Contacts of the strand formed by residues 61 - 79 (chain J) in PDB entry 6MZL


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 61 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24J  TYR*     3.7    34.1    -      -       +      +
     56J  VAL      3.4     1.2    -      -       -      +
     57J  ARG*     3.2     3.0    -      -       -      -
     58J  VAL      2.9    36.7    +      -       -      +
     59J  ASP*     3.7    11.0    -      -       +      +
     60J  ARG*     1.3    77.7    -      -       -      +
     62J  PRO*     1.3    75.8    -      -       +      +
     63J  LEU*     3.7     4.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 62 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55J  ILE*     3.8    22.9    -      -       +      -
     56J  VAL      3.7     3.6    -      -       -      +
     57J  ARG*     4.1    10.5    -      -       +      +
     60J  ARG      3.4    10.3    -      -       -      +
     61J  VAL*     1.3    89.2    -      -       +      +
     63J  LEU*     1.3    68.0    +      -       -      +
     99J  VAL      5.3     2.6    -      -       -      +
    103J  LEU*     4.0    29.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 63 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20J  LEU*     4.5     6.7    -      -       +      -
     21J  PRO*     3.7    16.4    -      -       +      -
     24J  TYR*     3.7    56.3    -      -       +      +
     55J  ILE*     3.5     3.1    -      -       -      -
     56J  VAL      2.8    39.4    +      -       -      +
     58J  VAL*     4.5     4.9    -      -       +      -
     61J  VAL*     4.4     5.4    -      -       +      +
     62J  PRO*     1.3    81.7    -      -       -      +
     64J  ALA*     1.3    64.9    +      -       -      +
     65J  SER*     3.3     1.9    +      -       -      -
     97J  SER*     3.9    14.8    -      -       -      -
     98J  THR      3.5    15.3    -      -       -      +
     99J  VAL*     3.8    19.3    -      -       +      +
    103J  LEU*     4.2     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 64 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54J  GLY      3.9     5.2    -      -       -      +
     63J  LEU*     1.3    70.1    -      -       -      +
     65J  SER*     1.3    58.9    +      -       -      +
     96J  VAL      3.7     1.2    -      -       -      +
     97J  SER*     3.5     0.3    -      -       -      -
     98J  THR*     2.8    37.4    +      -       -      +
     99J  VAL      5.4     0.6    -      -       -      -
    100J  ASP      3.9    14.1    -      -       -      +
    101J  GLY*     3.9    18.4    -      -       -      +
    102J  ASP      3.8    22.0    -      -       -      +
    103J  LEU*     3.8    14.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 65 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53J  HIS*     3.5     9.2    -      -       -      +
     54J  GLY      2.9    41.2    +      -       -      +
     56J  VAL*     3.3    12.7    -      -       -      +
     63J  LEU      3.3     7.4    +      -       -      -
     64J  ALA*     1.3    72.7    -      -       -      +
     66J  LYS*     1.3    61.8    +      -       -      +
     95J  LEU*     3.7    22.9    -      -       -      -
     96J  VAL      3.0     7.6    -      -       -      -
     97J  SER*     2.6    26.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 66 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52J  ARG      3.6     2.9    -      -       -      -
     53J  HIS*     4.3    17.4    +      -       +      +
     65J  SER*     1.3    76.4    -      -       -      +
     67J  LEU*     1.3    62.0    +      -       -      +
     68J  VAL*     3.5    15.6    +      -       +      +
     94J  MET      3.3     4.0    -      -       -      +
     95J  LEU*     3.8     2.9    -      -       -      -
     96J  VAL*     2.9    37.2    +      -       +      +
    129J  LYS*     4.0    25.8    -      -       -      +
    130J  PHE*     3.6    36.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 67 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    620A  LEU*     4.1    25.4    -      -       +      -
     16J  PHE*     4.9     6.3    -      -       +      -
     47J  LEU*     5.9     4.9    -      -       +      -
     51J  GLY      3.4    21.1    -      -       -      +
     52J  ARG*     2.7    35.2    +      -       -      +
     66J  LYS*     1.3    70.0    -      -       -      +
     68J  VAL*     1.3    60.1    +      -       -      +
     93J  GLN*     3.4    45.1    -      -       +      +
     94J  MET      3.6    15.5    -      -       -      +
     95J  LEU*     3.9    17.6    -      -       +      +
    130J  PHE*     3.5    22.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 68 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66J  LYS*     4.0    28.0    -      -       +      +
     67J  LEU*     1.3    78.3    -      -       -      +
     69J  ASP*     1.3    62.8    +      -       -      +
     70J  LEU*     5.1     0.4    -      -       +      -
     93J  GLN*     3.3     6.6    -      -       -      +
     94J  MET*     2.9    54.8    +      -       +      +
     96J  VAL*     4.2    14.4    -      -       +      -
    129J  LYS      4.5     1.8    -      -       -      +
    130J  PHE*     3.3    19.3    -      -       -      +
    131J  ILE      5.3     0.2    -      -       -      -
    132J  TRP*     3.8    35.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 69 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52J  ARG*     3.3    29.6    +      -       -      -
     68J  VAL*     1.3    71.8    -      -       -      +
     70J  LEU*     1.3    66.6    +      -       -      +
     92J  CYS*     3.5     7.0    -      -       -      +
     93J  GLN*     3.3    28.7    +      -       -      +
    130J  PHE*     3.0    15.4    +      -       -      +
    131J  ILE*     5.1     6.7    -      -       +      +
    132J  TRP*     3.2    25.8    +      -       -      +
    144J  ARG*     3.8     9.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    617A  ARG*     4.5     5.9    +      -       -      -
     17J  ILE*     4.3    17.9    -      -       +      -
     68J  VAL*     3.8     0.6    +      -       +      -
     69J  ASP*     1.3    75.6    -      -       -      +
     71J  PRO*     1.3    70.7    -      -       +      +
     72J  CYS      3.4    12.4    -      -       -      +
     74J  MET*     4.4    11.9    -      -       +      -
     91J  ILE*     4.7     3.4    -      -       +      +
     92J  CYS*     2.5    41.1    +      -       -      +
     93J  GLN      4.1    11.4    -      -       -      +
     94J  MET*     3.9    19.7    -      -       +      -
    132J  TRP*     3.7    27.6    -      -       +      -
    134J  HIS      4.6     1.3    -      -       -      +
    136J  ILE*     3.8    28.7    -      -       +      -
    144J  ARG*     4.2     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 71 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    617A  ARG*     3.1    21.7    +      -       -      -
    686A  GLU*     4.6     2.8    -      -       -      +
     69J  ASP      3.7     0.2    -      -       -      -
     70J  LEU*     1.3    87.0    -      -       +      +
     72J  CYS*     1.3    60.0    +      -       +      +
    132J  TRP*     3.4    19.5    -      -       +      +
    133J  ASN      4.1     0.2    -      -       -      -
    134J  HIS      3.4    28.9    -      -       -      +
    135J  GLY*     5.0     0.4    -      -       -      -
    143J  VAL*     3.7    16.6    -      -       +      -
    144J  ARG*     3.4    33.0    -      -       +      +
    148J  PHE*     3.7    25.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 72 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    617A  ARG*     4.0     2.9    -      -       -      +
    682A  GLU*     3.8    28.4    -      -       +      +
    683A  TYR      3.5    22.0    -      -       -      +
    684A  SER*     4.6     3.4    -      -       -      -
    685A  GLU      5.4     1.3    -      -       -      -
    686A  GLU*     5.5     0.2    -      -       -      +
     70J  LEU*     4.1    15.6    -      -       -      +
     71J  PRO*     1.3    82.6    -      -       +      +
     73J  VAL*     1.3    64.9    +      -       -      +
     74J  MET*     3.5     6.6    +      -       -      +
     91J  ILE      4.2     3.5    -      -       -      +
     92J  CYS*     4.7     1.2    -      -       -      -
    135J  GLY*     5.2     0.7    -      -       -      -
    140J  LEU*     4.5     7.9    -      -       -      -
    143J  VAL*     4.1    20.4    -      -       -      -
    148J  PHE*     3.6    27.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 73 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    616A  HIS*     3.3    29.8    -      -       +      +
    617A  ARG*     3.3    23.8    -      -       -      +
    682A  GLU*     4.0     0.3    -      -       -      -
    683A  TYR*     3.1    36.6    +      -       +      +
    685A  GLU      3.8    12.3    +      -       -      +
    686A  GLU      3.7    18.6    -      -       -      +
    687A  ASN*     5.7     0.2    -      -       -      -
    688A  GLY      5.8     0.2    -      -       -      +
    691A  MET*     3.9    30.1    -      -       +      -
     72J  CYS*     1.3    73.3    -      -       -      +
     74J  MET*     1.3    62.5    +      -       -      +
     75J  GLU*     5.1     1.3    -      -       +      -
     90J  ASP*     4.4     8.3    -      -       -      +
     91J  ILE      4.3     2.0    -      -       -      -
     92J  CYS*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 74 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    680A  LEU*     3.7    28.3    -      -       +      -
    681A  ALA      3.4    15.3    -      -       -      +
    682A  GLU*     3.5    38.6    -      -       +      +
    757A  MET*     5.4     0.4    -      -       -      -
    779A  ILE*     4.1    13.7    -      -       +      -
     17J  ILE*     4.6    15.9    -      -       -      -
     70J  LEU*     4.4    10.8    -      -       +      -
     72J  CYS      3.5     4.0    +      -       -      +
     73J  VAL*     1.3    76.7    -      -       -      +
     75J  GLU*     1.3    60.7    +      -       -      +
     90J  ASP*     3.4     8.0    -      -       -      +
     91J  ILE*     2.8    48.1    +      -       +      +
    136J  ILE*     3.7    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 75 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    680A  LEU*     3.4     4.0    -      -       -      -
    681A  ALA*     2.5    46.8    +      -       +      +
    683A  TYR*     2.6    46.6    +      -       +      +
    691A  MET*     3.5    11.7    -      -       +      +
    692A  MET*     3.6    16.2    +      -       -      +
     73J  VAL*     5.1     0.7    -      -       +      -
     74J  MET*     1.3    74.3    -      -       -      +
     76J  SER*     1.3    57.4    +      -       -      +
     77J  LEU*     3.4    17.4    -      -       +      +
     87J  LYS*     2.9    35.1    +      -       +      +
     89J  ALA      3.4     5.2    -      -       -      +
     90J  ASP*     3.3    17.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 76 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    678A  LEU*     5.1     2.9    -      -       -      -
    679A  ILE      3.5     9.2    -      -       -      -
    680A  LEU*     3.7    21.3    -      -       -      -
    763A  LEU*     5.0     4.5    -      -       -      -
     15J  GLN*     2.7    28.1    +      -       -      -
     75J  GLU*     1.3    72.1    -      -       -      +
     77J  LEU*     1.3    53.4    +      -       -      +
     87J  LYS*     3.7     1.6    -      -       -      +
     88J  THR*     2.5    52.8    +      -       -      -
     89J  ALA*     2.9    19.3    +      -       -      +
     91J  ILE*     4.0     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 77 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    678A  LEU*     3.2     7.3    -      -       -      +
    679A  ILE*     2.9    48.1    +      -       +      +
    681A  ALA*     3.8    14.8    -      -       +      -
    692A  MET*     4.5     9.2    -      -       +      -
    698A  THR*     3.8    19.7    -      -       +      -
    743A  PHE*     4.7     6.1    -      -       +      -
     75J  GLU*     3.4    37.7    -      -       +      +
     76J  SER*     1.3    73.9    -      -       -      +
     78J  LYS*     1.3    59.8    +      -       -      +
     85J  PHE*     3.7    30.7    -      -       +      -
     86J  TYR      3.3     6.7    -      -       -      +
     87J  LYS*     3.7    18.6    -      -       +      +
     88J  THR*     3.9     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 78 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    650A  ARG*     3.7    15.4    -      -       -      +
    665A  MET*     4.1    17.5    -      -       -      -
    670A  ASP      2.4    33.5    +      -       -      +
    671A  LEU*     4.1     4.9    -      -       -      +
    672A  THR      3.2    15.5    +      -       -      +
    675A  ASP*     3.1    31.1    +      -       -      -
    676A  GLY*     5.0     2.7    -      -       -      -
    677A  ASP      3.4     5.2    -      -       -      +
    678A  LEU*     3.7    15.9    -      -       +      -
     77J  LEU*     1.3    73.9    -      -       -      +
     79J  THR*     1.3    64.4    +      -       -      +
     80J  ILE*     5.3     3.4    -      -       -      -
     85J  PHE*     3.4     3.7    -      -       -      +
     86J  TYR*     2.6    54.9    +      -       +      +
     88J  THR*     3.6    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 79 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    676A  GLY*     4.1     1.0    -      -       -      -
    677A  ASP*     2.6    57.0    +      -       +      +
    678A  LEU*     5.2     1.8    -      -       -      -
    679A  ILE*     5.6     0.9    -      -       +      -
    719A  TYR*     4.7     4.7    -      -       +      -
     78J  LYS*     1.3    80.9    -      -       -      +
     80J  ILE*     1.3    77.3    +      -       -      +
     81J  ASP      3.6     0.3    +      -       -      -
     82J  LYS*     3.0    34.4    +      -       +      +
     84J  THR      3.3    15.7    +      -       -      -
     85J  PHE*     3.4    26.0    -      -       +      -
     86J  TYR*     5.4     2.5    -      -       -      -
----------------------------------------------------------
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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