Contacts of the helix formed by residues 48 - 65 (chain G) in PDB entry 5JGH


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 SER 48 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47G  THR*     1.3    84.7    -      -       -      +
     49G  ALA*     1.3    65.1    +      -       -      +
     50G  TYR*     3.8     8.3    +      -       -      +
     51G  PHE      3.3    12.0    +      -       -      -
     52G  LEU*     3.4    11.4    +      -       -      +
     96G  ARG*     3.4    12.1    -      -       -      +
     15K    T      2.3    30.7    +      -       -      -
     16K    T      3.9    22.7    -      -       -      -
      7L    A      4.2     8.9    +      -       -      -
      8L    A      3.7     9.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 49 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48G  SER*     1.3    75.6    -      -       -      +
     50G  TYR*     1.3    63.9    +      -       -      +
     52G  LEU*     3.1    24.4    +      -       -      +
     53G  TYR*     3.2     8.8    +      -       -      +
     81G  TRP*     3.9    13.3    -      -       +      -
     92G  TYR*     3.8    21.3    -      -       -      +
     93G  ILE*     4.0    22.4    -      -       +      -
     96G  ARG*     3.8    15.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 50 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48G  SER*     3.4     2.3    +      -       -      +
     49G  ALA*     1.3    78.2    -      -       -      +
     51G  PHE*     1.3    83.1    +      +       -      +
     53G  TYR*     3.4     5.4    +      +       -      +
     54G  LEU*     2.7    54.6    +      -       +      +
     74G  SER*     3.4     9.4    +      -       -      -
     77G  ALA*     3.8    29.1    -      -       +      +
     78G  GLY*     4.0     2.0    -      -       -      -
     81G  TRP*     3.8    40.8    -      +       +      +
     14K    A      3.1    38.3    +      +       +      +
     15K    T      3.1    37.7    -      +       -      +
----------------------------------------------------------
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Residues in contact with PHE 51 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47G  THR*     3.1    23.1    -      -       +      -
     48G  SER*     3.3     3.6    +      -       -      +
     49G  ALA      3.1     1.0    -      -       -      -
     50G  TYR*     1.3   108.4    -      +       -      +
     52G  LEU*     1.3    54.5    +      -       -      +
     54G  LEU*     3.4    11.4    -      -       +      +
     55G  GLN*     2.7    37.2    +      -       -      +
     14K    A      3.6    15.9    -      +       -      -
     15K    T      4.1     5.6    -      -       -      -
      8L    A      3.3    68.4    -      +       +      -
      9L    T      3.5    47.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 52 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47G  THR*     4.7    12.0    -      -       -      +
     48G  SER      3.4     8.0    +      -       -      +
     49G  ALA*     3.1    10.2    +      -       -      +
     51G  PHE*     1.3    80.2    -      -       -      +
     53G  TYR*     1.3    62.2    +      -       -      +
     55G  GLN*     3.5     9.3    +      -       -      +
     56G  ASP*     3.4    20.4    +      -       -      +
     92G  TYR*     3.6    44.5    -      -       +      +
     95G  GLU*     4.3    12.6    -      -       +      -
     96G  ARG*     3.8    24.7    -      -       +      +
     99G  LEU*     4.3    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 53 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49G  ALA      3.2     3.2    +      -       -      -
     50G  TYR*     3.4    11.2    -      +       -      +
     52G  LEU*     1.3    76.2    -      -       -      +
     54G  LEU*     1.3    67.4    +      -       -      +
     56G  ASP      3.4     1.0    +      -       -      -
     57G  HIS*     3.0    59.3    +      +       +      +
     61G  PHE*     2.9    33.4    -      +       -      -
     77G  ALA*     4.4    11.0    -      -       +      -
     80G  LYS*     3.1    24.7    -      -       +      +
     81G  TRP*     3.3    46.0    -      +       +      -
     84G  LEU*     3.8    23.1    -      -       +      +
     92G  TYR*     3.4    25.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with LEU 54 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50G  TYR*     2.7    53.9    +      -       +      +
     51G  PHE*     3.1    17.9    +      -       +      +
     53G  TYR*     1.3    76.0    -      -       -      +
     55G  GLN*     1.3    60.9    +      -       +      +
     57G  HIS      5.3     0.4    -      -       -      -
     58G  ARG*     2.7    66.1    +      -       +      +
     61G  PHE*     5.4     5.2    -      -       +      -
     74G  SER*     4.9     3.1    -      -       -      +
     77G  ALA*     5.1     7.2    -      -       +      -
     14K    A      4.0     8.5    -      -       +      +
      9L    T      3.9    35.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 55 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51G  PHE*     2.7    19.8    +      -       +      +
     52G  LEU*     4.0    10.0    -      -       -      +
     54G  LEU*     1.3    82.8    -      -       +      +
     56G  ASP*     1.3    65.2    +      -       -      +
     58G  ARG*     4.0    18.0    +      -       -      +
     59G  SER*     5.0     1.9    +      -       -      -
      8L    A      6.1     0.2    -      -       -      +
      9L    T      4.6    27.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 56 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52G  LEU      3.4     9.9    +      -       -      +
     53G  TYR      3.4     1.4    +      -       -      -
     54G  LEU      3.2     0.6    -      -       -      -
     55G  GLN*     1.3    85.6    -      -       -      +
     57G  HIS*     1.3    67.2    +      -       +      +
     58G  ARG      3.8     0.2    +      -       -      -
     59G  SER*     4.9     4.5    +      -       -      -
     60G  GLN*     4.6    11.1    +      -       -      +
     92G  TYR*     3.8    26.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 57 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53G  TYR*     3.0    40.7    +      +       +      +
     54G  LEU      3.6     0.9    -      -       -      -
     56G  ASP*     1.3    80.2    -      -       +      +
     58G  ARG*     1.3    64.6    +      -       -      +
     59G  SER      3.4     1.3    -      -       -      -
     60G  GLN*     3.7    24.6    +      -       -      +
     61G  PHE*     3.0    47.3    +      +       +      -
     88G  ILE*     5.5     6.4    -      -       +      +
     92G  TYR*     3.0    27.3    +      +       -      -
----------------------------------------------------------
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Residues in contact with ARG 58 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54G  LEU*     2.7    48.7    +      -       +      +
     55G  GLN*     4.1    14.4    +      -       -      +
     56G  ASP      3.4     2.0    -      -       -      -
     57G  HIS*     1.3    72.7    -      -       -      +
     59G  SER*     1.3    74.0    +      -       -      +
     61G  PHE*     2.9    23.4    +      -       +      +
     62G  VAL*     3.1    28.9    +      -       +      +
     73G  ILE*     5.5     4.9    -      -       +      -
      9L    T      4.5     7.3    +      -       -      +
     10L    A      3.3    65.5    +      -       -      +
     11L    T      5.3     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 59 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55G  GLN      5.0     1.6    +      -       -      -
     56G  ASP      4.9     3.7    +      -       -      -
     57G  HIS      3.4     0.2    -      -       -      -
     58G  ARG*     1.3    86.7    -      -       -      +
     60G  GLN*     1.3    65.5    +      -       -      +
     62G  VAL*     3.0    22.6    +      -       -      +
     63G  LYS*     3.4    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 60 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56G  ASP      4.6    12.6    +      -       -      +
     57G  HIS*     3.7    27.6    +      -       -      +
     58G  ARG      3.4     0.2    -      -       -      -
     59G  SER*     1.3    78.7    +      -       -      +
     61G  PHE*     1.3    62.9    +      -       +      +
     63G  LYS*     3.1    37.7    +      -       +      +
     64G  GLU*     3.1    31.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 61 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53G  TYR*     2.9    37.7    -      +       -      -
     54G  LEU*     5.1     3.6    -      -       +      -
     57G  HIS*     3.0    42.6    +      +       +      -
     58G  ARG*     2.9    16.0    +      -       +      +
     60G  GLN*     1.3    78.0    -      -       +      +
     62G  VAL*     1.3    61.0    +      -       -      +
     64G  GLU*     3.1    24.2    +      -       -      +
     65G  ASN*     3.4    22.3    +      -       -      +
     73G  ILE*     4.1    18.9    -      -       +      +
     76G  ILE*     5.9     8.7    -      -       +      -
     77G  ALA*     3.9    29.8    -      -       +      -
     80G  LYS*     4.5     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 62 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58G  ARG*     3.2    29.4    -      -       +      +
     59G  SER*     3.0    11.8    +      -       -      +
     61G  PHE*     1.3    78.3    -      -       -      +
     63G  LYS*     1.3    61.3    +      -       +      +
     65G  ASN      3.0    23.6    -      -       -      +
     66G  PRO*     3.8     7.3    -      -       -      +
     68G  LEU*     6.3     1.1    -      -       +      -
     73G  ILE*     3.7    22.2    -      -       +      -
    202G  ACT      5.3    10.0    -      -       -      +
     10L    A      6.6     0.2    -      -       +      -
     11L    T      6.5     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 63 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59G  SER*     3.4    23.1    +      -       -      +
     60G  GLN*     3.1    34.1    +      -       +      +
     62G  VAL*     1.3    77.4    -      -       +      +
     64G  GLU*     1.3    66.4    +      -       +      +
     65G  ASN      3.1     2.3    +      -       -      -
     66G  PRO*     4.0    10.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 64 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60G  GLN*     3.1    31.2    +      -       -      +
     61G  PHE*     3.1    34.6    -      -       -      +
     62G  VAL      3.5     0.2    -      -       -      -
     63G  LYS*     1.3    77.1    -      -       +      +
     65G  ASN*     1.3    67.3    +      -       -      +
     66G  PRO*     3.8     5.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 65 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61G  PHE      3.4    10.0    +      -       -      +
     62G  VAL*     3.0    16.8    -      -       -      +
     63G  LYS      3.1     0.6    -      -       -      -
     64G  GLU*     1.3    87.1    -      -       -      +
     66G  PRO*     1.3    69.1    -      -       -      +
     67G  THR      3.8     1.1    -      -       -      -
     68G  LEU*     3.3    40.9    -      -       +      +
     76G  ILE*     3.7    29.4    -      -       +      +
----------------------------------------------------------
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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