Contacts of the strand formed by residues 10 - 24 (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 THR 10 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  GLU      3.3     9.3    +      -       -      -
      9A  MET*     1.3    78.0    +      -       -      +
     11A  PHE*     1.3    68.5    +      -       -      +
     12A  GLN*     4.2     6.3    -      -       +      +
     85A  SER      4.2    12.6    -      -       -      +
     86A  ILE*     3.3    24.1    -      -       -      +
     87A  ALA*     3.0    17.1    +      -       -      +
     89A  ILE*     4.4     4.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 11 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     1.3    77.0    -      -       -      +
     12A  GLN*     1.3    65.6    +      -       -      +
     13A  ILE*     3.8    21.8    -      -       +      -
     84A  PHE*     3.9    27.6    -      +       -      -
     86A  ILE*     3.6    16.6    -      -       +      -
     97A  CYS*     5.7     6.1    -      -       +      -
    101A  TYR*     3.7    37.0    -      +       -      -
    102A  CYS*     3.5    28.5    -      -       -      -
    105A  ILE*     4.3     7.4    -      -       +      -
    132C  ASN*     6.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 12 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     4.8     7.0    -      -       +      -
     11A  PHE*     1.3    79.9    -      -       -      +
     13A  ILE*     1.3    83.6    +      -       -      +
     14A  GLN*     4.7     1.8    -      -       -      +
     84A  PHE*     3.5     6.2    -      -       -      +
     85A  SER*     2.8    50.8    +      -       -      +
     86A  ILE*     4.3     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 13 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     3.8    19.1    -      -       +      -
     12A  GLN*     1.3    89.6    +      -       -      +
     14A  GLN*     1.3    64.1    +      -       -      +
     15A  ARG      3.8    11.4    -      -       -      +
     16A  ILE*     3.6    27.4    -      -       +      -
     83A  ILE      3.9     4.7    -      -       -      +
     84A  PHE*     3.8    15.9    -      -       +      -
    105A  ILE*     3.3    35.2    -      -       +      -
    130C  PRO*     3.8    33.5    -      -       +      +
    132C  ASN*     6.5     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 14 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  GLN*     3.5     5.8    +      -       -      -
     13A  ILE*     1.3    73.8    -      -       -      +
     15A  ARG*     1.4    73.2    +      -       -      +
     55A  VAL*     5.4     3.4    -      -       +      -
     83A  ILE*     2.9    52.2    +      -       +      +
     85A  SER*     3.3    24.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 15 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ILE*     3.4     4.0    -      -       -      +
     14A  GLN*     1.4    96.5    -      -       -      +
     16A  ILE*     1.3    67.7    +      -       -      +
     17A  TYR*     3.7    15.5    -      -       +      -
     82A  GLY*     3.2     3.1    -      -       -      -
     83A  ILE*     2.8    36.6    +      -       +      +
     32B  PHE*     3.5    53.9    +      -       -      +
    122B  THR*     2.9    51.7    +      -       +      +
    130C  PRO*     6.0     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 16 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ILE*     3.6    22.4    -      -       +      +
     15A  ARG*     1.3    78.0    -      -       -      +
     17A  TYR*     1.3    69.1    +      -       -      +
     80A  GLN*     3.6    15.3    -      -       -      +
     81A  GLY      3.6     4.0    -      -       -      -
     82A  GLY*     4.5     0.4    -      -       -      -
     84A  PHE*     5.1     0.2    -      -       +      -
    105A  ILE*     3.9    17.9    -      -       +      -
    106A  LEU*     3.9    21.8    -      -       +      -
    109A  TYR*     3.6    50.3    -      -       +      -
    120B  ARG      4.4     0.5    -      -       -      +
    122B  THR*     3.3    15.4    -      -       -      +
    111C  ARG*     4.5    10.6    +      -       -      +
    130C  PRO*     3.8    22.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 17 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ARG*     3.7    16.4    -      -       +      -
     16A  ILE*     1.3    82.5    -      -       -      +
     18A  THR*     1.3    65.1    +      -       -      +
     19A  LYS*     3.3    18.4    +      -       +      -
     57A  GLU*     2.9    23.2    +      -       -      -
     80A  GLN*     3.1     8.5    -      -       -      -
     81A  GLY*     2.8    35.6    +      -       -      +
     83A  ILE*     3.5    25.6    -      -       +      +
     25B  ALA*     5.5     0.2    -      -       +      -
     28B  ALA*     3.5    24.5    -      -       +      -
     29B  PRO*     3.2    24.6    -      -       -      +
     32B  PHE*     3.5    22.0    -      +       -      -
    120B  ARG      3.1    18.4    -      -       -      +
    121B  GLY*     3.7     5.8    -      -       -      -
    122B  THR*     3.5    16.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  TYR*     1.3    72.0    -      -       -      +
     19A  LYS*     1.3    61.2    +      -       -      +
     20A  ASP      3.3     3.1    -      -       -      -
     21A  ILE*     3.3    23.2    -      -       -      +
     78A  VAL*     3.8    15.0    -      -       +      -
     79A  GLN      3.6     6.3    -      -       -      -
     80A  GLN*     3.3    28.9    -      -       -      +
    113A  CYS*     3.8    14.6    -      -       +      -
     23B  PHE*     3.1    22.3    -      -       -      -
    120B  ARG*     3.0    33.0    +      -       +      +
    121B  GLY*     3.5     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  TYR*     3.5    17.9    -      -       +      +
     18A  THR*     1.3    72.1    -      -       -      +
     20A  ASP*     1.3    62.1    +      -       +      +
     49A  SER*     4.7     3.8    +      -       -      -
     57A  GLU*     2.9    39.9    +      -       -      +
     59A  VAL*     3.8    24.4    -      -       +      +
     79A  GLN*     3.0    10.7    +      -       +      +
     81A  GLY*     3.9    13.9    -      -       -      +
     23B  PHE      3.8     1.5    -      -       -      +
     24B  GLU*     3.8     0.7    -      -       -      -
     25B  ALA*     2.9    46.7    +      -       -      +
     26B  PRO      5.9     0.7    -      -       -      -
     29B  PRO*     3.3    26.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  THR*     4.3     0.3    -      -       -      -
     19A  LYS*     1.3    81.3    -      -       +      +
     21A  ILE*     1.3    83.2    +      -       -      +
     22A  SER*     4.7     4.9    -      -       -      -
     77A  GLU*     4.0    14.2    -      -       -      +
     78A  VAL*     3.6     1.6    -      -       -      +
     79A  GLN*     2.9    68.8    +      -       +      +
     23B  PHE      3.1     9.2    -      -       -      +
     24B  GLU*     4.0    16.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  THR*     3.3    30.1    -      -       -      +
     20A  ASP*     1.3    87.9    -      -       -      +
     22A  SER*     1.3    65.7    +      -       -      +
     77A  GLU      3.6     4.9    -      -       -      -
     78A  VAL*     4.2     2.9    -      -       +      -
    113A  CYS*     3.7    13.5    -      -       -      -
    117A  MET*     3.6    27.4    -      -       +      -
     21B  ILE*     3.6    20.0    -      -       +      -
     22B  SER*     3.4     6.4    +      -       -      -
     23B  PHE*     2.8    37.2    +      -       +      +
     24B  GLU*     5.3     0.2    -      -       -      +
    117B  MET*     3.4    34.5    -      -       +      -
    120B  ARG*     3.8     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ASP*     4.7     8.7    -      -       -      -
     21A  ILE*     1.3    75.7    -      -       -      +
     23A  PHE*     1.3    62.7    +      -       -      +
     24A  GLU*     4.3    18.0    +      -       -      +
     75A  LEU*     4.4     3.0    -      -       -      +
     76A  CYS*     3.7     0.2    -      -       -      -
     77A  GLU*     2.8    52.2    +      -       -      +
    117A  MET*     3.6     7.0    -      -       -      +
     21B  ILE      3.3     6.0    +      -       -      -
     22B  SER*     4.8     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  SER*     1.3    71.4    +      -       -      +
     24A  GLU*     1.3    61.2    +      -       -      +
     25A  ALA*     3.7     6.5    -      -       +      -
     74A  PHE*     3.8    14.6    -      -       +      -
     75A  LEU      3.2    22.7    -      -       -      -
     76A  CYS*     3.3    27.6    -      -       -      -
    117A  MET*     3.3    27.4    -      -       +      -
    118A  VAL*     4.8     0.7    -      -       -      -
    121A  GLY*     4.2     6.7    -      -       -      -
    123A  PHE*     3.6    29.6    -      +       -      -
     18B  THR*     3.2    26.0    -      -       +      -
     19B  LYS      3.4    26.7    -      -       -      -
     20B  ASP*     3.0    36.0    -      -       -      +
     21B  ILE*     2.8    30.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  SER*     4.3    14.3    +      -       -      +
     23A  PHE*     1.3    78.6    -      -       -      +
     25A  ALA*     1.3    58.2    +      -       -      +
     26A  PRO*     3.5    15.2    -      -       +      +
     72A  THR*     4.9     1.2    -      -       -      +
     74A  PHE*     3.5     2.4    -      -       -      -
     75A  LEU*     2.9    64.9    +      -       +      +
     19B  LYS      4.0     0.9    -      -       -      -
     20B  ASP*     4.2     9.2    -      -       -      +
----------------------------------------------------------
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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