Contacts of the strand formed by residues 161 - 170 (chain A) in PDB entry 1JEY


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 MET 161 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  GLY      4.5     3.7    +      -       -      -
     35A  ARG      3.3    10.1    -      -       -      +
     37A  SER*     2.8    31.9    -      -       -      +
     82A  LEU*     4.8     2.9    -      -       +      -
    108A  LEU*     4.6     0.7    -      -       -      -
    154A  PHE*     3.1    32.3    -      -       +      +
    157A  VAL*     3.3    35.0    -      -       +      +
    159A  PHE      3.9     0.4    +      -       -      -
    160A  LYS*     1.3    81.7    -      -       -      +
    162A  SER*     1.3    66.5    +      -       -      +
    163A  HIS      4.9     0.7    -      -       -      +
    164A  LYS*     3.2    41.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  GLY*     3.4    26.5    +      -       -      -
     35A  ARG      3.2     5.4    +      -       -      -
     36A  ASP*     3.0    16.9    +      -       -      -
    161A  MET*     1.3    77.9    -      -       -      +
    163A  HIS*     1.3    72.4    +      -       -      +
    164A  LYS*     3.7    14.7    +      -       -      +
     34D    C      5.1     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  ASP*     3.2    12.8    +      -       -      +
     37A  SER*     2.7    34.2    +      -       -      -
    161A  MET*     4.9     0.2    -      -       -      +
    162A  SER*     1.3    84.6    +      -       -      +
    164A  LYS*     1.3    58.4    +      -       -      +
    165A  ARG*     4.0     9.2    +      -       -      -
    199A  PHE*     3.7    38.2    -      +       -      -
    252A  ARG*     3.6    47.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  PHE*     3.7    36.6    -      -       +      -
    161A  MET*     3.2    38.0    +      -       +      +
    162A  SER      3.7    15.9    +      -       -      +
    163A  HIS*     1.3    77.4    +      -       -      +
    165A  ARG*     1.3    60.3    +      -       -      +
    196A  THR      5.6     3.7    +      -       -      +
    197A  GLY      4.3    11.4    +      -       -      +
    198A  ILE*     3.4    22.4    -      -       +      +
    199A  PHE*     2.9    29.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  SER      2.8     9.9    +      -       -      +
     38A  LEU*     3.3    19.0    -      -       +      +
     39A  ILE      2.9    25.5    +      -       -      -
    154A  PHE*     3.5     5.2    -      -       -      -
    163A  HIS*     4.7     8.9    +      -       +      -
    164A  LYS*     1.3    75.0    -      -       -      +
    166A  ILE*     1.3    68.3    +      -       -      +
    167A  MET*     4.1     8.5    -      -       +      -
    199A  PHE*     3.3    27.6    -      -       +      +
    201A  ASP*     2.6    42.5    +      -       -      +
    249A  LYS*     3.7    29.0    -      -       -      +
    252A  ARG*     3.1    47.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ILE*     3.5    10.8    -      -       +      +
     41A  LEU*     4.1    29.8    -      -       +      -
    147A  LEU*     4.4     6.3    -      -       +      +
    150A  CYS*     3.6    29.8    -      -       +      -
    151A  ALA      4.8     2.5    -      -       -      +
    154A  PHE*     3.7    17.7    -      -       +      -
    165A  ARG*     1.3    78.3    -      -       -      +
    167A  MET*     1.3    60.3    +      -       -      +
    168A  LEU      4.0     0.8    +      -       -      +
    193A  LEU*     4.3    19.5    -      -       +      -
    198A  ILE*     4.0    19.5    -      -       +      -
    199A  PHE      2.7    12.2    +      -       -      +
    200A  LEU*     3.3    12.5    -      -       +      +
    201A  ASP*     2.7    34.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  LEU*     3.9    21.5    -      -       +      -
     39A  ILE      2.9    13.9    +      -       -      +
     40A  PHE*     4.3    13.2    -      -       +      -
     41A  LEU      2.8    29.0    +      -       -      +
    165A  ARG*     4.1    11.6    -      -       -      -
    166A  ILE*     1.3    73.8    -      -       -      +
    168A  LEU*     1.3    58.9    +      -       -      +
    169A  PHE*     3.5    14.1    -      -       +      -
    201A  ASP*     3.4     8.3    -      -       -      +
    203A  MET*     3.5    37.5    -      -       +      -
    246A  VAL*     3.9    29.6    -      -       -      -
    249A  LYS*     3.9    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  LEU*     3.5    22.9    -      -       +      +
     88A  TYR*     3.5    37.7    -      -       +      +
    143A  LEU*     5.0     7.4    -      -       +      -
    147A  LEU*     6.2     0.7    -      -       +      -
    166A  ILE*     4.0     1.5    +      -       +      -
    167A  MET*     1.3    73.2    -      -       -      +
    169A  PHE*     1.3    65.2    +      -       -      +
    170A  THR*     4.1     7.9    -      -       +      -
    200A  LEU*     4.7    17.9    -      -       +      -
    201A  ASP      2.9    16.0    +      -       -      +
    202A  LEU*     3.8     9.4    -      -       +      +
    203A  MET*     2.7    32.8    +      -       -      +
    217A  TYR*     3.4    42.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  PHE*     3.9    33.2    -      +       +      -
     41A  LEU      2.8    23.8    +      -       -      +
     42A  VAL*     4.3     6.7    -      -       +      -
     43A  ASP*     3.0    27.2    +      -       -      +
     48A  MET*     3.6     5.1    -      -       +      +
     63A  SER*     3.4    39.3    -      -       -      +
     66A  CYS*     4.2    12.1    -      -       -      -
     67A  ILE*     4.1     8.7    -      -       +      -
    167A  MET*     3.5    30.3    -      -       +      -
    168A  LEU*     1.3    73.8    -      -       -      +
    170A  THR*     1.3    60.8    +      -       -      +
    203A  MET*     3.6    14.8    -      -       +      -
    205A  LEU*     4.2     2.0    -      -       +      -
    242A  LEU*     4.2    10.3    -      -       +      -
    246A  VAL*     4.0    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  ASP*     2.9    25.5    +      -       -      -
     48A  MET*     3.7     9.4    -      -       -      -
     88A  TYR*     3.8     7.6    +      -       -      -
    168A  LEU*     4.1     5.2    -      -       +      -
    169A  PHE*     1.3    76.0    -      -       -      +
    171A  ASN*     1.3    60.6    +      -       -      +
    172A  GLU*     3.0    27.0    +      -       -      +
    175A  PRO*     6.1     0.2    -      -       -      +
    202A  LEU*     3.9    24.2    -      -       +      -
    203A  MET      3.6     4.4    +      -       -      -
    204A  HIS*     3.3     5.2    -      -       -      -
    205A  LEU*     2.9    24.4    +      -       -      +
    211A  PHE*     3.7     4.0    -      -       +      -
    217A  TYR*     4.1    13.1    +      -       +      +
----------------------------------------------------------
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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