.6    +      -       -      -
    163B  ARG*     1.3    73.5    -      -       -      +
    165B  GLN*     1.3    66.8    +      -       -      +
    194B  ASN*     4.3     3.4    -      -       -      +
    196B  PHE*     3.7    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 165 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158B  MET*     4.2     4.0    -      -       -      -
    159B  ARG*     2.8    36.5    +      -       -      +
    163B  ARG*     4.6     6.3    -      -       +      +
    164B  ALA*     1.3    80.9    -      -       -      +
    166B  LYS*     1.3    65.7    +      -       -      +
    167B  VAL*     3.6     1.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 166 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  ARG*     4.3     8.9    -      -       -      +
    208A  SER      5.4     5.8    +      -       -      -
    211A  ASP*     4.3     4.9    +      -       -      -
    156B  ASN*     4.0    16.2    -      -       +      +
    157B  LEU      3.5     6.7    -      -       -      +
    158B  MET*     3.5    23.2    -      -       +      +
    165B  GLN*     1.3    76.8    -      -       -      +
    167B  VAL*     1.3    62.9    +      -       -      +
    168B  VAL*     3.9     6.9    -      -       -      +
    169B  THR*     2.7    41.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  ILE*     4.7     3.5    -      -       -      +
    100A  ARG*     4.0    12.0    +      -       -      -
    115A  ILE*     3.9    36.1    -      -       +      +
    157B  LEU*     2.7    33.6    +      -       +      +
    158B  MET      4.3     0.7    -      -       -      -
    159B  ARG*     3.6    44.6    -      -       +      +
    165B  GLN      4.2     0.7    -      -       -      +
    166B  LYS*     1.3    77.5    -      -       -      +
    168B  VAL*     1.3    70.6    +      -       +      +
    185B  MET*     4.7     4.5    -      -       +      -
    187B  LEU*     4.1    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  ILE*     3.9    22.9    -      -       +      -
    115A  ILE*     4.9     0.4    -      -       +      -
    211A  ASP*     3.3    23.1    -      -       +      +
    213A  VAL*     4.8     0.4    -      -       +      -
    155B  VAL      3.9     0.3    -      -       -      +
    156B  ASN*     3.5     4.2    -      -       -      +
    157B  LEU*     2.9    39.2    +      -       +      +
    166B  LYS*     3.6     7.2    -      -       -      +
    167B  VAL*     1.3    90.8    +      -       +      +
    169B  THR*     1.3    62.9    +      -       -      +
    170B  PHE*     3.6    29.4    -      -       +      -
    185B  MET*     3.6    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  GLU      3.4    25.4    -      -       -      +
    210A  ALA*     3.4     2.4    -      -       -      -
    211A  ASP*     2.7    40.9    +      -       -      +
    154B  CYS*     4.4     6.7    -      -       +      -
    155B  VAL      3.3     7.0    -      -       -      +
    156B  ASN*     2.6    25.6    +      -       -      +
    166B  LYS*     2.7    27.2    +      -       -      +
    168B  VAL*     1.3    72.9    -      -       -      +
    170B  PHE*     1.3    63.3    +      -       -      +
    171B  CYS*     4.0    15.9    -      -       -      -
    200B  THR*     5.2     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  GLN*     4.6     9.6    -      -       +      -
    178A  VAL*     5.5     9.0    -      -       +      -
    210A  ALA*     4.6     0.4    -      -       -      -
    211A  ASP      4.0    15.9    -      -       -      +
    213A  VAL*     3.4    34.8    -      -       +      -
    145B  TYR*     3.3    35.7    +      +       -      +
    153B  LEU*     3.9     1.0    -      -       -      +
    154B  CYS*     3.2     1.9    -      -       -      -
    155B  VAL*     2.9    39.1    +      -       +      +
    157B  LEU*     4.8     9.6    -      -       +      -
    168B  VAL*     3.6    24.9    -      -       +      -
    169B  THR*     1.3    72.6    -      -       -      +
    171B  CYS*     1.3    62.8    +      -       -      +
    172B  ASP      4.3     0.2    -      -       -      -
    181B  THR*     5.9     1.1    -      -       -      +
    182B  THR      4.4     6.3    -      -       -      +
    183B  GLY*     3.8    22.4    -      -       -      -
    184B  GLY      3.7    18.4    -      -       -      -
    197B  LEU*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  LEU*     3.5    14.1    -      -       -      +
    176A  PHE*     3.7    28.3    -      -       +      -
    178A  VAL*     3.4    19.6    -      -       -      +
    209A  GLU*     4.0    12.3    -      -       -      -
    210A  ALA*     3.8    25.9    -      -       +      +
    211A  ASP      5.6     0.2    +      -       -      -
    153B  LEU      3.3     3.4    -      -       -      -
    154B  CYS*     2.1    46.9    -      -       -      -
    169B  THR*     4.0     3.1    -      -       -      -
    170B  PHE*     1.3    74.4    -      -       -      +
    172B  ASP*     1.3    60.7    +      -       -      +
    173B  TYR*     4.1     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  PHE      3.4     7.7    -      -       -      +
    177A  GLN*     3.4     4.7    -      -       -      +
    178A  VAL*     3.3    26.0    +      -       +      +
    153B  LEU*     2.8    24.4    +      -       +      +
    171B  CYS*     1.3    73.6    -      -       -      +
    173B  TYR*     1.3    62.8    +      -       -      +
    179B  GLN*     2.8    30.6    +      -       -      +
    180B  VAL      4.5     2.1    -      -       -      +
    181B  THR*     2.7    45.8    +      -       +      +
   1224B   CA      2.3    26.6    -      -       -      -
----------------------------------------------------------
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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