Contacts of the strand formed by residues 91 - 101 (chain C) in PDB entry 6OY5


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 91 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76C  PRO*     3.3    10.6    -      -       -      +
     77C  PRO*     3.3    27.3    -      -       +      +
     78C  PHE      5.7     0.2    +      -       -      -
     83C  CYS*     5.3     0.4    -      -       -      -
     89C  THR*     3.3    35.2    +      -       +      +
     90C  TYR*     1.3    75.8    -      -       -      +
     92C  ALA*     1.3    59.4    +      -       -      +
    117C  HIS*     3.4    42.4    +      -       +      +
    118C  ILE      3.1    21.8    -      -       -      +
    119C  PRO*     3.8     4.5    -      -       +      +
    120C  LEU*     3.9     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 92 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73C  LEU*     4.5    12.5    -      -       +      +
     74C  GLY      3.5    23.6    -      -       -      +
     75C  GLU      4.4     2.7    -      -       -      -
     91C  GLN*     1.3    73.9    -      -       -      +
     93C  PRO*     1.3    70.6    -      -       +      +
     94C  LEU*     3.5     0.3    +      -       -      -
    117C  HIS*     3.2     5.0    -      -       -      -
    118C  ILE*     2.8    39.3    +      -       -      +
    120C  LEU*     4.0    25.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 93 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72C  ARG      4.0     0.3    -      -       -      +
     73C  LEU*     3.6     3.8    -      -       -      +
     74C  GLY*     2.9    40.8    +      -       -      -
     75C  GLU      3.2    22.9    -      -       -      +
     77C  PRO*     4.1     8.1    -      -       +      -
     92C  ALA*     1.3    83.3    -      -       +      +
     94C  LEU*     1.3    60.2    +      -       -      +
     95C  TYR*     4.0    21.2    +      -       +      +
    114C  PHE*     3.7    19.1    -      -       +      -
    116C  GLY      3.7     6.3    -      -       -      +
    117C  HIS*     3.6    18.1    -      -       +      +
    283F  GLY      4.2     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 94 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  ILE*     5.6     1.3    -      -       +      -
     48C  PHE*     4.4     3.1    -      -       +      -
     71C  TYR*     3.9    23.8    -      -       +      -
     72C  ARG      3.4    17.5    -      -       -      +
     73C  LEU*     3.8    20.2    -      -       +      -
     92C  ALA      3.5     2.2    +      -       -      +
     93C  PRO*     1.3    73.1    -      -       -      +
     95C  TYR*     1.3    68.6    +      -       -      +
    114C  PHE*     3.5     7.3    -      -       -      -
    115C  LEU*     2.9    50.4    +      -       +      +
    116C  GLY      2.7    16.9    +      -       -      +
    118C  ILE*     4.0    26.9    -      -       +      -
    344C  PHE*     4.1    21.3    -      -       +      -
    378C  LEU*     4.7     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71C  TYR*     3.4     6.9    -      -       -      +
     72C  ARG*     3.0    79.9    +      -       +      +
     74C  GLY*     4.9     0.4    -      -       -      -
     93C  PRO*     4.0    33.3    -      -       +      +
     94C  LEU*     1.3    75.7    -      -       -      +
     96C  ALA*     1.3    61.1    +      -       -      +
    112C  GLU*     3.8    29.6    -      -       +      +
    113C  VAL      3.5     4.9    -      -       -      +
    114C  PHE*     3.5    35.0    -      +       +      -
    115C  LEU*     4.9     0.7    -      -       -      -
    282F  LEU      5.1     0.2    +      -       -      -
    283F  GLY*     3.8    21.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  PHE*     4.3    16.2    -      -       +      -
     68C  PHE*     5.1     1.1    -      -       +      -
     70C  GLU      3.7     7.9    -      -       -      +
     71C  TYR*     4.8     0.2    -      -       +      -
     95C  TYR*     1.3    77.1    -      -       -      +
     97C  ARG*     1.3    62.1    +      -       -      +
     98C  LEU*     3.5    14.4    +      -       +      +
    112C  GLU*     3.3     4.1    -      -       -      -
    113C  VAL*     2.9    46.3    +      -       +      +
    115C  LEU*     3.8    24.2    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     68C  PHE*     4.3     0.3    -      -       -      -
     69C  LEU*     2.8    59.9    +      -       +      +
     70C  GLU*     2.9    48.1    +      -       +      +
     71C  TYR*     4.9     0.2    -      -       -      +
     72C  ARG*     5.9     3.6    -      -       -      +
     96C  ALA*     1.3    70.3    -      -       -      +
     98C  LEU*     1.3    59.8    +      -       -      +
    110C  GLU*     4.8     8.0    +      -       +      +
    111C  ASP      3.7    11.4    -      -       -      +
    112C  GLU*     4.2    25.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  PHE*     6.0     0.7    -      -       +      -
     52C  PHE*     4.4    18.2    -      -       +      -
     66C  LEU*     4.1    20.2    -      -       +      -
     67C  ASP      3.4    15.7    -      -       -      +
     68C  PHE*     3.8    20.4    -      -       +      -
     69C  LEU*     4.6     1.1    -      -       -      -
     96C  ALA*     3.9    15.3    -      -       +      +
     97C  ARG*     1.3    85.0    -      -       -      +
     99C  GLN*     1.3    59.4    +      -       -      +
    100C  LEU      4.2     0.4    -      -       -      -
    110C  GLU*     3.3     5.6    -      -       -      +
    111C  ASP      3.0    33.5    +      -       -      +
    113C  VAL*     3.6    25.8    -      -       +      -
    351C  LEU*     6.4     0.4    -      -       +      -
    369C  PRO*     3.9     8.8    -      -       +      +
    373C  VAL*     4.0    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 99 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  VAL      4.0     0.2    -      -       -      +
     66C  LEU*     3.7     3.6    -      -       -      -
     67C  ASP*     2.9    50.6    +      -       +      +
     69C  LEU*     3.3    28.0    -      -       +      +
     98C  LEU*     1.3    72.4    -      -       -      +
    100C  LEU*     1.3    63.1    +      -       -      +
    101C  ILE*     3.5    26.3    +      -       +      +
    108C  ILE*     4.9    12.2    -      -       +      +
    109C  LYS      3.7     3.8    -      -       -      +
    110C  GLU*     3.4    28.0    +      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
     64C  LEU*     4.3    16.6    -      -       +      -
     65C  VAL      3.9    10.3    -      -       -      +
     66C  LEU*     3.7    13.9    -      -       +      +
     98C  LEU      4.2     0.6    -      -       -      -
     99C  GLN*     1.3    71.5    -      -       -      +
    101C  ILE*     1.3    78.6    +      -       -      +
    107C  LEU*     3.6    15.4    -      -       +      +
    108C  ILE*     3.2    28.1    -      -       -      +
    109C  LYS*     2.7    24.3    +      -       +      +
    359C  MET*     5.5     1.3    -      -       -      -
    365C  ASP      5.7     0.2    -      -       -      +
    367C  LEU*     3.2    33.4    -      -       +      +
    368C  THR*     4.3     9.0    -      -       -      +
    369C  PRO*     4.1     9.8    -      -       +      +
    372C  LEU*     4.3    18.4    -      -       +      -
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Residues in contact with ILE 101 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64C  LEU*     3.7     4.2    -      -       -      +
     65C  VAL*     2.9    51.2    +      -       +      +
     67C  ASP*     4.5    11.4    -      -       +      +
     99C  GLN*     3.5    30.3    -      -       +      +
    100C  LEU*     1.3    90.2    -      -       -      +
    102C  HIS*     1.3    74.3    +      -       -      +
    103C  LYS*     5.6     0.4    -      -       -      -
    106C  GLY*     5.2     2.9    -      -       -      +
    107C  LEU      3.4     8.7    -      -       -      +
    108C  ILE*     4.8    12.8    -      -       +      -
----------------------------------------------------------
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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