Contacts of the helix formed by residues 768 - 779 (chain M) in PDB entry 4G7Z


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 768 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    766M  GLU*     2.8    14.4    +      -       -      +
    767M  PRO*     1.3    71.3    -      -       -      +
    769M  PRO*     1.3    71.0    -      -       +      +
    770M  GLU*     3.3    23.1    -      -       +      +
    771M  GLU*     2.5    48.8    +      -       -      +
    772M  ARG*     3.0     7.4    +      -       -      +
    347P  GLN*     4.2    18.8    -      -       +      +
    350P  LEU*     5.7     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 769 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    766M  GLU*     5.8     5.2    -      -       +      +
    767M  PRO      3.3     5.1    -      -       -      +
    768M  THR*     1.3    92.7    -      -       +      +
    770M  GLU*     1.3    71.3    +      -       -      +
    772M  ARG*     4.0     6.8    +      -       -      +
    773M  LEU*     4.0    15.1    +      -       -      +
     65N  ARG*     3.3    33.7    -      -       -      +
    347P  GLN*     5.8     0.4    -      -       -      +
    373P  LYS*     4.6     5.7    -      -       -      +
    374P  GLY      3.6    24.4    -      -       -      +
    375P  LEU*     4.5    13.9    +      -       -      +
    378P  GLY*     5.0     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 770 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    768M  THR*     3.0    21.2    -      -       -      +
    769M  PRO*     1.3    90.0    -      -       -      +
    771M  GLU*     1.3    63.8    +      -       -      +
    772M  ARG      3.3     0.7    -      -       -      -
    773M  LEU*     3.3     5.9    +      -       -      +
    774M  LEU*     3.2    20.6    +      -       -      +
    347P  GLN*     3.5    19.8    +      -       -      +
    350P  LEU*     3.5    27.3    -      -       +      +
    351P  SER*     3.3    29.5    +      -       -      +
    354P  LEU*     3.6    23.8    -      -       +      +
    375P  LEU*     4.8    16.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 771 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    762M  LYS*     6.0     0.2    +      -       -      -
    765M  SER*     6.2     0.2    -      -       -      -
    766M  GLU      3.2    10.6    -      -       -      +
    767M  PRO*     3.3     6.6    -      -       +      +
    768M  THR*     2.5    49.5    +      -       -      +
    770M  GLU*     1.3    73.2    -      -       -      +
    772M  ARG*     1.3    60.7    +      -       -      +
    774M  LEU*     3.3     9.1    +      -       +      +
    775M  ARG*     3.1    42.8    +      -       +      +
    350P  LEU*     4.4     8.0    -      -       +      +
    423P  ASP*     5.4     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 772 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    767M  PRO*     3.4    46.2    -      -       +      +
    768M  THR      3.0     6.8    +      -       -      +
    769M  PRO*     4.2     7.1    -      -       -      +
    770M  GLU      3.3     0.2    -      -       -      -
    771M  GLU*     1.3    76.5    -      -       -      +
    773M  LEU*     1.3    60.4    +      -       -      +
    775M  ARG*     3.2    29.8    +      -       -      +
    776M  SER*     3.0    16.2    +      -       -      -
     65N  ARG*     2.9    20.1    -      -       -      +
    373P  LYS*     3.4    53.4    +      -       +      +
    380P  GLU*     2.7    42.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 773 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    769M  PRO      4.0     8.8    +      -       -      +
    770M  GLU      3.3     9.0    +      -       -      +
    771M  GLU      3.3     0.4    -      -       -      -
    772M  ARG*     1.3    79.1    -      -       -      +
    774M  LEU*     1.3    63.6    +      -       -      +
    776M  SER*     3.1    25.0    +      -       -      -
    777M  ILE*     3.1    22.9    +      -       +      +
    354P  LEU*     3.7    28.9    -      -       +      -
    358P  LEU*     4.7    13.0    -      -       +      -
    369P  LEU*     4.7    24.9    -      -       +      +
    370P  LYS*     6.4     0.9    -      -       -      -
    373P  LYS*     4.7    21.4    -      -       +      +
    375P  LEU*     3.9    21.3    -      -       +      -
    405P  LEU*     5.3     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 774 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    770M  GLU      3.2    10.7    +      -       -      +
    771M  GLU*     3.7    11.0    -      -       +      +
    772M  ARG      3.3     0.2    -      -       -      -
    773M  LEU*     1.3    73.3    -      -       -      +
    775M  ARG*     1.3    66.8    +      -       -      +
    776M  SER      3.0     2.0    -      -       -      -
    777M  ILE*     3.0    37.3    +      -       +      +
    778M  PHE*     3.2    14.0    +      -       -      +
    350P  LEU*     5.1     9.0    -      -       +      -
    354P  LEU*     4.8     6.2    -      -       +      +
    418P  LEU*     4.2    27.8    -      -       +      +
    421P  PHE*     3.5    45.8    -      -       +      +
    422P  LEU*     4.1    16.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 775 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    762M  LYS*     5.9     2.4    -      -       -      +
    765M  SER*     5.3     7.1    +      -       -      -
    766M  GLU      5.3     0.2    -      -       -      -
    767M  PRO*     3.6    32.5    -      -       -      +
    771M  GLU*     3.1    39.0    +      -       +      +
    772M  ARG*     3.2    18.7    +      -       -      +
    774M  LEU*     1.3    75.6    -      -       -      +
    776M  SER*     1.3    56.9    +      -       -      +
    778M  PHE*     3.9     1.9    +      -       -      +
    779M  GLY*     3.1    23.0    +      -       -      -
    780M  GLU      3.4    20.9    +      -       -      +
    781M  LYS*     5.8     0.4    -      -       -      -
    782M  ALA*     3.4    39.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 776 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    772M  ARG      3.0     8.3    +      -       -      -
    773M  LEU*     3.1    16.4    +      -       -      -
    774M  LEU      3.0     0.4    -      -       -      -
    775M  ARG*     1.3    77.4    -      -       -      +
    777M  ILE*     1.3    63.6    +      -       -      +
    779M  GLY*     3.3    12.0    +      -       -      -
    373P  LYS*     2.9    31.5    +      -       -      +
    405P  LEU*     3.6    30.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 777 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    773M  LEU*     3.1    21.4    +      -       +      +
    774M  LEU*     3.0    35.3    +      -       +      +
    776M  SER*     1.3    79.4    -      -       -      +
    778M  PHE*     1.3    64.0    +      -       +      +
    779M  GLY*     4.4     0.2    -      -       -      -
    354P  LEU*     4.5    10.8    -      -       +      -
    405P  LEU*     4.0    15.9    -      -       +      +
    408P  LEU*     5.6    16.2    -      -       +      -
    409P  LYS*     3.1    34.1    -      -       +      +
    413P  SER*     3.6    26.7    -      -       -      +
    418P  LEU*     4.3    16.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 778 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    728M  HIS*     5.5     1.3    -      +       -      -
    774M  LEU      3.2    10.3    +      -       -      +
    775M  ARG*     4.6     1.6    -      -       -      +
    777M  ILE*     1.3    82.4    -      -       +      +
    779M  GLY*     1.3    56.5    +      -       -      +
    780M  GLU*     3.2    42.5    +      -       +      +
    409P  LYS*     4.5    24.5    -      -       -      +
    413P  SER*     5.1     3.6    -      -       -      -
    419P  ARG*     3.4    44.4    -      -       -      -
    422P  LEU*     4.0    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 779 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    775M  ARG      3.1    12.2    +      -       -      -
    776M  SER*     3.7     9.6    -      -       -      -
    777M  ILE      3.2     2.8    -      -       -      -
    778M  PHE*     1.3    76.7    -      -       -      +
    780M  GLU*     1.3    62.8    +      -       -      +
    781M  LYS      3.5     2.1    +      -       -      -
----------------------------------------------------------
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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