Contacts of the strand formed by residues 395 - 399 (chain A) 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 PHE 395 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  ILE*     4.4     7.9    -      -       +      -
    303A  ILE*     3.8    33.9    -      -       +      -
    306A  LYS*     3.9    31.2    -      -       +      -
    307A  LEU*     4.8     6.5    -      -       +      -
    320A  GLN      3.2    11.3    +      -       -      -
    321A  VAL*     3.3    28.8    -      -       +      +
    322A  VAL      2.9    25.8    +      -       -      +
    393A  THR*     3.4     4.4    -      -       -      +
    394A  ARG*     1.3   103.8    -      -       +      +
    396A  VAL*     1.3    62.0    +      -       -      +
    397A  VAL*     4.0     1.1    -      -       +      -
    427A  GLN*     3.1    43.1    -      -       +      -
    429A  LEU*     4.7     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 396 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322A  VAL*     3.5    13.7    -      -       +      +
    324A  VAL*     5.9     1.3    -      -       +      -
    393A  THR*     3.7    19.7    -      -       +      -
    395A  PHE*     1.3    75.2    -      -       -      +
    397A  VAL*     1.3    61.5    +      -       -      +
    398A  LEU*     4.5    14.4    -      -       +      -
    416A  ILE*     5.9     3.8    -      -       +      -
    417A  MET*     4.4    25.1    -      -       +      -
    422A  MET*     4.0    17.9    -      -       +      -
    426A  HIS*     4.0    19.7    -      -       +      +
    427A  GLN      2.9    10.5    +      -       -      +
    428A  THR*     3.3    11.3    -      -       +      +
    429A  LEU*     2.8    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 397 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  PHE*     3.9    36.3    -      -       +      -
    303A  ILE*     3.5    32.1    -      -       +      -
    321A  VAL*     4.8     2.9    -      -       +      -
    322A  VAL      2.9     8.2    +      -       -      +
    323A  ILE*     3.4    21.9    -      -       +      -
    324A  VAL*     2.9    26.5    +      -       -      +
    396A  VAL*     1.3    80.9    -      -       -      +
    398A  LEU*     1.3    74.2    +      -       -      +
    399A  ASP      3.9     0.2    +      -       -      -
    429A  LEU*     3.3    23.6    -      -       +      +
    431A  PHE*     4.6     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 398 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    324A  VAL*     4.0    16.6    -      -       +      -
    396A  VAL*     4.5    13.9    -      -       +      +
    397A  VAL*     1.3    81.0    -      -       -      +
    399A  ASP*     1.3    63.0    +      -       -      +
    401A  ALA*     3.3    17.0    -      -       +      +
    404A  MET*     4.4     7.4    -      -       +      -
    405A  LEU*     4.1    26.5    -      -       +      -
    413A  MET*     3.7    28.5    -      -       +      -
    416A  ILE*     6.5     0.2    -      -       +      -
    417A  MET*     3.9    24.9    -      -       +      -
    428A  THR*     5.5     1.6    -      -       +      -
    429A  LEU      2.8    11.8    +      -       -      +
    430A  MET*     3.6    17.9    -      -       +      -
    431A  PHE      3.2    23.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 399 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  LYS*     5.5     2.3    -      -       -      +
    296A  THR*     5.1     1.7    +      -       -      -
    299A  PHE*     4.3    20.2    -      -       +      -
    323A  ILE*     4.9     1.6    -      -       +      -
    324A  VAL      3.1    18.2    +      -       -      +
    325A  SER*     5.2     0.7    -      -       -      -
    326A  PRO*     4.0     1.9    -      -       -      +
    330A  LEU*     4.2     7.9    -      -       +      +
    334A  ILE*     3.4    31.7    -      -       +      +
    397A  VAL*     3.8     3.9    +      -       -      +
    398A  LEU*     1.3    71.0    -      -       -      +
    400A  GLU*     1.3    89.9    +      -       +      +
    401A  ALA      2.9     1.4    +      -       -      -
    404A  MET*     3.5    11.3    -      -       -      +
    431A  PHE*     3.9    16.9    -      -       -      +
    432A  SER*     5.4     0.7    -      -       -      -
   2801A   MG      3.4    24.9    -      -       -      -
----------------------------------------------------------
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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