Contacts of the helix formed by residues 780 - 788 (chain C) in PDB entry 4YZ9


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 GLN 780 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    777C  LYS*     3.4    11.4    +      -       +      +
    779C  LEU*     1.3    89.4    -      -       +      +
    781C  ARG*     1.3    59.4    +      -       -      +
    782C  GLN      3.0     3.4    -      -       -      -
    783C  ALA*     3.0    15.0    +      -       +      +
    784C  ASN*     2.9    42.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 781 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    734C  THR      4.5     5.7    -      -       -      +
    735C  GLU      3.1    26.4    +      -       -      +
    736C  GLY*     3.7    14.1    -      -       -      +
    737C  TRP*     4.2    11.5    -      -       -      +
    773C  HIS*     3.5    44.7    +      -       -      +
    775C  PHE*     3.4    26.7    +      -       +      +
    776C  GLY      2.9    28.2    +      -       -      +
    777C  LYS*     3.1    12.6    +      -       -      +
    778C  SER*     3.4    34.8    -      -       -      +
    779C  LEU      3.4     0.6    -      -       -      -
    780C  GLN*     1.3    77.3    -      -       -      +
    782C  GLN*     1.3    58.5    +      -       -      +
    784C  ASN*     3.7     1.4    -      -       -      +
    785C  ILE*     3.0    33.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 782 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    735C  GLU*     5.0     5.5    -      -       -      +
    736C  GLY*     4.1    23.3    -      -       -      +
    738C  ILE*     5.1     4.0    -      -       -      +
    743C  LEU*     3.1    42.7    -      -       +      +
    778C  SER      4.7     1.5    +      -       -      +
    779C  LEU      4.5     6.8    +      -       -      +
    780C  GLN      3.0     1.7    -      -       -      -
    781C  ARG*     1.3    80.6    -      -       +      +
    783C  ALA*     1.3    64.7    +      -       -      +
    785C  ILE*     3.4    10.7    +      -       -      +
    786C  LEU*     3.3    33.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 783 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    780C  GLN*     3.0    18.0    +      -       +      +
    782C  GLN*     1.3    78.5    -      -       -      +
    784C  ASN*     1.3    59.1    +      -       -      +
    786C  LEU*     3.4    10.1    +      -       -      +
    787C  LEU*     3.0    39.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 784 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    775C  PHE*     2.7    33.2    +      -       +      +
    776C  GLY*     4.8     2.0    -      -       -      -
    780C  GLN*     2.9    36.3    +      -       -      +
    781C  ARG      3.7     2.7    -      -       -      +
    782C  GLN      3.2     0.2    -      -       -      -
    783C  ALA*     1.3    76.9    -      -       -      +
    785C  ILE*     1.3    60.5    +      -       -      +
    787C  LEU*     3.1    10.3    +      -       -      +
    788C  GLY      2.8    24.8    +      -       -      -
    789C  ALA*     2.9    38.2    +      -       -      +
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Residues in contact with ILE 785 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    736C  GLY*     3.1    38.4    -      -       -      +
    738C  ILE      3.9    14.4    -      -       -      +
    740C  PRO*     3.7    37.5    -      -       +      +
    743C  LEU*     4.6     5.4    -      -       +      -
    758C  PHE*     3.9     9.0    -      -       +      -
    775C  PHE*     3.5    33.4    -      -       +      -
    781C  ARG*     3.0    23.1    +      -       +      +
    782C  GLN*     3.8    11.7    -      -       -      +
    783C  ALA      3.4     0.2    -      -       -      -
    784C  ASN*     1.3    75.7    -      -       -      +
    786C  LEU*     1.3    62.8    +      -       -      +
    788C  GLY*     3.0    10.6    +      -       -      -
    815C  MET*     3.8    12.6    -      -       -      +
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Residues in contact with LEU 786 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    740C  PRO*     4.4    13.5    -      -       +      +
    743C  LEU*     4.1    33.9    -      -       +      -
    744C  SER*     4.8    10.3    -      -       -      +
    782C  GLN*     3.3    23.8    +      -       +      +
    783C  ALA*     3.8    10.8    -      -       -      +
    784C  ASN      3.3     0.2    -      -       -      -
    785C  ILE*     1.3    76.9    -      -       -      +
    787C  LEU*     1.3    61.2    +      -       +      +
    815C  MET*     4.1    10.0    -      -       -      +
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Residues in contact with LEU 787 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    783C  ALA*     3.0    29.7    +      -       +      +
    784C  ASN*     3.1    13.9    +      -       -      +
    786C  LEU*     1.3    80.2    -      -       +      +
    788C  GLY*     1.3    59.1    +      -       -      +
    789C  ALA*     3.5    11.4    +      -       +      +
    815C  MET*     3.6     9.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 788 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    775C  PHE*     4.4     9.4    -      -       -      -
    784C  ASN      2.8     6.0    +      -       -      -
    785C  ILE      3.0     9.6    +      -       -      -
    786C  LEU      3.4     0.2    -      -       -      -
    787C  LEU*     1.3    78.4    -      -       -      +
    789C  ALA*     1.3    60.0    +      -       -      +
    790C  CYS*     3.7     8.6    +      -       -      -
    815C  MET*     3.4    23.0    -      -       -      +
----------------------------------------------------------
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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