Contacts of the strand formed by residues 435 - 440 (chain A) in PDB entry 2FY5


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 THR 435 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418A  GLN*     4.9     1.1    -      -       -      +
    422A  GLN*     3.3    24.9    +      -       -      +
    433A  VAL*     2.8    14.8    +      -       -      +
    434A  PRO*     1.3    74.4    +      -       -      +
    436A  TYR*     1.3    72.6    +      -       -      +
    451A  ASN*     3.9     5.7    +      -       -      -
    452A  ILE      3.8     0.8    -      -       -      +
    453A  ARG*     3.7    25.9    -      -       -      +
    454A  SER*     4.6     8.7    -      -       -      -
    455A  ALA*     3.8    13.6    -      -       -      +
    535A  PHE*     4.0     4.6    -      -       -      -
    537A  LEU*     3.1    39.4    -      -       +      +
    539A  THR*     4.4     7.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 436 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  TRP*     5.1     1.9    +      -       -      -
     84A  MET*     4.7    26.6    -      -       +      +
    435A  THR*     1.3    77.2    -      -       -      +
    437A  GLU*     1.3    59.0    +      -       -      +
    438A  SER*     3.4    30.8    +      -       -      -
    449A  VAL*     3.6    26.5    -      -       -      +
    450A  ASP      4.5     2.1    +      -       -      -
    451A  ASN*     3.0    36.1    -      -       +      -
    452A  ILE      4.0     0.2    -      -       -      -
    503A  ASP*     5.4     0.2    -      -       -      -
    535A  PHE*     3.5    42.6    -      +       +      -
    537A  LEU      2.9     9.0    +      -       -      +
    538A  SER*     4.1    15.7    -      -       -      +
    539A  THR*     2.7    40.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 437 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    414A  ASP*     2.5    32.4    -      -       -      +
    418A  GLN*     2.9    34.5    -      -       -      +
    436A  TYR*     1.3    76.2    -      -       -      +
    438A  SER*     1.3    71.0    +      -       -      +
    439A  ALA      3.2     1.4    +      -       -      -
    451A  ASN*     2.9     9.4    +      -       -      +
    452A  ILE*     3.1    47.3    +      -       +      +
    454A  SER*     4.1     0.7    -      -       -      +
    489A  GLN*     3.0    16.5    +      -       -      -
    493A  THR*     4.7     0.2    +      -       -      -
    539A  THR*     3.3    18.8    -      -       -      +
    540A  SER*     4.7     2.9    -      -       -      -
    541A  GLN*     5.4     0.7    -      -       -      +
    564A  TYR*     3.5     2.4    +      -       -      +
   2000A  SOP      3.9    10.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 438 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    436A  TYR*     3.4    23.9    +      -       -      -
    437A  GLU*     1.3    77.0    -      -       -      +
    439A  ALA*     1.3    59.2    +      -       -      +
    440A  SER      4.0     0.2    -      -       -      -
    449A  VAL*     4.7     8.1    -      -       -      +
    450A  ASP      4.3     2.5    -      -       -      -
    539A  THR      3.3     5.5    +      -       -      -
    540A  SER*     3.5    19.4    -      -       -      -
    541A  GLN      5.3     0.3    +      -       -      -
   2000A  SOP      3.5    57.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 439 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    437A  GLU      3.2     0.4    +      -       -      -
    438A  SER*     1.3    71.4    -      -       -      +
    440A  SER*     1.3    63.0    +      -       -      +
    441A  ILE*     4.4     0.4    -      -       +      +
    449A  VAL*     3.1     6.0    -      -       -      +
    450A  ASP      2.9    42.6    +      -       -      +
    452A  ILE*     3.4    34.3    -      -       +      -
    496A  ALA*     3.8    15.5    -      -       +      +
    497A  ILE*     4.1     9.2    -      -       +      +
   2000A  SOP      3.8     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 440 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  LEU*     6.0     0.3    -      -       -      +
    330A  ILE*     5.4     2.9    -      -       -      -
    438A  SER      4.0     1.0    -      -       -      -
    439A  ALA*     1.3    72.0    -      -       -      +
    441A  ILE*     1.3    61.2    +      -       -      +
    442A  ARG*     3.3    31.7    +      -       -      +
    443A  ARG*     5.5     2.8    +      -       -      +
    448A  ARG      3.7     7.4    -      -       -      -
    449A  VAL*     4.1     2.9    -      -       -      -
    497A  ILE*     3.7    21.3    -      -       -      +
   2000A  SOP      2.8    40.7    +      -       -      +
----------------------------------------------------------
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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