Contacts of the strand formed by residues 798 - 806 (chain C) in PDB entry 5VO8


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 GLY 798 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    747C  ALA      3.4     0.3    -      -       -      +
    748C  GLU*     3.7     2.3    -      -       -      +
    749C  VAL*     3.0    39.1    +      -       -      +
    797C  GLY*     1.3    74.2    -      -       -      -
    799C  ILE*     1.3    67.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 799 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  HIS*     3.6    32.1    -      -       +      -
     64A  GLU*     6.0     0.9    -      -       +      +
     65A  PHE*     4.3    22.3    -      -       +      -
    159A  LYS*     6.1     2.2    -      -       -      +
    746C  GLY*     3.9     8.1    -      -       -      -
    747C  ALA      3.2    14.4    -      -       -      +
    748C  GLU*     3.5    27.4    -      -       +      +
    749C  VAL*     5.3     0.4    -      -       -      -
    798C  GLY*     1.3    76.8    -      -       -      +
    800C  VAL*     1.3    74.2    +      -       -      +
    801C  VAL*     3.1    13.2    +      -       +      +
    826C  TYR      4.1     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 800 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  HIS*     3.9     0.5    -      -       -      -
    743C  VAL*     3.7    31.6    -      -       +      -
    744C  ARG      3.8    13.5    -      -       -      +
    745C  ILE*     3.6     5.2    -      -       -      +
    746C  GLY*     2.7    31.0    +      -       -      +
    747C  ALA      3.1     8.5    +      -       -      +
    749C  VAL*     3.8    29.6    -      -       +      -
    755C  LEU*     4.7     1.3    -      -       +      -
    799C  ILE*     1.3    72.7    -      -       -      +
    801C  VAL*     1.3    59.8    +      -       -      +
    802C  ARG      4.0    10.8    -      -       -      +
    803C  THR*     4.2     7.4    -      -       +      -
    825C  VAL*     3.7    28.0    -      -       +      -
    826C  TYR      3.7     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 801 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  HIS*     3.7    32.9    +      -       +      +
     65A  PHE*     3.8    24.0    -      -       +      -
    705C  ILE*     4.9    13.9    -      -       +      -
    745C  ILE*     3.7    17.5    -      -       -      +
    799C  ILE      3.4    14.6    -      -       -      +
    800C  VAL*     1.3    73.1    -      -       -      +
    802C  ARG*     1.3    65.2    +      -       +      +
    826C  TYR*     3.0    26.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 802 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85C  GLU*     3.4    28.7    +      -       -      -
    745C  ILE*     3.8     9.6    -      -       +      +
    800C  VAL*     3.7     3.7    -      -       -      +
    801C  VAL*     1.3    82.6    -      -       +      +
    803C  THR*     1.3    75.0    +      -       -      +
    804C  VAL*     3.7    22.1    -      -       -      +
    824C  ARG*     5.3     1.6    -      -       -      +
    825C  VAL*     3.5     0.3    -      -       -      -
    826C  TYR*     2.8    47.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 803 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    742C  VAL*     3.8    30.5    -      -       +      +
    743C  VAL      4.0    11.4    -      -       -      +
    745C  ILE*     4.0    17.4    -      -       +      +
    800C  VAL*     4.2     9.0    -      -       +      -
    802C  ARG*     1.3    85.4    +      -       -      +
    804C  VAL*     1.3    68.4    +      -       -      +
    805C  ARG*     4.2     1.7    +      -       -      -
    823C  VAL*     5.3     2.0    -      -       -      -
    824C  ARG      3.2     6.5    -      -       -      -
    825C  VAL*     4.2    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 804 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85C  GLU*     3.8    20.0    -      -       -      +
    802C  ARG*     3.7    32.1    -      -       -      +
    803C  THR*     1.3    78.6    -      -       -      +
    805C  ARG*     1.3    63.9    +      -       -      +
    806C  LEU*     4.0    26.7    -      -       +      -
    822C  VAL      4.0     0.7    -      -       -      +
    823C  VAL*     3.3     4.8    -      -       -      +
    824C  ARG*     2.7    70.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 805 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    722C  ILE*     4.4    15.6    +      -       -      +
    740C  GLU*     2.5    56.4    +      -       -      +
    742C  VAL*     4.2    15.2    -      -       +      +
    803C  THR*     4.2     2.2    -      -       -      +
    804C  VAL*     1.3    77.8    -      -       -      +
    806C  LEU*     1.3    71.9    +      -       -      +
    807C  ARG*     3.4    44.8    +      -       +      +
    810C  ASP*     5.2     0.7    -      -       -      +
    821C  GLU*     2.9    26.6    +      -       -      -
    822C  VAL      3.6     1.8    -      -       -      +
    823C  VAL*     3.6    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 806 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85C  GLU*     5.6     3.8    -      -       -      +
     86C  LYS*     5.7    11.9    -      -       +      +
    804C  VAL*     4.0    22.4    -      -       +      -
    805C  ARG*     1.3    83.1    -      -       -      +
    807C  ARG*     1.3    62.8    +      -       -      +
    810C  ASP*     4.9     0.9    -      -       -      -
    813C  VAL*     4.1    26.5    -      -       +      -
    815C  LEU*     4.3    12.9    -      -       +      +
    821C  GLU*     3.1     2.3    -      -       -      +
    822C  VAL*     2.6    59.0    +      -       +      +
    824C  ARG*     4.7    13.7    -      -       -      +
----------------------------------------------------------
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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