Contacts of the strand formed by residues 109 - 119 (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 LYS 109 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100C  LEU*     2.7    47.7    +      -       +      +
    107C  LEU*     4.3    10.2    -      -       +      +
    108C  ILE*     1.4    71.6    -      -       -      +
    110C  GLU*     1.3    80.1    +      -       -      +
    111C  ASP*     4.5    11.7    +      -       -      +
    367C  LEU      5.0     2.2    -      -       -      +
    368C  THR*     3.6    34.3    -      -       +      -
    369C  PRO*     3.6    13.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 110 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69C  LEU*     3.7    25.4    -      -       +      +
     97C  ARG*     4.8     8.2    +      -       +      +
     98C  LEU      3.3     5.6    -      -       -      +
     99C  GLN*     3.4    35.5    +      -       +      -
    108C  ILE*     4.4     9.3    +      -       +      +
    109C  LYS*     1.3    92.0    +      -       -      +
    111C  ASP*     1.3    65.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 111 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  ALA      3.6     1.0    -      -       -      +
     97C  ARG*     3.7     6.1    -      -       -      +
     98C  LEU*     3.0    34.1    +      -       -      +
    109C  LYS*     4.5    10.6    +      -       -      -
    110C  GLU*     1.3    78.0    -      -       -      +
    112C  GLU*     1.3    72.4    +      -       -      +
    113C  VAL*     3.8     3.8    +      -       +      +
    368C  THR*     5.3     1.8    +      -       -      -
    369C  PRO*     4.0    20.7    -      -       +      +
    370C  ALA*     3.2    30.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 112 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72C  ARG*     3.2    34.4    +      -       -      +
     95C  TYR*     3.8    32.5    -      -       +      +
     96C  ALA      3.3    12.6    -      -       -      +
     97C  ARG*     4.2    24.0    +      -       +      +
    111C  ASP*     1.3    85.0    +      -       -      +
    113C  VAL*     1.3    60.6    +      -       -      +
    114C  PHE      4.0     1.0    +      -       -      -
    370C  ALA*     6.0     0.2    -      -       -      +
    280F  GLN      5.2     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 113 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95C  TYR*     3.5     2.8    -      -       -      -
     96C  ALA*     2.9    39.3    +      -       +      +
     98C  LEU*     3.6    21.5    -      -       +      -
    111C  ASP*     4.6     2.9    -      -       -      +
    112C  GLU*     1.3    75.3    -      -       -      +
    114C  PHE*     1.3    62.5    +      -       -      +
    115C  LEU*     3.6    18.6    +      -       +      +
    369C  PRO*     3.8    17.9    -      -       +      +
    370C  ALA*     3.6    35.9    -      -       +      +
    373C  VAL*     4.4     6.7    -      -       +      -
    280F  GLN*     3.4    15.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 114 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93C  PRO*     3.7    20.2    -      -       +      -
     94C  LEU      3.5     9.0    -      -       -      -
     95C  TYR*     3.5    28.0    -      +       +      -
    112C  GLU      4.0     2.0    +      -       -      +
    113C  VAL*     1.3    70.6    -      -       -      +
    115C  LEU*     1.3    61.4    +      -       -      +
    116C  GLY*     3.4    37.5    -      -       -      -
    117C  HIS*     3.7    14.1    -      +       -      -
    373C  VAL*     5.6     0.2    -      -       -      +
    375C  SER*     3.7    13.7    +      -       -      -
    379C  GLU*     5.6     0.2    -      -       -      -
    279F  GLN*     3.2    48.6    +      -       +      -
    280F  GLN*     3.9    35.6    +      -       -      +
    283F  GLY*     3.6    17.9    -      -       -      -
    284F  ARG*     3.8     5.2    -      -       -      -
    285F  GLU*     5.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 115 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  PHE*     3.9    24.2    -      -       +      -
     94C  LEU*     2.9    26.2    +      -       +      +
     96C  ALA*     3.8    22.9    -      -       +      -
     98C  LEU*     6.2     0.4    -      -       +      -
    113C  VAL*     4.0    23.8    -      -       +      +
    114C  PHE*     1.3    79.1    -      -       -      +
    116C  GLY*     1.3    59.2    +      -       -      +
    348C  LEU*     5.2     2.5    -      -       +      -
    351C  LEU*     4.3    11.2    -      -       +      -
    373C  VAL*     4.3    11.7    -      -       +      -
    375C  SER*     3.9    21.2    -      -       -      -
    378C  LEU*     4.0    29.4    -      -       +      +
    379C  GLU*     3.5    14.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 116 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94C  LEU*     2.7    34.6    +      -       -      +
    114C  PHE*     3.4    32.8    -      -       -      -
    115C  LEU*     1.3    80.2    -      -       -      +
    117C  HIS*     1.3    55.9    +      -       -      -
    375C  SER*     4.7     0.4    +      -       -      -
    379C  GLU*     3.9    19.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 117 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77C  PRO*     3.8    24.4    -      -       +      +
     91C  GLN*     3.4    43.2    +      -       +      +
     92C  ALA      3.2     7.4    -      -       -      +
     93C  PRO*     3.6    26.2    -      -       +      +
    114C  PHE*     3.7    21.0    -      +       -      -
    116C  GLY*     1.3    76.7    -      -       -      -
    118C  ILE*     1.3    66.1    +      -       -      +
    119C  PRO*     4.2     4.6    -      -       -      +
    379C  GLU*     4.6    12.4    +      -       -      +
    382C  ILE*     4.9     6.6    -      -       -      +
    283F  GLY      4.3     5.2    -      -       -      -
    284F  ARG*     4.0    16.5    -      -       +      +
    285F  GLU*     4.9     7.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 118 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  TYR*     3.9     8.1    -      -       -      +
     30C  LEU*     4.5    17.9    -      -       +      -
     44C  ILE*     5.2     3.1    -      -       +      -
     73C  LEU*     4.6    13.7    -      -       +      -
     91C  GLN*     3.7     2.7    -      -       -      -
     92C  ALA*     2.8    40.6    +      -       -      +
     94C  LEU*     4.0    21.7    -      -       +      +
    117C  HIS*     1.3    78.4    -      -       -      +
    119C  PRO*     1.3    82.3    -      -       +      +
    120C  LEU*     3.5     2.1    +      -       +      +
    340C  MET*     3.9    21.8    -      -       +      -
    344C  PHE*     3.8    30.3    -      -       +      -
    382C  ILE*     4.8     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 119 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  TYR*     2.5    32.2    +      -       -      +
     89C  THR*     4.2     9.9    -      -       +      -
     90C  TYR      3.3    13.9    -      -       -      +
     91C  GLN*     3.8     3.6    -      -       +      +
    117C  HIS      4.2     3.1    -      -       -      +
    118C  ILE*     1.3    92.6    -      -       +      +
    120C  LEU*     1.3    60.3    +      -       -      +
    127C  PHE*     4.2     9.4    -      -       +      -
    129C  ILE*     4.0    23.8    -      -       +      -
    382C  ILE*     3.9    20.0    -      -       +      -
    383C  ARG*     6.5     0.4    -      -       -      -
    386C  PHE*     4.2    23.1    -      -       +      -
----------------------------------------------------------
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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