Contacts of the strand formed by residues 71 - 87 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ASN*     3.6    21.2    -      -       +      +
     30A  HIS*     3.1    33.3    +      -       -      +
     31A  VAL*     3.3    21.5    -      -       +      +
     34A  LYS*     2.9    42.9    +      -       -      +
     67A  SER*     3.4     3.1    -      -       -      -
     68A  LEU*     2.9    35.5    +      -       +      +
     70A  GLU*     1.3    85.6    -      -       +      +
     72A  THR*     1.3    63.9    +      -       -      +
     73A  ALA      3.8     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  GLU      4.9     2.9    -      -       -      +
     26A  PRO*     4.8     6.4    -      -       +      +
     27A  ASN*     3.1    37.0    +      -       -      +
     65A  THR*     4.3    10.3    -      -       -      +
     66A  ALA      3.6     7.4    -      -       -      +
     67A  SER*     3.8    11.1    -      -       -      -
     70A  GLU      4.2     1.7    +      -       -      -
     71A  GLU*     1.3    72.2    -      -       -      +
     73A  ALA*     1.3    63.2    +      -       -      +
     74A  PHE*     3.5    28.3    -      -       -      +
     75A  LEU*     4.5     7.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  ALA*     3.9    10.8    -      -       -      +
     28A  ALA*     4.2     6.6    +      -       -      -
     31A  VAL*     3.7    24.8    -      -       +      +
     36A  TRP*     4.1    17.5    -      -       +      -
     38A  PRO*     4.7     5.8    -      -       +      -
     66A  ALA*     2.8    19.9    +      -       +      +
     67A  SER*     4.2     0.9    -      -       -      +
     68A  LEU      5.1     1.3    -      -       -      +
     71A  GLU      3.8     3.2    +      -       -      -
     72A  THR*     1.3    74.0    -      -       -      +
     74A  PHE*     1.3    74.9    +      -       +      +
    123A  PHE*     3.4    15.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     3.8    17.7    -      -       +      -
     24A  GLU      3.5     9.2    -      -       -      -
     25A  ALA*     4.5     0.2    -      -       +      -
     36A  TRP*     3.7    22.4    -      +       -      -
     38A  PRO*     5.1     0.9    -      -       +      -
     40A  VAL*     5.1     5.2    -      -       +      -
     64A  VAL*     4.0    19.5    -      -       +      -
     65A  THR*     3.7     0.3    -      -       -      -
     66A  ALA*     3.0    50.5    +      -       +      +
     72A  THR*     3.5     8.0    -      -       -      +
     73A  ALA*     1.3    86.6    -      -       +      +
     75A  LEU*     1.3    59.9    +      -       -      +
     76A  CYS*     3.3    23.6    -      -       -      -
    118A  VAL*     3.7    20.9    -      -       +      -
    123A  PHE*     3.7    33.9    -      +       +      -
    124A  PRO      5.5     2.7    -      -       -      -
    126A  LEU*     4.1    14.1    -      -       +      -
    470E  LEU*     5.5     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  SER*     5.6     3.4    -      -       -      +
     23A  PHE*     3.2    10.8    -      -       -      -
     24A  GLU*     2.9    67.9    +      -       +      +
     63A  THR*     3.9    22.9    -      -       +      -
     64A  VAL      3.0    27.1    -      -       -      +
     65A  THR*     4.2     9.9    -      -       -      +
     72A  THR*     4.7     8.1    -      -       +      -
     74A  PHE*     1.3    74.4    -      -       -      +
     76A  CYS*     1.3    62.4    +      -       -      +
     77A  GLU*     4.1    13.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     3.3    29.8    -      -       -      -
     62A  VAL      3.6     3.6    -      -       -      +
     64A  VAL*     2.9    38.6    +      -       +      +
     74A  PHE*     3.3    12.1    -      -       -      -
     75A  LEU*     1.3    70.0    -      -       -      +
     77A  GLU*     1.3    60.3    +      -       -      +
     78A  VAL      4.3     0.2    -      -       -      -
    114A  ILE*     3.7    23.1    -      -       +      +
    117A  MET*     3.4    19.3    -      -       -      -
    118A  VAL*     3.3    31.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ASP*     4.0    15.6    -      -       -      +
     21A  ILE*     3.6     1.0    -      -       -      -
     22A  SER*     2.8    51.3    +      -       -      +
     61A  ARG*     2.9    47.8    +      -       +      +
     62A  VAL      3.5     3.6    -      -       -      -
     63A  THR*     3.1    31.9    +      -       +      +
     75A  LEU*     4.1    11.5    -      -       +      +
     76A  CYS*     1.3    73.2    -      -       -      +
     78A  VAL*     1.3    66.6    +      -       -      +
     79A  GLN*     4.3     2.5    +      -       +      -
    117A  MET*     4.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  THR*     3.8    18.2    -      -       +      -
     20A  ASP      3.6     4.7    -      -       -      +
     21A  ILE*     4.2     4.5    -      -       +      -
     60A  LEU      3.2     6.2    -      -       -      +
     61A  ARG*     4.2     0.9    -      -       -      -
     62A  VAL*     3.0    31.5    +      -       -      +
     77A  GLU*     1.3    80.8    -      -       -      +
     79A  GLN*     1.3    61.4    +      -       -      +
     80A  GLN*     3.2    15.8    +      -       +      +
    110A  ALA*     4.4     3.6    -      -       +      -
    113A  CYS*     3.4    40.6    -      -       +      -
    114A  ILE*     3.8    20.0    -      -       +      -
    117A  MET*     3.6    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  THR*     3.6     0.3    -      -       -      -
     19A  LYS*     3.0    27.9    +      -       +      +
     20A  ASP*     2.9    53.8    +      -       +      +
     47A  ALA*     5.1     6.8    -      -       -      +
     59A  VAL*     3.7    21.2    -      -       +      +
     60A  LEU      3.7     5.4    -      -       -      -
     61A  ARG*     3.7    34.3    -      -       +      +
     77A  GLU*     4.3     4.5    +      -       -      +
     78A  VAL*     1.3    67.6    -      -       -      +
     80A  GLN*     1.3    59.8    +      -       -      +
     81A  GLY      3.2     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ILE*     3.6     4.6    -      -       -      +
     17A  TYR*     3.1    39.1    +      -       -      +
     18A  THR*     3.3    21.0    +      -       -      +
     59A  VAL*     4.2     0.2    -      -       -      -
     60A  LEU      2.9    37.3    +      -       -      +
     78A  VAL*     3.2     5.6    +      -       +      +
     79A  GLN*     1.3    68.9    -      -       -      +
     81A  GLY*     1.3    57.2    +      -       -      +
    106A  LEU*     3.3    43.0    -      -       +      +
    109A  TYR*     3.3    39.4    +      -       +      +
    110A  ALA*     3.4    17.6    -      -       +      +
    113A  CYS*     4.5     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ILE*     3.6     1.6    -      -       -      -
     17A  TYR*     2.8    41.6    +      -       -      +
     19A  LYS*     3.9    20.6    -      -       -      +
     57A  GLU*     4.9     1.8    -      -       -      -
     58A  VAL      3.7     5.8    -      -       -      -
     59A  VAL*     3.9     7.9    -      -       -      -
     79A  GLN      3.2     6.9    +      -       -      -
     80A  GLN*     1.3    74.3    -      -       -      +
     82A  GLY*     1.3    57.6    +      -       -      -
    106A  LEU*     3.7     5.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ARG      3.2    11.9    -      -       -      -
     17A  TYR*     5.2     0.4    -      -       -      -
     57A  GLU*     3.4     6.2    -      -       -      +
     58A  VAL      2.9    33.5    +      -       -      -
     81A  GLY*     1.3    74.5    -      -       -      -
     83A  ILE*     1.3    61.5    +      -       -      -
     84A  PHE*     3.2    14.4    -      -       -      -
    106A  LEU*     3.6    17.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ILE*     3.8     1.0    -      -       -      +
     14A  GLN*     2.9    59.5    +      -       +      +
     15A  ARG*     2.8    25.7    +      -       +      +
     17A  TYR*     3.5    29.4    -      -       +      +
     51A  LEU*     3.6    28.5    -      -       +      -
     55A  VAL*     3.9    15.7    -      -       +      -
     56A  TYR      4.7     1.1    -      -       -      +
     57A  GLU*     3.6    21.1    -      -       -      +
     82A  GLY*     1.3    71.7    -      -       -      -
     84A  PHE*     1.3    65.3    +      -       -      +
     29B  PRO*     4.1    14.1    -      -       +      +
     32B  PHE*     4.8     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     3.9    17.7    -      +       +      -
     12A  GLN      3.5     2.7    -      -       -      +
     13A  ILE*     3.8    42.2    -      -       +      -
     14A  GLN*     4.6     0.4    -      -       -      -
     55A  VAL*     4.1     1.7    -      -       -      +
     56A  TYR      2.9    40.3    +      -       -      +
     58A  VAL*     4.0    22.0    -      -       +      -
     82A  GLY*     3.2    29.4    -      -       -      -
     83A  ILE*     1.3    78.3    -      -       -      +
     85A  SER*     1.3    59.0    +      -       -      +
     86A  ILE*     3.2    24.9    -      -       +      +
    102A  CYS*     3.7    44.0    -      -       +      -
    105A  ILE*     4.4     3.6    -      -       +      -
    106A  LEU*     4.0    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     4.2     7.4    -      -       -      +
     11A  PHE      4.1     0.5    -      -       -      -
     12A  GLN*     2.8    43.5    +      -       -      +
     14A  GLN*     3.3    27.8    -      -       -      +
     54A  ASP      4.3     6.5    -      -       -      -
     55A  VAL*     5.0    10.9    -      -       -      +
     84A  PHE*     1.3    67.7    -      -       -      +
     86A  ILE*     1.3    59.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     3.3    13.7    -      -       -      +
     11A  PHE*     3.6    32.5    -      -       +      -
     12A  GLN      4.3     0.9    -      -       -      +
     54A  ASP*     2.8    21.0    +      -       -      +
     56A  TYR*     3.6    27.6    -      -       +      +
     84A  PHE*     3.2    33.0    +      -       +      +
     85A  SER*     1.3    78.7    -      -       -      +
     87A  ALA*     1.3    63.9    +      -       -      +
     89A  ILE*     4.5     7.4    -      -       +      -
     94A  MET*     5.7     2.2    -      -       +      -
     97A  CYS*     6.4     2.9    -      -       +      -
    102A  CYS*     5.6     3.1    -      -       -      -
    451E  VAL*     3.2    31.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  THR*     3.8    20.0    -      -       +      +
      8A  GLU      3.9     4.5    -      -       -      +
      9A  MET*     3.1     2.3    -      -       -      -
     10A  THR*     3.0    30.4    +      -       -      +
     54A  ASP*     3.3    25.1    -      -       +      +
     86A  ILE*     1.3    78.8    -      -       -      +
     88A  GLY*     1.3    58.9    +      -       -      +
     89A  ILE*     3.2    13.8    -      -       -      +
    451E  VAL*     4.2     8.5    -      -       -      -
----------------------------------------------------------
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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