Contacts of the strand formed by residues 613 - 619 (chain D) in PDB entry 5ON2


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 613 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    573D  ALA      3.8     0.2    -      -       -      +
    574D  PHE*     3.5     6.1    -      -       -      -
    575D  TYR*     2.7    75.7    +      -       +      +
    576D  TYR*     5.2     2.0    -      -       -      -
    577D  VAL*     5.9     2.9    -      -       +      +
    611D  GLU      4.7     4.9    -      -       -      +
    612D  LEU*     1.3    79.4    -      -       -      +
    614D  TYR*     1.3    69.5    +      -       -      +
    615D  THR*     5.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 614 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572D  ASP*     2.8    37.9    +      -       +      -
    573D  ALA      3.9     4.7    -      -       -      -
    574D  PHE*     3.5    27.6    -      +       +      -
    601D  ILE*     3.8    42.7    -      -       +      +
    612D  LEU      4.3     0.4    -      -       -      -
    613D  VAL*     1.3    78.2    -      -       -      +
    615D  THR*     1.3    63.9    +      -       -      +
    616D  GLY*     3.5    35.6    +      -       -      -
    617D  MET*     3.7     8.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 615 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    573D  ALA*     2.7    36.3    +      -       -      +
    575D  TYR*     3.5    37.2    -      -       +      -
    583D  ARG*     5.0     4.3    -      -       -      +
    585D  TRP*     3.6    14.8    -      -       +      -
    613D  VAL*     5.2     1.1    -      -       +      -
    614D  TYR*     1.3    73.7    -      -       -      +
    616D  GLY*     1.3    63.8    +      -       -      +
    618D  SER*     4.8     6.4    -      -       -      -
    624D  LYS*     4.8     9.7    +      -       -      -
     69E    G      4.9     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 616 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    571D  ALA      3.8     0.2    -      -       -      +
    573D  ALA*     3.5    19.9    +      -       -      +
    614D  TYR*     3.5    32.5    -      -       -      -
    615D  THR*     1.3    80.9    -      -       -      +
    617D  MET*     1.3    60.8    +      -       -      -
    618D  SER      3.1     7.4    +      -       -      -
     69E    G      3.3    11.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 617 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    570D  LEU*     4.2    14.4    -      -       +      +
    571D  ALA*     3.6    31.0    -      -       -      -
    572D  ASP*     3.7    19.7    -      -       -      +
    595D  ARG*     5.7     3.8    -      -       -      +
    614D  TYR*     3.7    11.0    +      -       -      +
    616D  GLY*     1.3    67.0    -      -       -      -
    618D  SER*     1.3    60.3    +      -       -      +
    657D  GLU*     3.5    52.0    -      -       +      +
    658D  TRP      5.5     4.0    -      -       -      +
     68E    C      5.1     3.8    -      -       -      +
     69E    G      2.9    42.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 618 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    570D  LEU*     3.4     5.0    -      -       -      -
    571D  ALA      2.8    31.1    +      -       -      +
    573D  ALA*     3.4    24.5    -      -       -      +
    615D  THR      4.8     3.8    -      -       -      -
    616D  GLY      3.1     4.9    +      -       -      -
    617D  MET*     1.3    74.6    -      -       -      +
    619D  LYS*     1.3    64.2    +      -       -      +
    624D  LYS*     3.6    29.1    -      -       -      +
    626D  ASN*     3.5     8.3    +      -       -      -
     70E    G      3.4    14.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 619 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    532D  GLU*     2.8    27.4    +      -       -      +
    568D  MET*     4.6    11.2    -      -       +      -
    569D  VAL      4.1     2.0    -      -       -      +
    570D  LEU*     3.9    12.8    -      -       +      +
    618D  SER*     1.3    78.5    +      -       -      +
    620D  MET*     1.3    68.0    +      -       -      +
    621D  SER*     3.4    19.0    +      -       -      +
    624D  LYS*     5.2     2.8    -      -       -      +
    626D  ASN*     3.2    12.6    +      -       -      +
    901D  LSS      3.9    13.0    -      -       -      +
     70E    G      3.2    24.9    +      -       -      +
     71E    G      2.8    29.8    +      -       -      +
     75E    C      3.4    25.8    +      -       -      +
     76E    A      4.2     1.4    +      -       -      -
----------------------------------------------------------
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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