Contacts of the strand formed by residues 395 - 399 (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 PHE 395 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279D  ILE*     4.5     8.7    -      -       +      -
    303D  ILE*     3.8    35.7    -      -       +      -
    306D  LYS*     4.0    26.2    -      -       +      -
    307D  LEU*     4.2    16.8    -      -       +      -
    320D  GLN      3.2     3.6    +      -       -      -
    321D  VAL*     3.2    33.4    -      -       +      -
    322D  VAL      2.8    26.5    +      -       -      +
    393D  THR*     3.5     4.2    -      -       -      +
    394D  ARG*     1.3   104.3    -      -       +      +
    396D  VAL*     1.3    62.3    +      -       -      +
    397D  VAL*     4.0     1.6    -      -       +      -
    427D  GLN*     3.4    39.7    -      -       +      -
    429D  LEU*     4.7     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 396 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322D  VAL*     3.4    14.6    -      -       +      +
    324D  VAL*     5.9     1.6    -      -       +      -
    393D  THR*     3.8    19.1    -      -       +      -
    395D  PHE*     1.3    74.4    -      -       -      +
    397D  VAL*     1.3    58.5    +      -       -      +
    398D  LEU*     4.2    13.9    +      -       +      -
    416D  ILE*     5.9     4.7    -      -       +      -
    417D  MET*     4.4    24.5    -      -       +      -
    422D  MET*     4.0    13.5    -      -       +      -
    426D  HIS*     4.0    18.2    -      -       +      +
    427D  GLN      2.8    12.8    +      -       -      +
    428D  THR*     3.3    15.6    -      -       +      +
    429D  LEU*     2.8    32.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 397 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299D  PHE*     3.8    37.5    -      -       +      -
    303D  ILE*     3.5    31.0    -      -       +      -
    321D  VAL*     4.9     2.7    -      -       +      -
    322D  VAL      2.8     9.3    +      -       -      +
    323D  ILE*     3.3    24.7    -      -       +      -
    324D  VAL*     2.9    27.2    +      -       -      +
    395D  PHE*     5.0     0.2    -      -       +      -
    396D  VAL*     1.3    79.8    -      -       -      +
    398D  LEU*     1.3    74.0    +      -       -      +
    399D  ASP      3.9     0.4    +      -       -      +
    429D  LEU*     3.3    19.7    -      -       +      +
    431D  PHE*     4.8     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 398 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    324D  VAL*     4.1    14.6    -      -       +      -
    396D  VAL*     4.5    11.0    -      -       +      -
    397D  VAL*     1.3    81.6    -      -       -      +
    399D  ASP*     1.3    62.1    -      -       -      +
    401D  ALA*     3.5    10.4    -      -       +      +
    404D  MET*     4.3     7.2    -      -       +      -
    405D  LEU*     4.1    21.5    -      -       +      -
    413D  MET*     3.6    42.6    -      -       +      -
    417D  MET*     4.1    21.3    -      -       +      -
    428D  THR*     5.5     1.1    -      -       +      -
    429D  LEU      2.8     8.7    +      -       -      +
    430D  MET*     3.5    24.5    -      -       +      -
    431D  PHE*     3.1    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 399 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295D  LYS*     5.4     2.9    -      -       -      +
    296D  THR*     5.0     1.6    +      -       -      -
    299D  PHE*     4.3    20.5    -      -       +      -
    323D  ILE*     5.0     2.2    -      -       +      -
    324D  VAL      3.2    18.8    +      -       -      +
    325D  SER*     5.2     1.8    -      -       -      -
    326D  PRO*     4.0     1.6    -      -       -      +
    330D  LEU*     4.1     9.9    -      -       +      +
    334D  ILE*     3.2    30.6    -      -       +      +
    397D  VAL*     3.9     3.3    -      -       -      +
    398D  LEU*     1.3    69.7    -      -       -      +
    400D  GLU*     1.3    90.1    +      -       +      +
    401D  ALA      2.9     1.7    +      -       -      -
    404D  MET*     3.4    11.8    -      -       -      +
    431D  PHE*     3.9    17.0    -      -       -      +
    432D  SER*     5.5     0.3    -      -       -      -
   2804D   MG      3.6    24.3    -      -       -      -
----------------------------------------------------------
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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