Contacts of the strand formed by residues 395 - 399 (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 PHE 395 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279B  ILE*     4.2     8.7    -      -       +      -
    303B  ILE*     3.6    37.9    -      -       +      -
    306B  LYS*     3.8    31.0    -      -       +      -
    307B  LEU*     4.3    13.5    -      -       +      -
    320B  GLN      3.3     1.2    +      -       -      -
    321B  VAL*     3.4    30.4    -      -       +      -
    322B  VAL      2.9    25.3    +      -       -      -
    393B  THR*     3.2     7.3    -      -       -      +
    394B  ARG*     1.3   103.1    -      -       +      +
    396B  VAL*     1.3    63.0    +      -       -      +
    397B  VAL*     4.1     2.0    -      -       +      -
    427B  GLN*     3.1    44.2    -      -       +      +
    429B  LEU*     4.3     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 396 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322B  VAL*     3.3    17.5    -      -       +      +
    324B  VAL*     5.7     1.6    -      -       +      -
    393B  THR*     3.6    17.3    -      -       +      -
    395B  PHE*     1.3    79.2    -      -       -      +
    397B  VAL*     1.3    64.2    +      -       -      +
    398B  LEU*     4.3    11.4    -      -       +      -
    416B  ILE*     5.4     4.0    -      -       +      -
    417B  MET*     3.5    33.4    -      -       +      -
    422B  MET*     4.1    17.9    -      -       +      -
    426B  HIS*     3.9    20.0    -      -       +      +
    427B  GLN      3.0     8.3    +      -       -      +
    428B  THR*     3.4     5.4    -      -       +      +
    429B  LEU*     3.0    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 397 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299B  PHE*     3.9    32.1    -      -       +      -
    303B  ILE*     3.6    31.2    -      -       +      -
    322B  VAL      2.7    10.9    +      -       -      +
    323B  ILE*     3.4    35.2    -      -       +      -
    324B  VAL*     2.9    28.6    +      -       -      +
    395B  PHE*     4.9     1.8    -      -       +      -
    396B  VAL*     1.3    78.8    -      -       -      +
    398B  LEU*     1.3    75.8    +      -       -      +
    429B  LEU*     3.5    15.9    -      -       +      +
    431B  PHE*     4.7     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 398 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    324B  VAL*     4.2     9.9    -      -       +      -
    396B  VAL*     4.3    17.9    -      -       +      -
    397B  VAL*     1.3    83.1    -      -       -      +
    399B  ASP*     1.3    62.0    +      -       -      +
    401B  ALA*     3.5    16.1    -      -       +      +
    404B  MET*     4.3     8.7    -      -       +      -
    405B  LEU*     4.2    17.9    -      -       +      -
    413B  MET*     3.9    39.0    -      -       +      -
    417B  MET*     4.6     6.7    -      -       -      -
    428B  THR*     5.2     4.5    -      -       +      -
    429B  LEU      2.8    11.7    +      -       -      +
    430B  MET*     3.6    29.9    -      -       +      -
    431B  PHE*     3.1    23.9    +      -       -      +
    446B  PHE*     5.4     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 399 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295B  LYS*     5.3     3.5    -      -       -      +
    296B  THR*     4.7     1.2    +      -       -      -
    299B  PHE*     4.1    21.7    -      -       +      -
    323B  ILE*     4.9     1.6    -      -       +      -
    324B  VAL      3.2    18.1    +      -       -      +
    325B  SER*     5.2     1.8    -      -       -      -
    326B  PRO*     4.0     2.3    -      -       -      +
    330B  LEU*     4.2     7.4    -      -       +      +
    334B  ILE*     3.2    32.2    -      -       +      +
    397B  VAL*     3.8     4.3    -      -       -      +
    398B  LEU*     1.3    71.2    -      -       -      +
    400B  GLU*     1.3    90.0    +      -       +      +
    401B  ALA      3.0     1.9    +      -       -      -
    404B  MET*     3.3    12.5    -      -       -      +
    431B  PHE*     4.0    16.5    -      -       -      +
    432B  SER*     5.4     0.2    -      -       -      -
   2802B   MG      3.6    23.5    -      -       -      -
----------------------------------------------------------
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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