Contacts of the strand formed by residues 465 - 471 (chain D) in PDB entry 2DB3


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 465 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462D  CYS*     2.7    33.3    -      -       +      +
    463D  SER      3.0     2.6    -      -       -      +
    464D  ASP*     1.3    78.5    -      -       -      +
    466D  LYS*     1.3    64.8    +      -       -      +
    467D  GLN*     3.2    10.7    +      -       +      +
    577D  ILE*     3.7    40.4    -      -       +      +
    580D  THR*     4.6    11.7    -      -       -      +
    581D  GLY*     5.0     0.9    -      -       -      -
    587D  GLY      3.4    12.6    -      -       -      +
    588D  ARG*     4.0     3.4    -      -       -      +
    589D  ALA*     3.9    31.4    -      -       +      +
    614D  GLN*     3.4    11.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 466 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464D  ASP      3.7     3.2    +      -       -      +
    465D  VAL*     1.3    69.7    -      -       -      +
    467D  GLN*     1.3    68.8    +      -       -      +
    468D  THR*     4.0    10.5    +      -       -      +
    587D  GLY      2.9    15.0    +      -       -      +
    588D  ARG*     3.4    10.3    -      -       +      +
    589D  ALA      2.9    26.9    +      -       -      +
    614D  GLN*     3.5    12.6    -      -       -      +
    615D  THR*     5.3     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 467 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461D  ALA*     3.6    13.3    -      -       -      +
    462D  CYS      4.4     0.2    +      -       -      -
    465D  VAL*     3.3    20.4    +      -       +      +
    466D  LYS*     1.3    76.6    -      -       -      +
    468D  THR*     1.3    61.7    +      -       -      +
    469D  ILE*     4.3     0.9    +      -       -      +
    573D  TYR*     2.7    41.2    +      -       -      +
    577D  ILE*     3.5    18.7    -      -       +      +
    589D  ALA*     3.5     7.0    -      -       +      +
    608D  ILE*     4.0     3.5    -      -       -      +
    609D  LEU*     3.6    17.7    -      -       +      +
    612D  SER*     3.2    27.1    +      -       -      -
    614D  GLN*     2.7    37.5    +      -       +      +
    615D  THR*     4.8     9.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 468 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466D  LYS*     4.7    12.3    +      -       -      +
    467D  GLN*     1.3    75.5    +      -       -      +
    469D  ILE*     1.3    68.5    +      -       -      +
    470D  TYR*     3.9    33.7    -      -       +      +
    588D  ARG*     6.1     0.7    -      -       -      +
    589D  ALA      3.0    11.7    +      -       -      +
    590D  THR*     3.3    12.4    +      -       -      +
    591D  SER*     2.9    24.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 469 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467D  GLN      4.3     0.4    +      -       -      +
    468D  THR*     1.3    87.0    -      -       -      +
    470D  TYR*     1.3    69.6    +      -       -      +
    566D  MET*     5.8     0.4    -      -       -      -
    573D  TYR*     3.7    23.6    -      -       -      +
    591D  SER*     3.5    19.5    -      -       -      +
    593D  PHE*     3.9    17.5    -      -       +      -
    605D  LEU*     3.9    27.4    -      -       +      -
    609D  LEU*     4.1    26.9    -      -       +      -
    615D  THR      5.8     0.4    -      -       -      +
    617D  PRO*     4.0    19.8    -      -       +      +
    619D  PHE*     3.7    29.3    -      -       +      -
    620D  LEU*     4.4     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 470 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468D  THR*     3.9    22.1    -      -       +      +
    469D  ILE*     1.3    79.5    -      -       -      +
    471D  GLU*     1.3    59.1    +      -       -      +
    472D  VAL*     3.5    16.3    +      -       +      -
    480D  LYS*     3.8    34.1    +      -       -      -
    484D  ILE*     4.5     4.5    -      -       +      -
    590D  THR*     3.7    32.5    -      -       +      -
    591D  SER      2.8     9.4    +      -       -      +
    592D  PHE*     3.6     6.1    -      +       +      -
    593D  PHE*     2.7    34.8    +      -       -      +
    619D  PHE*     3.7     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 471 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    470D  TYR*     1.3    72.4    -      -       -      +
    472D  VAL*     1.3    61.9    +      -       -      +
    593D  PHE*     3.4     4.8    -      -       -      -
    595D  PRO*     3.4    34.7    -      -       +      +
    619D  PHE*     3.6    53.2    -      -       +      +
----------------------------------------------------------
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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