Contacts of the strand formed by residues 702 - 713 (chain C) in PDB entry 6M6A


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 SER 702 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    569C  VAL*     4.3    14.0    -      -       -      +
    570C  PRO*     3.6    22.1    +      -       -      +
    571C  LEU*     4.3     0.9    -      -       -      -
    635C  THR*     6.1     0.2    -      -       -      -
    700C  TYR      3.3     1.8    +      -       -      -
    701C  THR*     1.3    73.9    -      -       -      +
    703C  ILE*     1.3    71.1    +      -       -      +
    704C  HIS*     3.7    22.5    +      -       -      -
    830C  LYS*     3.9     0.9    -      -       -      +
    831C  ARG*     2.6    41.3    +      -       -      +
    996C  LYS*     3.5    20.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 703 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  GLU*     4.0    12.1    -      -       -      +
     65A  PHE*     3.6    42.8    -      -       +      -
     76A  VAL*     5.8     4.3    -      -       +      -
    570C  PRO      5.1     0.6    +      -       -      -
    572C  ILE*     4.8    20.4    -      -       +      -
    635C  THR*     4.5     1.6    -      -       -      -
    636C  ALA*     4.1    24.6    +      -       +      +
    701C  THR*     5.1     2.5    -      -       +      +
    702C  SER*     1.3    85.3    +      -       -      +
    704C  HIS*     1.3    70.7    +      -       -      +
    705C  ILE*     6.0     0.7    -      -       +      -
    828C  ALA*     4.6     2.5    -      -       +      -
    829C  GLN      3.3    21.3    -      -       -      +
    830C  LYS*     3.7    16.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 704 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    569C  VAL*     5.5     6.1    -      -       +      +
    570C  PRO*     6.0     0.2    -      -       +      -
    633C  GLN      4.3     2.2    +      -       -      -
    634C  GLY      3.3    15.2    +      -       -      +
    635C  THR*     3.5    26.1    -      -       +      +
    702C  SER*     3.7    17.8    +      -       -      -
    703C  ILE*     1.3    80.3    -      -       -      +
    705C  ILE*     1.3    63.7    +      -       -      +
    828C  ALA*     3.4     1.4    -      -       -      -
    829C  GLN*     2.7    45.6    +      -       +      +
    831C  ARG*     3.2    58.4    +      -       -      +
    998C  TYR*     3.5    27.3    +      +       -      -
   1000C  MET*     4.5     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 705 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    628C  PHE*     3.4    29.2    -      -       +      +
    630C  ARG*     3.0    57.0    +      -       +      +
    634C  GLY*     2.7    20.5    +      -       -      +
    635C  THR      4.3     0.2    -      -       -      -
    636C  ALA*     3.7    28.9    -      -       +      +
    703C  ILE*     5.7     0.9    -      -       +      -
    704C  HIS*     1.3    78.0    -      -       -      +
    706C  GLU*     1.3    63.9    +      -       -      +
    801C  VAL*     4.8     9.6    -      -       +      -
    802C  ARG*     5.0     3.6    -      -       -      +
    826C  TYR*     4.4    18.4    -      -       +      -
    827C  VAL      3.6     9.6    -      -       -      +
    828C  ALA*     4.2     7.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 706 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    630C  ARG*     3.4    10.0    +      -       -      +
    705C  ILE*     1.3    75.4    -      -       -      +
    707C  ARG*     1.3    80.1    +      -       -      +
    708C  TYR*     3.4    37.9    +      -       +      +
    796C  GLU*     4.9     3.8    -      -       -      +
    825C  VAL      3.5     1.4    -      -       -      +
    826C  TYR*     3.3     2.3    -      -       -      -
    827C  VAL*     2.6    48.3    +      -       +      +
    829C  GLN*     4.5    20.1    +      -       -      +
    831C  ARG*     5.6     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 707 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  ASP*     4.6    13.5    +      -       -      -
    630C  ARG*     3.0    32.9    -      -       -      +
    706C  GLU*     1.3    90.7    -      -       -      +
    708C  TYR*     1.3    68.9    +      -       -      +
    709C  GLU*     2.4    37.4    +      -       +      +
    824C  ARG*     3.4    21.5    -      -       -      +
    825C  VAL      3.3     3.6    -      -       -      -
    826C  TYR*     3.5    26.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 708 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    706C  GLU*     3.4    31.1    -      -       +      +
    707C  ARG*     1.3    83.7    -      -       -      +
    709C  GLU*     1.3    62.4    +      -       -      +
    749C  VAL*     6.2     0.2    -      -       -      +
    755C  LEU*     5.2    13.7    -      -       +      -
    790C  LEU*     4.9    13.7    -      -       +      -
    792C  VAL*     4.7     7.0    -      -       +      +
    793C  PRO*     4.2    16.9    -      -       +      +
    796C  GLU*     2.3    39.7    +      -       -      +
    797C  GLY      5.2     1.0    +      -       -      -
    824C  ARG*     3.3     1.9    -      -       -      -
    825C  VAL*     2.4    71.6    +      -       +      +
    827C  VAL*     3.7    28.1    -      -       +      +
    829C  GLN*     5.9     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 709 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  ASP*     4.6     2.8    -      -       -      +
    707C  ARG*     2.4    38.7    +      -       +      +
    708C  TYR*     1.3    79.5    -      -       -      +
    710C  ILE*     1.3    62.1    +      -       -      +
    790C  LEU*     4.9     5.6    -      -       -      +
    822C  VAL*     3.5    25.1    -      -       +      +
    823C  VAL      3.3     7.4    -      -       -      +
    824C  ARG*     3.4    27.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 710 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    709C  GLU*     1.3    74.3    -      -       -      +
    711C  GLU*     1.3    64.1    +      -       -      +
    722C  ILE*     5.0     6.1    -      -       +      -
    755C  LEU*     5.3     1.3    -      -       +      -
    756C  VAL*     3.7    25.1    -      -       +      -
    758C  ARG*     3.5    39.7    -      -       +      +
    788C  THR      4.1     4.7    -      -       -      +
    790C  LEU*     3.7    39.4    -      -       +      +
    822C  VAL*     3.4     4.9    -      -       -      +
    823C  VAL*     2.5    59.1    +      -       +      +
    825C  VAL*     5.8     1.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 711 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    710C  ILE*     1.3    78.1    -      -       -      +
    712C  ALA*     1.3    76.1    +      -       -      +
    713C  ARG*     3.1    44.1    +      -       -      +
    722C  ILE*     5.0     3.6    -      -       -      -
    758C  ARG*     2.4    42.5    +      -       -      +
    816C  LYS*     4.9     3.0    +      -       -      -
    819C  VAL*     3.3    13.0    -      -       +      +
    821C  GLU      3.3    13.7    -      -       -      +
    822C  VAL*     3.7    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 712 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711C  GLU*     1.3    79.0    -      -       -      +
    713C  ARG*     1.3    58.3    +      -       -      +
    720C  GLU*     3.4    18.4    -      -       +      +
    722C  ILE*     3.9     6.0    -      -       +      +
    758C  ARG*     3.7    21.3    -      -       -      +
    820C  ARG*     3.2     4.0    +      -       -      +
    821C  GLU*     2.9    61.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 713 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711C  GLU*     3.1    30.1    +      -       -      +
    712C  ALA*     1.3    74.3    -      -       -      +
    714C  ASP*     1.3    76.7    +      -       -      +
    715C  THR*     4.1     4.3    +      -       -      +
    719C  PRO*     3.3    16.5    -      -       -      +
    720C  GLU*     3.4    18.1    +      -       -      +
    758C  ARG*     6.0     0.4    -      -       -      +
    816C  LYS*     3.2    27.7    -      -       -      +
    818C  GLY      3.2    12.3    -      -       -      +
    819C  VAL*     3.7     7.0    -      -       +      -
    820C  ARG*     3.8     9.2    -      -       -      +
    531D  ASP*     3.6    24.4    +      -       -      -
    532D  GLY*     5.0     9.4    -      -       -      -
----------------------------------------------------------
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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