Contacts of the helix formed by residues 63 - 80 (chain A) in PDB entry 2XJC


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 PRO 63 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  SER*     4.7     6.3    -      -       -      -
     62A  SER*     1.4    85.6    -      -       -      +
     64A  GLU*     1.3    72.3    +      -       -      +
     65A  TYR      3.4     2.2    -      -       -      -
     66A  GLU*     3.4     7.5    +      -       -      +
     67A  SER*     2.9    32.3    +      -       -      -
     91A  TYR*     4.2     9.9    -      -       +      -
     93A  SER*     3.9    29.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  LYS*     3.5     8.6    +      -       -      +
     62A  SER      3.4    20.6    +      -       -      +
     63A  PRO*     1.3    86.8    -      -       -      +
     65A  TYR*     1.3    58.1    +      -       -      +
     67A  SER*     3.5     6.5    +      -       -      -
     68A  LEU*     3.0    22.3    +      -       -      +
    224A  LYS*     4.1    30.7    -      -       +      +
    225A  TYR*     3.5    25.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  ASP*     5.5     0.2    +      -       -      -
     55A  TYR*     3.4    20.9    -      -       -      -
     60A  TYR*     3.4    46.0    -      +       +      -
     61A  LYS      2.8    23.8    +      -       -      +
     64A  GLU*     1.3    72.4    -      -       -      +
     66A  GLU*     1.3    65.8    +      -       +      +
     68A  LEU*     3.2     4.3    +      -       +      +
     69A  GLY*     3.0    21.1    +      -       -      -
    157A  PHE*     3.6    31.1    -      +       -      -
    160A  PRO*     5.2     0.2    -      -       -      +
    209A  HIS*     4.5     1.0    +      -       -      -
    214A  LEU*     3.6    34.5    -      -       +      +
    215A  LYS*     6.2     0.2    -      -       -      +
    218A  THR*     3.4    23.9    +      -       -      -
    225A  TYR*     3.9    22.4    -      +       +      +
    255A  TYR*     4.5     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  TRP*     4.0     8.4    +      -       -      -
     55A  TYR*     4.6     8.3    +      -       -      +
     60A  TYR      5.0     0.3    -      -       -      +
     61A  LYS      3.6     3.6    -      -       -      +
     62A  SER*     2.6    44.8    +      -       -      -
     63A  PRO*     3.4     5.6    +      -       -      +
     65A  TYR*     1.3    77.3    -      -       +      +
     67A  SER*     1.3    52.6    +      -       -      +
     69A  GLY      3.3     0.7    +      -       -      -
     70A  PHE*     2.8    33.4    +      -       -      +
     91A  TYR*     3.5    33.7    +      -       +      +
     93A  SER*     5.4     1.7    -      -       -      -
    156A  LEU*     4.5     5.6    -      -       -      +
    159A  LEU*     4.0    29.9    -      -       +      +
    160A  PRO*     3.3    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  PRO*     2.9    22.6    +      -       -      -
     64A  GLU*     3.6     7.6    -      -       -      -
     66A  GLU*     1.3    70.7    -      -       -      +
     68A  LEU*     1.3    59.3    +      -       -      +
     70A  PHE*     3.6     1.2    -      -       -      +
     71A  GLU*     2.9    46.2    +      -       -      +
     91A  TYR*     3.6    30.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  GLU      3.0    14.6    +      -       -      +
     65A  TYR*     3.2     9.2    +      -       +      +
     67A  SER*     1.3    71.2    -      -       -      +
     69A  GLY*     1.3    66.3    +      -       -      +
     71A  GLU*     3.5    14.4    +      -       +      +
     72A  LEU*     3.1    36.1    +      -       +      +
    214A  LEU*     3.6    24.0    -      -       +      -
    217A  LYS*     3.9    38.8    -      -       +      -
    218A  THR*     4.1     9.4    -      -       -      +
    225A  TYR*     3.7    39.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  TYR*     3.0    14.6    +      -       -      -
     66A  GLU      3.7     2.7    -      -       -      -
     68A  LEU*     1.3    76.4    -      -       -      +
     70A  PHE*     1.3    57.1    +      -       -      +
     72A  LEU*     3.8     3.5    -      -       -      +
     73A  THR*     2.8    37.1    +      -       -      -
    160A  PRO*     4.2     9.6    -      -       -      -
    208A  VAL*     4.9     2.4    -      -       -      +
    209A  HIS*     6.4     0.2    -      -       -      -
    214A  LEU*     4.4    19.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  GLU      2.8    18.7    +      -       -      +
     67A  SER      3.6     4.7    -      -       -      +
     69A  GLY*     1.3    76.1    -      -       -      +
     71A  GLU*     1.3    63.2    +      -       +      +
     73A  THR*     3.3     4.4    +      -       -      -
     74A  VAL*     2.9    46.3    +      -       +      +
     89A  PHE*     3.6    38.6    -      +       +      -
     90A  ALA*     3.9     1.1    -      -       -      -
     91A  TYR*     3.6    39.3    -      +       +      -
    160A  PRO*     3.6    28.3    -      -       +      +
    163A  TYR*     3.5    26.0    -      +       -      -
    164A  LEU*     3.6    29.4    -      -       +      -
    167A  CYS*     4.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  SER*     2.9    35.0    +      -       -      +
     68A  LEU*     3.8    18.0    -      -       +      +
     70A  PHE*     1.3    79.3    -      -       +      +
     72A  LEU*     1.3    62.1    +      -       +      +
     74A  VAL*     3.4     5.6    +      -       -      +
     75A  GLU*     2.9    46.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  LEU*     3.1    34.8    +      -       +      +
     69A  GLY      4.0     0.9    -      -       -      +
     71A  GLU*     1.3    79.0    -      -       +      +
     73A  THR*     1.3    60.5    +      -       -      +
     75A  GLU*     3.9    18.7    -      -       -      +
     76A  ARG*     3.1    22.0    +      -       -      +
    207A  TRP*     5.2     1.3    -      -       +      -
    208A  VAL*     3.4    25.9    -      -       +      +
    213A  SER*     3.7    17.3    -      -       -      +
    214A  LEU*     3.5    42.8    -      -       +      +
    217A  LYS*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  GLY      2.8    23.4    +      -       -      -
     70A  PHE*     3.8     4.7    -      -       -      -
     72A  LEU*     1.3    73.0    -      -       -      +
     74A  VAL*     1.3    68.0    +      -       -      +
     76A  ARG*     3.2     4.3    +      -       -      +
     77A  LEU*     3.1    23.9    +      -       +      +
    160A  PRO*     5.5     2.9    -      -       -      +
    161A  GLU*     6.1     0.2    -      -       -      -
    164A  LEU*     3.5    25.1    -      -       +      -
    201A  VAL      4.3     2.2    -      -       -      +
    204A  ALA*     3.8    16.8    -      -       +      -
    205A  VAL*     3.7    33.5    -      -       +      +
    208A  VAL*     3.9    16.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  PHE*     2.9    38.8    +      -       +      +
     71A  GLU*     3.7     6.5    -      -       -      +
     73A  THR*     1.3    76.5    -      -       -      +
     75A  GLU*     1.3    62.1    +      -       +      +
     77A  LEU*     3.2    10.3    +      -       -      +
     78A  VAL*     3.0    22.0    +      -       -      +
     86A  LEU*     3.5    34.7    -      -       +      +
     87A  LEU*     4.2    14.8    -      -       +      -
     89A  PHE*     4.5     6.1    -      -       +      +
    164A  LEU*     3.7    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  GLU*     2.9    32.9    +      -       -      +
     72A  LEU*     3.9    21.7    -      -       -      +
     73A  THR      3.3     0.2    -      -       -      -
     74A  VAL*     1.3    76.3    -      -       +      +
     76A  ARG*     1.3    58.1    +      -       -      +
     78A  VAL*     3.5     6.8    +      -       -      +
     79A  SER*     3.0    29.7    +      -       -      -
     87A  LEU*     4.4    16.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  LEU      3.1    15.6    +      -       -      +
     73A  THR      3.5     8.7    -      -       -      +
     74A  VAL      3.2     0.2    -      -       -      -
     75A  GLU*     1.3    77.6    -      -       -      +
     77A  LEU*     1.3    56.8    +      -       -      +
     79A  SER*     3.0    26.7    +      -       -      -
     80A  ILE*     3.1    40.2    +      -       +      +
    204A  ALA*     3.9    22.8    -      -       +      +
    207A  TRP*     3.4    74.1    -      -       +      +
    208A  VAL*     4.4     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  THR*     3.1    16.9    +      -       +      +
     74A  VAL*     3.6     6.5    -      -       -      +
     76A  ARG*     1.3    72.3    -      -       -      +
     78A  VAL*     1.3    63.6    +      -       -      +
     80A  ILE*     3.3    13.1    -      -       +      +
     81A  GLY      3.2     6.2    +      -       -      -
     82A  TYR*     2.8    51.0    +      -       +      +
     86A  LEU*     3.8    22.9    -      -       +      -
    164A  LEU*     3.9    27.8    -      -       +      -
    168A  LEU*     4.3    15.5    -      -       +      -
    200A  ASP*     3.7    31.2    -      -       +      +
    201A  VAL*     4.3     4.3    -      -       +      +
    204A  ALA*     3.9     8.3    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     74A  VAL      3.0    19.7    +      -       -      +
     75A  GLU      3.9     4.3    -      -       -      +
     77A  LEU*     1.3    75.5    -      -       -      +
     79A  SER*     1.3    63.7    +      -       -      +
     81A  GLY*     3.1    14.0    +      -       -      -
     82A  TYR      3.7    11.9    -      -       -      +
     83A  PRO      3.8     8.7    -      -       -      +
     84A  GLN*     3.6    31.7    +      -       -      +
     86A  LEU*     3.7    28.0    -      -       +      -
     87A  LEU*     3.9    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  GLU      3.0    16.9    +      -       -      -
     76A  ARG*     3.0    28.8    +      -       -      -
     77A  LEU      3.3     0.2    -      -       -      -
     78A  VAL*     1.3    77.9    -      -       -      +
     80A  ILE*     1.3    58.6    +      -       -      +
     81A  GLY*     3.3     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  ARG*     3.1    51.6    +      -       +      +
     77A  LEU*     3.3    23.8    -      -       +      +
     79A  SER*     1.3    77.2    -      -       -      +
     81A  GLY*     1.3    57.0    +      -       -      +
     82A  TYR*     4.2    21.5    -      -       +      -
    200A  ASP*     4.7    12.8    -      -       +      +
    204A  ALA*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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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