Contacts of the strand formed by residues 93 - 104 (chain C) in PDB entry 6RI7


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 93 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78C  PRO*     3.8    17.5    -      -       -      +
     79C  VAL*     5.4     3.9    +      -       -      +
     90C  VAL*     5.7     1.7    -      -       -      +
     91C  THR*     3.2    23.4    +      -       -      -
     92C  TYR*     1.3    82.1    -      -       -      +
     94C  ALA*     1.3    63.2    +      -       -      +
    126C  GLU*     2.6    40.4    +      -       -      +
    127C  ILE      3.1    20.4    -      -       -      -
    128C  PRO*     3.7     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 94 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75C  LEU*     4.6     8.7    -      -       +      -
     76C  GLY      4.4     6.3    -      -       -      +
     78C  PRO*     4.5     3.8    -      -       +      -
     93C  SER*     1.3    79.9    +      -       -      +
     95C  PRO*     1.3    79.3    -      -       +      +
    126C  GLU*     3.1    22.6    -      -       -      +
    127C  ILE*     2.7    19.1    +      -       +      +
    129C  LEU*     3.9    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75C  LEU*     3.2    27.7    -      -       -      +
     76C  GLY*     3.1    35.0    -      -       -      +
     77C  GLU      3.9    13.2    -      -       -      +
     78C  PRO*     4.3     4.9    -      -       +      -
     79C  VAL*     5.4     6.5    -      -       +      +
     94C  ALA*     1.3    87.7    -      -       -      +
     96C  LEU*     1.3    59.9    +      -       -      +
     97C  ARG*     3.4    30.3    -      -       +      +
    123C  TYR*     6.3     0.2    -      -       +      -
    126C  GLU*     3.5    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  LEU*     4.8     9.4    -      -       +      -
     53C  PHE*     5.7     2.7    -      -       +      -
     73C  TYR*     4.1    14.8    -      -       +      -
     74C  ARG      4.0     0.2    -      -       -      -
     75C  LEU*     3.7    30.7    -      -       +      -
     94C  ALA      4.7     1.8    -      -       -      +
     95C  PRO*     1.3    74.3    -      -       -      +
     97C  ARG*     1.3    62.9    +      -       -      +
     98C  VAL*     4.4     6.1    -      -       +      -
    123C  TYR*     3.1     4.8    -      -       -      +
    124C  MET*     2.9    52.1    +      -       +      +
    125C  GLY      3.2    21.1    +      -       -      +
    126C  GLU*     5.0     1.1    -      -       -      -
    127C  ILE*     4.8    16.2    -      -       +      +
    464C  PHE*     3.8    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 97 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73C  TYR*     3.1    22.6    -      -       -      +
     74C  ARG*     3.1    49.1    +      -       -      +
     76C  GLY*     5.2     1.6    -      -       -      +
     95C  PRO*     3.4    33.3    -      -       +      +
     96C  LEU*     1.3    73.0    -      -       -      +
     98C  VAL*     1.3    62.0    +      -       -      +
    121C  GLU*     3.2    43.3    +      -       +      +
    122C  VAL      3.7     2.2    -      -       -      -
    123C  TYR*     3.2    37.9    -      -       -      +
    126C  GLU*     5.6     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53C  PHE*     4.3    10.5    -      -       +      -
     57C  PHE*     5.6     0.4    -      -       +      -
     70C  TYR*     4.6     7.6    -      -       +      -
     72C  SER      3.8     7.4    -      -       -      +
     73C  TYR*     4.0     9.0    -      -       +      +
     96C  LEU*     4.1     7.2    -      -       +      +
     97C  ARG*     1.3    83.2    -      -       -      +
     99C  LYS*     1.3    64.1    +      -       -      +
    100C  LEU*     3.8    27.4    +      -       +      -
    119C  GLU      4.4     0.3    -      -       -      +
    121C  GLU*     3.0     5.4    +      -       -      -
    122C  VAL*     2.9    41.9    +      -       +      +
    124C  MET*     3.5    42.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 99 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71C  VAL*     2.9    38.0    +      -       +      -
     72C  SER*     2.9    41.8    +      -       -      +
     73C  TYR*     4.6     1.5    -      -       -      +
     98C  VAL*     1.3    72.2    -      -       -      +
    100C  LEU*     1.3    65.8    +      -       -      +
    118C  LYS*     5.9     3.8    -      -       +      -
    119C  GLU      4.1     8.2    +      -       -      +
    120C  GLN*     5.2     3.4    -      -       -      +
    121C  GLU*     4.0    34.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 100 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  PHE*     3.5    31.4    -      -       +      -
     68C  LEU*     3.7    30.2    -      -       +      +
     69C  GLN      3.2    14.4    -      -       -      +
     70C  TYR*     3.6     5.4    -      -       -      -
     71C  VAL*     4.4     1.8    -      -       -      -
     98C  VAL*     3.8    22.2    +      -       +      +
     99C  LYS*     1.3    80.8    -      -       -      +
    101C  ARG*     1.3    61.7    +      -       -      +
    102C  LEU      3.5     0.3    +      -       -      -
    117C  ILE      3.5     1.9    -      -       -      +
    118C  LYS*     3.2    21.2    -      -       -      -
    119C  GLU*     3.3    12.3    +      -       +      +
    122C  VAL*     4.6    12.6    -      -       +      -
    124C  MET*     5.1     1.1    -      -       +      -
    489C  PRO*     4.7    13.0    -      -       +      +
    493C  ILE*     4.3    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 101 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68C  LEU*     3.2     3.5    -      -       -      +
     69C  GLN*     2.9    69.0    +      -       +      +
     71C  VAL*     3.7    22.5    -      -       +      +
    100C  LEU*     1.3    69.2    -      -       -      +
    102C  LEU*     1.3    60.3    +      -       -      +
    103C  VAL*     3.7    18.9    +      -       +      +
    116C  ASP*     4.6    12.9    +      -       +      +
    118C  LYS*     2.8    54.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 102 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66C  SER*     6.2     0.2    -      -       -      -
     67C  GLU      3.2    19.3    -      -       -      +
     68C  LEU*     3.6    25.8    -      -       +      -
    100C  LEU      3.5     0.4    +      -       -      -
    101C  ARG*     1.3    72.0    -      -       -      +
    103C  VAL*     1.3    64.2    +      -       -      +
    104C  ILE*     5.7     6.0    -      -       +      +
    115C  LYS      4.2     0.3    -      -       -      +
    116C  ASP*     3.2     2.8    -      -       -      -
    117C  ILE*     2.7    64.6    +      -       +      +
    479C  LEU*     5.4     6.1    -      -       +      -
    487C  LEU*     4.3    17.3    -      -       +      -
    489C  PRO*     3.8    28.5    -      -       +      -
    492C  MET*     4.4    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 103 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66C  SER*     3.5     2.5    -      -       -      -
     67C  GLU*     2.9    64.3    +      -       +      +
     68C  LEU*     5.4     0.2    -      -       -      -
     69C  GLN*     4.8     7.9    -      -       -      +
    101C  ARG*     3.7    24.7    -      -       +      +
    102C  LEU*     1.3    79.5    -      -       -      +
    104C  ILE*     1.3    69.5    +      -       -      +
    105C  TYR*     5.1     7.4    -      -       +      +
    113C  THR*     5.3    11.7    -      -       +      -
    115C  LYS      3.9     3.8    -      -       -      +
    116C  ASP*     3.6    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 104 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  ASN      3.2    13.9    -      -       -      +
     66C  SER*     3.5    17.0    -      -       -      +
    102C  LEU*     5.7     6.3    -      -       +      +
    103C  VAL*     1.3    78.3    -      -       -      +
    105C  TYR*     1.3    61.0    +      -       -      +
    107C  ARG*     4.4    21.1    -      -       -      +
    113C  THR*     3.4     3.7    -      -       -      -
    114C  VAL*     2.7    44.6    +      -       +      -
    115C  LYS*     3.3    16.0    +      -       +      +
    483C  ASP      4.5     7.0    -      -       -      +
    484C  LEU*     4.7    14.6    -      -       +      -
    485C  ASP*     4.5    26.2    -      -       +      +
----------------------------------------------------------
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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