Contacts of the strand formed by residues 143 - 153 (chain E) in PDB entry 1J8H


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 LYS 143 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168D  MET*     4.2     8.1    -      -       +      -
    171D  MET*     3.4    37.6    -      -       -      +
    173D  PHE*     3.7    41.4    -      -       +      -
    137E  GLU*     3.3    12.5    -      -       -      +
    138E  ILE*     3.3    22.0    +      -       -      -
    141E  THR*     3.2    22.1    +      -       -      +
    142E  GLN*     1.3    85.1    -      -       -      +
    144E  ALA*     1.3    62.1    +      -       -      +
    198E  ARG*     3.7    34.5    -      -       +      +
    199E  VAL      3.5    11.4    -      -       -      +
    200E  SER*     5.1     2.5    -      -       -      -
    201E  ALA*     3.8     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 144 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133E  PRO*     3.4    28.3    -      -       +      -
    137E  GLU*     3.9     0.9    -      -       -      -
    138E  ILE*     4.3     4.3    -      -       +      -
    143E  LYS*     1.3    75.3    -      -       -      +
    145E  THR*     1.3    62.9    +      -       -      +
    146E  LEU*     3.8     1.7    -      -       -      +
    197E  LEU      3.5     4.0    -      -       -      +
    198E  ARG*     4.1     0.7    -      -       -      -
    199E  VAL*     2.7    39.5    +      -       +      +
    200E  SER      4.6     1.3    -      -       -      +
    201E  ALA*     4.4     1.8    -      -       -      +
    204E  TRP*     3.6    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 145 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128D  LEU*     3.3    19.9    -      -       -      +
    140D  LEU*     3.5    29.1    -      -       +      +
    142D  THR*     5.4     0.9    +      -       -      -
    166D  LEU*     5.2     1.6    -      -       +      -
    177D  SER*     6.3     0.2    -      -       -      -
    133E  PRO*     3.4    12.4    -      -       -      +
    137E  GLU*     2.7    29.8    +      -       -      +
    144E  ALA*     1.3    72.5    -      -       -      +
    146E  LEU*     1.3    71.4    +      -       -      +
    147E  VAL*     4.5     1.3    -      -       +      -
    196E  ARG*     3.9    23.3    -      -       +      -
    197E  LEU      3.6     5.6    -      -       -      +
    198E  ARG*     3.0    24.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 146 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130E  VAL*     4.4    11.4    -      -       +      -
    131E  PHE      3.5     8.5    -      -       -      +
    132E  GLU*     5.3     0.7    -      -       -      -
    133E  PRO*     3.8    20.2    -      -       +      -
    144E  ALA      3.8    11.0    -      -       -      +
    145E  THR*     1.3    76.1    -      -       -      +
    147E  VAL*     1.3    63.4    +      -       -      +
    162E  TRP*     3.7    21.3    -      -       +      -
    196E  ARG*     3.3     6.1    -      -       -      -
    197E  LEU*     2.9    47.6    +      -       +      +
    199E  VAL*     4.5     5.8    -      -       +      -
    204E  TRP*     4.0    14.4    -      -       +      -
    211E  PHE*     3.7    49.1    -      -       +      -
    242E  ALA*     5.1     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 147 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128D  LEU*     3.8    22.2    -      -       +      -
    138D  VAL*     4.4    16.8    -      -       +      -
    140D  LEU*     4.8     4.3    -      -       +      -
    179D  VAL*     4.3    20.9    -      -       +      -
    130E  VAL*     3.4     5.4    -      -       -      +
    131E  PHE*     2.9    38.3    +      -       +      -
    145E  THR*     4.2     5.1    +      -       +      -
    146E  LEU*     1.3    80.3    -      -       -      +
    148E  CYS*     1.3    73.0    +      -       -      +
    149E  LEU*     4.2    16.2    -      -       +      -
    162E  TRP*     4.2     2.9    -      -       -      -
    194E  SER*     4.9     1.6    -      -       -      -
    195E  SER      3.3     9.9    -      -       -      +
    196E  ARG*     4.3    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 148 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128E  VAL*     3.6    16.8    -      -       -      -
    129E  ALA      3.6     4.5    -      -       -      -
    130E  VAL*     4.6     0.4    -      -       -      +
    147E  VAL*     1.3    74.7    -      -       -      +
    149E  LEU*     1.3    68.2    +      -       -      +
    150E  ALA      4.8     0.2    -      -       -      -
    160E  LEU*     4.2     7.6    -      -       +      +
    162E  TRP*     3.6    16.8    -      -       +      -
    193E  LEU      3.7     0.3    -      -       -      +
    194E  SER*     3.1     8.8    -      -       -      -
    195E  SER*     2.8    35.2    +      -       -      +
    213E  CYS*     2.0    50.9    -      -       +      -
    215E  VAL*     5.0     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 149 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  LYS*     3.9    21.1    -      -       +      -
    138D  VAL*     3.9    17.9    -      -       +      -
    179D  VAL*     5.1     0.4    -      -       +      -
    181D  TRP*     3.8    39.3    -      -       +      -
    127E  GLU      3.3     5.9    -      -       -      +
    128E  VAL*     3.3     1.2    -      -       -      -
    129E  ALA*     2.9    39.1    +      -       +      +
    131E  PHE*     3.8    15.9    -      -       +      -
    147E  VAL*     4.2    11.2    -      -       +      -
    148E  CYS*     1.3    86.1    -      -       -      +
    150E  ALA*     1.3    59.3    -      -       -      +
    151E  THR*     3.9     9.8    +      -       +      +
    193E  LEU      4.0     2.7    -      -       -      +
    194E  SER*     3.5    24.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 150 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126E  PRO*     4.5     7.4    -      -       +      -
    127E  GLU      3.3     7.4    -      -       -      +
    128E  VAL*     4.6     1.8    -      -       +      +
    148E  CYS*     4.1     0.8    -      -       -      -
    149E  LEU*     1.3    71.6    -      -       -      +
    151E  THR*     1.3    60.8    +      -       -      +
    153E  PHE*     3.5    16.6    -      -       +      -
    158E  VAL*     5.7     0.4    -      -       +      -
    160E  LEU*     4.8     4.7    -      -       +      +
    192E  SER*     3.2     2.1    -      -       -      -
    193E  LEU*     2.6    49.8    +      -       +      +
    215E  VAL*     4.0    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 151 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  LYS*     4.0    32.7    +      -       -      +
    181D  TRP*     5.0     2.0    -      -       +      +
    125E  PRO      4.4     0.2    -      -       -      +
    126E  PRO*     3.2     2.4    -      -       -      +
    127E  GLU*     2.8    47.3    +      -       -      +
    149E  LEU*     4.2    21.3    -      -       +      -
    150E  ALA*     1.3    79.3    -      -       -      +
    152E  GLY*     1.3    66.4    +      -       -      +
    153E  PHE*     3.3     3.8    -      -       -      -
    182E  GLU*     3.9     3.1    -      -       -      -
    191E  TYR      3.8     1.6    -      -       -      -
    192E  SER*     3.4    22.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 152 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124E  PHE*     3.5     8.0    -      -       -      +
    125E  PRO      3.6     4.9    -      -       -      +
    127E  GLU*     6.4     0.2    -      -       -      -
    151E  THR*     1.3    76.4    -      -       -      +
    153E  PHE*     1.3    58.9    +      -       -      +
    182E  GLU*     3.1    14.3    +      -       -      -
    190E  ARG*     3.0    45.0    +      -       -      -
    191E  TYR      3.0     8.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 153 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124E  PHE      3.3    12.1    -      -       -      +
    125E  PRO      4.0     0.7    -      -       -      -
    126E  PRO*     3.4    35.7    -      -       +      -
    150E  ALA*     3.5    30.3    -      -       +      -
    151E  THR      3.3     1.3    -      -       -      -
    152E  GLY*     1.3    79.7    -      -       -      +
    154E  PHE*     1.3    65.0    +      -       -      +
    155E  PRO      3.5    13.7    -      -       -      -
    156E  ASP*     4.0    14.4    -      -       -      -
    158E  VAL*     3.6    36.8    -      -       +      -
    179E  PRO*     4.3     4.5    -      -       +      -
    190E  ARG*     3.3     0.9    -      -       -      -
    191E  TYR*     2.7    64.0    +      -       +      -
    192E  SER*     3.9     2.2    -      -       -      -
    193E  LEU*     3.9    13.2    -      -       +      -
    217E  PHE*     4.4     3.1    -      -       +      -
----------------------------------------------------------
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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