Contacts of the strand formed by residues 465 - 471 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462B  CYS*     2.8    33.9    -      -       +      +
    463B  SER      3.1     2.4    -      -       -      -
    464B  ASP*     1.3    80.4    -      -       -      +
    466B  LYS*     1.3    63.5    +      -       -      +
    467B  GLN*     3.4    23.1    +      -       +      +
    577B  ILE*     4.0    20.4    -      -       +      +
    580B  THR*     3.6    37.0    -      -       +      +
    581B  GLY*     4.9     0.7    -      -       -      -
    587B  GLY*     3.2     7.9    -      -       -      +
    589B  ALA*     3.8    27.4    -      -       +      +
    614B  GLN*     3.5     7.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 466 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464B  ASP      4.1     1.4    +      -       -      -
    465B  VAL*     1.3    70.3    -      -       -      +
    467B  GLN*     1.3    69.7    +      -       -      +
    468B  THR*     4.0     7.8    +      -       -      +
    587B  GLY      3.0    11.9    +      -       -      +
    588B  ARG*     3.6     8.5    -      -       +      +
    589B  ALA      3.0    25.5    +      -       -      +
    613B  GLY      4.4     7.5    +      -       -      -
    614B  GLN*     3.2    27.8    +      -       -      +
    615B  THR*     4.7    19.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 467 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461B  ALA*     3.8     5.9    -      -       -      +
    465B  VAL*     3.5    22.2    +      -       +      +
    466B  LYS*     1.3    80.1    -      -       -      +
    468B  THR*     1.3    63.2    +      -       -      +
    469B  ILE*     4.3     2.3    +      -       +      +
    573B  TYR*     2.9    38.6    +      -       -      +
    577B  ILE*     3.5    23.8    -      -       +      +
    589B  ALA*     3.6     9.0    -      -       +      +
    608B  ILE*     3.7     6.4    -      -       -      +
    609B  LEU*     3.4    24.4    -      -       +      +
    612B  SER*     3.4    23.1    +      -       -      -
    614B  GLN*     2.7    31.1    +      -       -      +
    615B  THR*     4.8     7.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 468 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466B  LYS*     4.7     9.2    +      -       -      +
    467B  GLN*     1.3    73.6    +      -       -      +
    469B  ILE*     1.3    66.4    +      -       -      +
    470B  TYR*     3.7    40.6    +      -       +      +
    589B  ALA      2.9    12.4    +      -       -      +
    590B  THR*     3.5     8.8    -      -       -      +
    591B  SER      2.9    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 469 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467B  GLN      4.3     0.6    +      -       -      +
    468B  THR*     1.3    84.7    -      -       -      +
    470B  TYR*     1.3    65.3    +      -       -      +
    573B  TYR*     3.8    17.0    -      -       -      +
    589B  ALA      5.7     0.4    -      -       -      +
    591B  SER*     3.5    28.5    -      -       -      +
    593B  PHE*     3.7    27.4    -      -       +      +
    605B  LEU*     3.9    31.4    -      -       +      -
    609B  LEU*     4.3    22.2    -      -       +      -
    617B  PRO*     3.6    22.4    -      -       +      +
    619B  PHE*     3.2    25.9    -      -       +      -
    620B  LEU*     4.3     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 470 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468B  THR*     3.7    21.0    -      -       +      +
    469B  ILE*     1.3    78.6    -      -       -      +
    471B  GLU*     1.3    61.2    +      -       -      +
    472B  VAL*     4.0    15.0    -      -       +      -
    480B  LYS*     4.0    27.6    -      -       +      +
    484B  ILE*     4.6    10.8    -      -       +      -
    590B  THR*     3.8    31.9    -      -       +      -
    591B  SER      3.0     9.5    +      -       -      +
    592B  PHE*     3.9    11.3    -      +       +      -
    593B  PHE*     2.9    31.0    +      -       -      +
    619B  PHE*     3.7     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 471 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    470B  TYR*     1.3    71.2    -      -       -      +
    472B  VAL*     1.3    68.2    +      -       -      +
    480B  LYS*     5.0     3.8    -      -       -      -
    593B  PHE*     3.6     3.5    -      -       -      +
    595B  PRO*     3.2    35.8    -      -       +      +
    619B  PHE*     3.4    49.1    -      -       +      +
----------------------------------------------------------
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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