Contacts of the strand formed by residues 143 - 147 (chain F) in PDB entry 2NVX


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 143 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70F  LYS      4.9     4.0    -      -       -      -
     72F  LYS*     3.4    31.0    -      -       +      -
     73F  ALA*     2.9    49.5    +      -       +      +
     74F  ILE*     3.6     9.3    -      -       -      +
    135F  ARG*     3.7    47.6    -      -       +      -
    136F  ARG      2.8    19.3    -      -       -      +
    137F  TYR*     3.6    31.0    -      +       +      -
    138F  LEU*     6.1     0.2    -      -       -      -
    141F  GLY      4.1     4.5    -      -       -      -
    142F  SER*     1.3    72.8    -      -       -      +
    144F  GLU*     1.3    63.4    +      -       -      +
    145F  ASP*     3.9     8.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 144 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74F  ILE*     3.6    27.2    -      -       +      +
     78F  GLN      3.3    23.0    -      -       -      +
     79F  ARG*     3.3    20.4    -      -       +      +
     80F  ALA*     3.7     6.0    +      -       -      +
     81F  THR*     2.4    40.4    +      -       -      +
    134F  ILE      3.6     1.0    -      -       -      +
    136F  ARG*     2.8    34.1    +      -       +      +
    138F  LEU*     5.3    12.6    -      -       +      -
    143F  PHE*     1.3    73.9    -      -       -      +
    145F  ASP*     1.3    62.9    +      -       -      +
    146F  TRP*     3.3    24.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 145 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1444A  MET*     4.2     9.0    -      -       -      +
     74F  ILE      5.6     1.6    +      -       -      -
     79F  ARG*     2.8    37.3    +      -       -      +
    133F  VAL*     4.1    17.2    -      -       +      +
    134F  ILE      3.3     5.4    -      -       -      +
    135F  ARG*     3.1    41.1    +      -       -      +
    143F  PHE*     3.9     9.2    +      -       -      -
    144F  GLU*     1.3    72.4    -      -       -      +
    146F  TRP*     1.3    55.6    +      -       -      +
    150F  GLU*     4.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 146 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79F  ARG*     3.4    40.8    -      -       +      +
     81F  THR*     4.1    14.7    -      -       -      -
     83F  PRO*     4.0    26.7    -      -       +      -
    133F  VAL*     4.4     3.6    -      -       -      +
    134F  ILE*     2.7    45.5    +      -       +      +
    136F  ARG*     3.1    37.2    -      -       -      +
    144F  GLU*     3.3    42.0    +      -       -      +
    145F  ASP*     1.3    74.5    -      -       -      +
    147F  SER*     1.3    61.4    +      -       -      +
    150F  GLU*     3.3    43.5    -      -       +      -
    151F  LEU*     3.7    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 147 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132F  LEU      3.9     8.1    -      -       -      -
    133F  VAL*     4.4    14.3    -      -       -      +
    145F  ASP      4.4     0.2    -      -       -      -
    146F  TRP*     1.3    74.1    -      -       -      +
    148F  VAL*     1.3    59.1    +      -       -      +
    149F  GLU*     2.9    24.5    +      -       -      +
    150F  GLU*     3.4    32.8    +      -       -      +
    151F  LEU*     2.9    21.9    -      -       -      +
----------------------------------------------------------
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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