Contacts of the strand formed by residues 819 - 831 (chain C) in PDB entry 5D4C


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 VAL 819 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711C  GLU*     4.0    16.2    -      -       +      +
    712C  ALA      3.8     9.6    -      -       -      +
    713C  ARG*     4.0     7.9    -      -       +      +
    808C  ARG*     3.8    15.6    -      -       -      -
    815C  LEU*     3.8    20.2    -      -       +      +
    816C  LYS*     3.1    49.3    +      -       +      +
    817C  PRO      4.4     1.3    -      -       -      +
    818C  GLY*     1.3    78.0    -      -       -      +
    820C  ARG*     1.3    65.1    +      -       -      +
    821C  GLU      3.9     6.5    -      -       -      +
    822C  VAL*     3.8    28.7    -      -       +      -
    532D  GLY      5.7     1.1    -      -       -      +
    305F  GLU*     4.2     1.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 820 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    712C  ALA      2.6    16.5    +      -       -      +
    713C  ARG      3.8     6.3    -      -       -      -
    714C  ASP*     2.8    46.9    +      -       -      +
    719C  PRO*     3.6    21.5    -      -       -      +
    720C  GLU      3.4    22.8    +      -       -      -
    721C  ARG*     5.5     3.0    -      -       -      +
    807C  ARG*     4.6     0.5    -      -       -      +
    808C  ARG*     2.8    56.4    +      -       -      +
    815C  LEU*     3.8     1.2    -      -       -      +
    818C  GLY      3.6     0.2    +      -       -      -
    819C  VAL*     1.3    72.2    -      -       -      +
    821C  GLU*     1.3    70.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 821 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    710C  ILE      4.1     0.2    -      -       -      +
    711C  GLU*     3.6     2.6    -      -       -      -
    712C  ALA*     2.9    42.7    +      -       +      +
    720C  GLU      5.0     0.3    -      -       -      +
    721C  ARG*     4.1     7.3    -      -       -      +
    722C  ILE*     3.3    36.4    +      -       +      +
    805C  ARG*     2.7    35.3    +      -       -      +
    806C  LEU      3.2    15.3    -      -       -      +
    807C  ARG*     3.3    18.3    -      -       +      +
    815C  LEU*     4.8     1.6    -      -       -      -
    819C  VAL*     3.6     2.6    -      -       -      +
    820C  ARG*     1.3    85.8    +      -       +      +
    822C  VAL*     1.3    65.5    -      -       -      +
    823C  VAL*     5.5     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 822 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    709C  GLU*     3.7    28.0    -      -       +      +
    710C  ILE      3.6     7.9    -      -       -      +
    711C  GLU*     4.1    15.7    -      -       +      +
    804C  VAL      3.9     0.7    -      -       -      +
    805C  ARG*     3.6     2.8    -      -       -      -
    806C  LEU*     2.9    47.9    +      -       +      +
    815C  LEU*     4.0    15.5    -      -       +      -
    816C  LYS*     6.4     0.4    -      -       +      -
    819C  VAL*     3.8    19.1    -      -       +      -
    821C  GLU*     1.3    79.0    -      -       -      +
    823C  VAL*     1.3    68.8    +      -       -      +
    824C  ARG*     4.5    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 823 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    708C  TYR      4.0     0.2    -      -       -      +
    709C  GLU*     3.4     3.6    -      -       -      +
    710C  ILE*     2.9    45.1    +      -       +      +
    722C  ILE*     3.9    31.0    -      -       +      -
    742C  VAL*     3.9    21.5    -      -       +      -
    756C  VAL*     3.7    22.5    -      -       +      +
    790C  LEU*     5.8     0.3    -      -       -      +
    803C  THR*     5.5     0.2    -      -       -      -
    804C  VAL      3.4    10.8    -      -       -      +
    805C  ARG*     4.2    21.5    -      -       +      +
    821C  GLU*     5.3     0.9    -      -       +      -
    822C  VAL*     1.3    80.7    -      -       -      +
    824C  ARG*     1.3    70.4    +      -       -      +
    825C  VAL*     4.3     0.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 824 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85C  GLU*     3.4    25.9    +      -       -      -
     86C  LYS*     4.8     3.6    -      -       -      +
     87C  ASP*     4.1    15.4    +      -       -      +
    707C  ARG*     3.6    41.1    -      -       +      +
    708C  TYR      3.3     7.2    -      -       -      +
    709C  GLU*     2.7    49.3    +      -       +      -
    802C  ARG      4.1     0.2    -      -       -      +
    803C  THR*     3.3     6.8    -      -       -      -
    804C  VAL*     2.9    54.9    +      -       +      +
    806C  LEU*     4.0    24.0    -      -       -      +
    822C  VAL*     4.3     7.4    -      -       +      +
    823C  VAL*     1.3    73.4    -      -       -      +
    825C  VAL*     1.3    62.1    +      -       -      +
    826C  TYR*     4.2    19.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 825 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707C  ARG*     3.8     1.6    -      -       -      +
    708C  TYR*     2.9    45.7    +      -       +      +
    742C  VAL*     4.6     2.2    -      -       +      -
    743C  VAL*     4.2     3.4    -      -       +      -
    755C  LEU*     4.2    24.5    -      -       +      +
    756C  VAL*     3.7    31.0    -      -       +      -
    790C  LEU*     5.5     1.1    -      -       +      -
    800C  VAL*     3.8    24.9    -      -       +      -
    802C  ARG      3.7     3.6    -      -       -      +
    803C  THR*     4.4    10.5    -      -       +      -
    823C  VAL*     4.2     0.6    -      -       +      +
    824C  ARG*     1.3    76.8    -      -       -      +
    826C  TYR*     1.3    63.6    +      -       -      +
    827C  VAL*     3.9    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 826 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85C  GLU*     5.1     5.0    +      -       -      -
    630C  ARG*     4.4    14.6    -      -       +      -
    705C  ILE*     3.8    20.9    -      -       +      -
    706C  GLU      3.6     1.6    -      -       -      -
    707C  ARG*     3.5    40.3    +      -       +      -
    800C  VAL*     3.4     7.1    -      -       -      +
    801C  VAL*     3.0    32.0    +      -       +      -
    802C  ARG*     2.9    62.2    +      -       +      +
    804C  VAL*     4.5     7.8    -      -       +      +
    824C  ARG*     4.2    26.9    +      -       +      -
    825C  VAL*     1.3    75.7    -      -       -      +
    827C  VAL*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 827 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    704C  HIS      3.8     1.6    -      -       -      +
    705C  ILE*     3.6     1.9    -      -       -      -
    706C  GLU*     2.9    38.0    +      -       +      +
    708C  TYR*     3.7    26.5    -      -       +      +
    749C  VAL*     4.1     4.0    -      -       +      -
    755C  LEU*     4.2    10.5    -      -       +      -
    797C  GLY*     3.6    12.6    -      -       -      +
    798C  GLY*     3.4    37.9    -      -       -      +
    799C  ILE      3.4     2.0    -      -       -      -
    800C  VAL*     4.1    13.2    -      -       +      -
    825C  VAL*     3.9    18.2    -      -       +      -
    826C  TYR*     1.3    76.3    -      -       -      +
    828C  ALA*     1.3    62.1    +      -       -      +
    829C  GLN*     5.2     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 828 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  PHE*     4.0    17.4    -      -       +      -
    703C  ILE*     4.9     2.5    -      -       +      -
    704C  HIS      3.4     5.4    -      -       -      +
    705C  ILE*     3.9    22.7    -      -       +      +
    798C  GLY*     3.5     1.9    -      -       -      -
    799C  ILE*     2.7    38.0    +      -       -      +
    801C  VAL*     3.7    27.3    -      -       +      +
    826C  TYR      4.1     1.0    -      -       -      -
    827C  VAL*     1.3    74.1    -      -       -      +
    829C  GLN*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 829 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  PHE*     4.2     7.0    -      -       -      -
    702C  SER      3.7     0.9    -      -       -      +
    703C  ILE*     3.5     3.1    -      -       -      +
    704C  HIS*     2.9    43.7    +      -       +      +
    706C  GLU*     5.8     4.2    -      -       -      +
    796C  GLU*     4.9     2.5    -      -       -      +
    797C  GLY      2.5    36.4    +      -       -      +
    798C  GLY*     4.4     3.6    -      -       -      -
    799C  ILE*     6.0     0.4    -      -       -      -
    827C  VAL*     5.2     2.2    -      -       -      +
    828C  ALA*     1.3    77.1    -      -       -      +
    830C  LYS*     1.3    61.6    +      -       -      +
    831C  ARG*     2.7    42.5    +      -       +      +
   1002C  GLU*     3.3    20.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 830 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  GLU*     2.9    36.0    +      -       -      +
     65A  PHE*     4.1    16.5    -      -       +      -
     76A  VAL*     5.0     7.9    -      -       +      +
     79A  ILE*     6.0     1.2    -      -       -      +
     80A  LEU*     6.1     1.2    -      -       -      +
    154A  GLU*     5.7     1.8    -      -       -      +
    168A  ASP*     4.4    10.9    +      -       -      -
    572C  ILE*     4.7    10.0    -      -       +      +
    698C  ASP*     4.2    16.0    +      -       -      -
    701C  THR*     3.7    24.7    -      -       +      -
    702C  SER      3.7     1.6    -      -       -      -
    703C  ILE*     4.3    17.9    -      -       +      +
    829C  GLN*     1.3    73.2    -      -       -      +
    831C  ARG*     1.3    60.4    +      -       -      +
    832C  LYS*     3.7    10.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 831 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    701C  THR*     3.1     9.1    -      -       -      -
    702C  SER*     2.9    36.3    +      -       -      +
    704C  HIS*     3.4    34.8    +      -       +      +
    829C  GLN*     2.7    36.1    +      -       +      -
    830C  LYS*     1.3    72.5    -      -       -      +
    832C  LYS*     1.3    63.8    +      -       -      +
    834C  GLN*     6.3     0.4    -      -       -      +
    837C  ASP*     5.9     0.4    -      -       -      +
    996C  LYS*     3.7    12.4    +      -       -      +
   1000C  MET*     3.5    25.9    -      -       -      +
   1002C  GLU*     3.2    30.8    +      -       -      +
   1003C  ASP*     2.7    43.3    +      -       -      -
----------------------------------------------------------
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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