Contacts of the strand formed by residues 478 - 486 (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 VAL 478 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    474C  VAL*     3.4     1.3    -      -       -      -
    475C  VAL*     2.8    50.9    +      -       +      +
    477C  GLY*     1.3    77.4    -      -       -      +
    479C  VAL*     1.3    63.4    +      -       -      +
    480C  THR*     3.7     7.1    +      -       +      -
    506C  ASN*     3.6    31.9    -      -       +      +
    507C  ARG*     4.8    10.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 479 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    472C  ARG*     3.4    43.5    -      -       +      +
    473C  ARG      3.5    11.0    -      -       -      +
    474C  VAL*     3.8    19.7    -      -       +      +
    478C  VAL*     1.3    73.4    -      -       -      +
    480C  THR*     1.3    66.0    +      -       -      +
    503C  LEU*     4.4    13.7    -      -       +      -
    506C  ASN*     3.0    43.8    +      -       -      +
    508C  ILE*     4.0    20.6    -      -       +      -
    532C  MET*     4.1    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 480 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    472C  ARG*     3.0    29.2    +      -       -      +
    473C  ARG*     2.9    38.2    +      -       +      +
    475C  VAL*     4.4    21.5    -      -       +      -
    478C  VAL*     3.7     8.5    +      -       +      +
    479C  VAL*     1.3    73.8    -      -       -      +
    481C  ASP*     1.3    61.7    +      -       -      +
    482C  GLU*     3.4    16.4    +      -       -      +
    506C  ASN*     4.8     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 481 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10C  ARG*     3.2    27.2    +      -       -      -
     12C  VAL*     3.8    12.7    -      -       +      +
     13C  ILE*     5.7     0.5    -      -       -      +
    472C  ARG*     4.0    10.8    +      -       -      +
    480C  THR*     1.3    75.8    -      -       -      +
    482C  GLU*     1.3    61.8    +      -       -      +
    483C  VAL*     3.5    14.3    +      -       -      +
    506C  ASN*     4.1    15.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 482 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    472C  ARG*     3.7     3.1    -      -       -      -
    473C  ARG*     2.7    73.3    +      -       -      +
    480C  THR*     3.4    11.0    +      -       -      +
    481C  ASP*     1.3    76.3    -      -       -      +
    483C  VAL*     1.3    63.8    +      -       -      +
    484C  VAL*     4.1    13.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 483 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12C  VAL*     4.0    16.2    -      -       +      -
     13C  ILE*     3.8    35.2    -      -       +      -
    470C  PRO*     3.5    31.4    -      -       +      -
    471C  TYR      3.5     8.5    -      -       -      +
    472C  ARG*     4.5     5.2    -      -       +      -
    481C  ASP      3.5    12.3    +      -       -      +
    482C  GLU*     1.3    80.0    -      -       -      +
    484C  VAL*     1.3    69.0    +      -       -      +
    485C  TYR*     4.2     9.7    +      -       +      -
    534C  VAL*     4.3     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 484 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    469C  THR      3.6     0.5    -      -       -      +
    470C  PRO*     3.6     2.0    -      -       -      +
    471C  TYR*     2.9    35.8    +      -       -      +
    473C  ARG*     4.0    14.6    -      -       -      +
    482C  GLU*     4.2    16.8    -      -       +      +
    483C  VAL*     1.3    76.8    -      -       -      +
    485C  TYR*     1.3    68.1    +      -       -      +
    486C  MET*     3.6    33.4    +      -       +      +
    490C  GLU*     4.6     7.6    -      -       -      +
    531C  PHE*     4.0    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 485 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13C  ILE*     4.0    19.8    -      -       +      +
     16C  PRO*     3.7     8.5    -      -       -      +
    458C  TYR*     3.3    27.1    +      -       -      -
    460C  ARG*     3.0    50.3    +      -       +      -
    468C  ARG*     3.1    39.7    +      -       +      +
    469C  THR      3.7     4.3    -      -       -      -
    470C  PRO*     3.3    30.6    -      -       +      +
    483C  VAL*     4.2     7.2    +      -       +      -
    484C  VAL*     1.3    77.9    -      -       -      +
    486C  MET*     1.3    59.7    +      -       -      +
    490C  GLU*     4.4     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 486 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    437C  ARG*     3.4     5.9    +      -       -      +
    468C  ARG*     3.0    23.5    -      -       -      -
    469C  THR      3.1    17.2    +      -       -      +
    471C  TYR*     4.0    17.7    -      -       +      -
    484C  VAL*     3.8    24.2    -      -       +      +
    485C  TYR*     1.3    76.8    -      -       -      +
    487C  THR*     1.3    70.0    +      -       -      +
    490C  GLU*     4.1    14.1    -      -       -      +
    491C  GLU*     3.7    28.5    -      -       +      +
    494C  TYR*     3.3    30.5    -      -       +      -
    496C  ILE*     5.9     1.6    -      -       -      -
    531C  PHE*     3.4    35.0    -      -       +      -
----------------------------------------------------------
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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