Contacts of the strand formed by residues 71 - 87 (chain D) in PDB entry 5JTP


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 GLU 71 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  ASN*     3.1    25.1    +      -       -      +
     30D  HIS*     3.0    41.5    +      -       +      -
     31D  VAL*     3.6    23.7    -      -       +      -
     34D  LYS*     2.9    34.4    +      -       -      +
     67D  SER*     3.3     8.2    -      -       -      -
     68D  LEU      2.9    28.4    +      -       -      +
     69D  GLY      3.5     0.2    -      -       -      -
     70D  GLU*     1.3    90.9    -      -       -      +
     72D  THR*     1.3    58.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 72 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  PRO*     3.8    24.8    -      -       +      +
     27D  ASN*     3.0    24.9    +      -       -      +
     31D  VAL*     3.5     8.3    -      -       -      +
     65D  THR*     5.2     2.6    -      -       +      +
     66D  ALA      3.2    16.8    -      -       -      +
     67D  SER*     3.6    10.9    +      -       -      +
     71D  GLU*     1.3    73.1    -      -       -      +
     73D  ALA*     1.3    61.5    +      -       -      +
     74D  PHE      4.0     2.9    -      -       -      +
     75D  LEU*     3.7    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 73 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25D  ALA*     3.9     0.9    -      -       -      -
     26D  PRO*     3.5    15.1    -      -       -      +
     31D  VAL*     3.7    12.3    -      -       -      +
     38D  PRO*     3.5    34.5    -      -       +      -
     66D  ALA      3.0     8.8    +      -       -      +
     67D  SER*     3.4     4.3    -      -       -      +
     68D  LEU*     3.7    24.5    -      -       +      +
     72D  THR*     1.3    73.9    -      -       -      +
     74D  PHE*     1.3    60.5    +      -       +      +
    123D  PHE*     3.1    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 74 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  PHE*     3.8    25.8    -      +       +      -
     24D  GLU      3.6     5.4    -      -       -      -
     26D  PRO*     4.5     0.7    -      -       -      -
     37D  GLN*     5.0     3.1    -      -       -      -
     38D  PRO*     3.7    22.0    -      -       +      -
     40D  VAL*     3.9    13.9    -      -       +      -
     64D  VAL*     3.7    26.3    -      -       +      +
     66D  ALA*     2.9    53.0    +      -       +      +
     72D  THR      4.0     0.2    -      -       -      -
     73D  ALA*     1.3    80.6    -      -       -      +
     75D  LEU*     1.3    65.5    +      -       -      +
     76D  CYS*     4.8     1.3    -      -       +      -
    118D  VAL*     3.6    28.3    -      -       +      -
    123D  PHE*     3.7    44.4    -      +       +      -
    124D  PRO      5.2     1.1    -      -       -      -
    126D  LEU*     4.2     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 75 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  SER      4.3     1.1    -      -       -      -
     23D  PHE*     3.2    11.7    -      -       -      -
     24D  GLU*     2.8    62.9    +      -       +      +
     26D  PRO*     4.7     8.3    -      -       +      -
     64D  VAL      3.6     1.6    -      -       -      -
     65D  THR*     3.7    36.1    -      -       +      +
     72D  THR*     3.7    24.9    -      -       +      +
     74D  PHE*     1.3    75.8    -      -       -      +
     76D  CYS*     1.3    61.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 76 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  SER      3.2     6.9    +      -       -      -
     23D  PHE*     4.2     9.2    -      -       +      -
     63D  THR*     3.4     4.5    -      -       -      +
     64D  VAL*     2.8    39.2    +      -       +      +
     74D  PHE*     4.8     4.7    -      -       +      -
     75D  LEU*     1.3    76.4    -      -       -      +
     77D  GLU*     1.3    64.7    +      -       -      +
     78D  VAL*     4.3     0.2    -      -       -      -
    114D  ILE*     3.4    42.6    -      -       +      -
    117D  MET*     3.2    34.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 77 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20D  ASP*     4.3    12.4    -      -       -      +
     21D  ILE*     3.5     2.3    -      -       -      -
     22D  SER*     2.9    41.0    +      -       -      +
     61D  ARG*     3.0    46.1    +      -       +      +
     62D  VAL      3.3     7.2    -      -       -      +
     63D  THR*     3.0    32.8    +      -       +      +
     76D  CYS*     1.3    77.5    -      -       -      +
     78D  VAL*     1.3    66.3    +      -       -      +
     79D  GLN*     4.3     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 78 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  THR*     3.8     5.8    -      -       +      -
     20D  ASP      3.4    11.0    -      -       -      +
     21D  ILE*     4.3     3.4    -      -       +      -
     60D  LEU      3.0    13.5    -      -       -      +
     61D  ARG*     4.4     0.4    -      -       -      -
     62D  VAL*     3.0    25.6    +      -       +      +
     77D  GLU*     1.3    79.1    -      -       -      +
     79D  GLN*     1.3    62.0    +      -       -      +
     80D  GLN*     3.4    34.6    +      -       +      +
    110D  ALA*     4.6     4.9    -      -       -      +
    113D  CYS*     3.6    29.6    -      -       +      -
    114D  ILE*     3.8    18.4    -      -       +      -
    117D  MET*     3.6    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 79 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  THR*     3.8     0.5    -      -       -      -
     19D  LYS*     3.0    31.3    +      -       +      +
     20D  ASP*     2.9    47.0    +      -       +      +
     47D  ALA*     5.9     1.6    -      -       -      +
     59D  VAL*     3.7    22.8    -      -       +      +
     60D  LEU      3.3     5.8    -      -       -      -
     61D  ARG*     3.1    53.0    +      -       +      +
     77D  GLU*     4.3     0.8    -      -       -      +
     78D  VAL*     1.3    70.4    -      -       -      +
     80D  GLN*     1.3    60.2    +      -       -      +
     81D  GLY      3.2     3.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 80 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120C  ARG      5.2     0.2    -      -       -      +
     16D  ILE*     3.2    24.2    -      -       +      +
     17D  TYR*     3.6    11.5    -      -       -      +
     18D  THR*     3.3    26.0    -      -       -      +
     60D  LEU*     2.8    32.3    +      -       +      +
     78D  VAL*     3.4    13.3    +      -       +      +
     79D  GLN*     1.3    68.3    -      -       -      +
     81D  GLY*     1.3    59.2    +      -       -      +
    106D  LEU*     3.4    47.3    -      -       +      +
    109D  TYR*     3.3    32.0    +      -       +      +
    110D  ALA*     3.8     9.6    -      -       +      +
    113D  CYS*     4.0     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 81 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16D  ILE*     3.9     1.0    -      -       -      -
     17D  TYR*     2.8    49.0    +      -       -      +
     19D  LYS*     3.9    23.1    -      -       -      +
     57D  GLU*     4.8     0.4    -      -       -      -
     58D  VAL      3.4     7.4    -      -       -      -
     59D  VAL*     4.0     5.6    -      -       -      -
     79D  GLN      3.2     7.7    +      -       -      -
     80D  GLN*     1.3    72.8    -      -       -      +
     82D  GLY*     1.3    57.5    +      -       -      -
    106D  LEU*     3.9     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 82 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15D  ARG      3.3    10.8    -      -       -      -
     16D  ILE*     4.5     0.4    -      -       -      -
     57D  GLU*     3.2     6.7    -      -       -      +
     58D  VAL      2.9    33.2    +      -       -      -
     81D  GLY*     1.3    74.0    -      -       -      -
     83D  ILE*     1.3    63.9    +      -       -      -
     84D  PHE*     3.3    13.8    -      -       -      -
    106D  LEU*     3.7    17.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 83 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  PRO*     4.4     9.0    -      -       +      -
     32C  PHE*     5.2     1.1    -      -       +      -
     13D  ILE      3.7     1.0    -      -       -      -
     14D  GLN*     2.9    61.8    +      -       +      +
     15D  ARG*     2.9    26.9    +      -       +      +
     17D  TYR*     3.6    36.8    -      -       +      +
     51D  LEU*     3.7    20.9    -      -       +      -
     55D  VAL*     3.7    15.5    -      -       +      -
     56D  TYR      4.1     2.2    -      -       -      -
     57D  GLU*     4.4     3.4    -      -       -      +
     82D  GLY*     1.3    71.3    -      -       -      -
     84D  PHE*     1.4    64.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 84 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11D  PHE*     3.6    39.9    -      +       +      -
     12D  GLN      3.7     4.5    -      -       -      +
     13D  ILE*     3.9    20.0    -      -       +      -
     14D  GLN*     4.5     2.5    -      -       -      -
     16D  ILE*     4.9     0.9    -      -       +      -
     56D  TYR*     2.9    41.1    +      -       -      +
     58D  VAL*     3.9    21.1    -      -       +      -
     82D  GLY*     3.3    30.3    -      -       -      -
     83D  ILE*     1.4    77.6    -      -       -      +
     85D  SER*     1.3    59.6    +      -       -      +
     86D  ILE*     3.5     9.7    +      -       +      +
     98D  LEU*     5.3     0.4    -      -       +      -
    102D  CYS*     3.7    33.9    -      -       +      -
    105D  ILE*     3.9    22.0    -      -       +      -
    106D  LEU*     4.0    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 85 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  THR*     3.6     6.3    -      -       -      +
     11D  PHE*     3.1     9.9    +      -       -      -
     12D  GLN*     2.9    51.3    +      -       -      +
     14D  GLN*     2.8    35.6    +      -       -      +
     54D  ASP*     3.3    12.6    -      -       -      -
     55D  VAL*     4.2     6.0    -      -       -      +
     84D  PHE*     1.3    67.7    -      -       -      +
     86D  ILE*     1.3    59.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 86 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  THR*     3.6     4.5    -      -       -      -
     11D  PHE*     3.8    30.5    -      -       +      -
     50D  GLN*     5.9     0.2    -      -       -      +
     54D  ASP*     2.8    35.8    +      -       -      +
     56D  TYR*     3.7    30.3    -      -       +      -
     84D  PHE*     4.0    12.1    -      -       +      +
     85D  SER*     1.3    74.0    -      -       -      +
     87D  ALA*     1.3    64.8    +      -       -      +
     89D  ILE*     4.2    11.7    -      -       +      -
     94D  MET*     3.3    36.8    -      -       +      -
     97D  CYS*     5.1     2.5    -      -       -      -
     98D  LEU*     4.1    10.3    -      -       +      -
    451H  VAL*     4.4    14.3    -      -       +      +
    452H  VAL*     5.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 87 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  GLN*     4.8     1.3    -      -       -      +
      5D  ASN*     3.3    42.6    -      -       +      +
      9D  MET*     3.7     1.9    -      -       -      +
     10D  THR*     2.9    38.5    +      -       +      +
     54D  ASP*     3.9     5.4    -      -       +      +
     86D  ILE*     1.3    76.3    -      -       -      +
     88D  GLY*     1.3    59.7    +      -       -      +
     89D  ILE*     3.1    21.8    +      -       -      +
    451H  VAL*     5.4     4.5    -      -       -      -
----------------------------------------------------------
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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