Contacts of the strand formed by residues 431 - 435 (chain A) in PDB entry 1FLL


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 431 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429A  LYS*     4.6     8.1    -      -       -      +
    430A  VAL*     1.3    68.1    -      -       -      +
    432A  LEU*     1.3    60.8    +      -       -      +
    433A  MET*     3.7    25.1    -      -       +      +
    445A  GLY      5.1     1.3    -      -       -      +
    446A  ASP*     4.0    15.9    -      -       -      +
    447A  ALA*     3.2    18.7    -      -       +      +
    493A  LYS      3.6     3.3    -      -       -      +
    494A  VAL*     3.6     5.2    -      -       -      -
    495A  ILE*     2.7    54.5    +      -       +      +
    497A  ASP*     5.5     1.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 432 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409A  LEU*     3.4    43.3    -      -       +      +
    410A  PHE*     4.2     1.3    -      -       -      +
    411A  PHE*     3.7    24.5    -      -       +      +
    430A  VAL*     3.5    33.2    -      -       +      +
    431A  THR*     1.3    67.5    -      -       -      +
    433A  MET*     1.3    52.1    +      -       -      +
    445A  GLY*     2.7    29.2    -      -       -      -
    446A  ASP      2.4    30.5    +      -       -      +
    448A  PHE*     4.1    18.6    -      -       +      -
    469A  GLY*     4.2     3.8    -      -       -      -
    470A  CYS*     4.8     7.2    -      -       -      +
    473A  PHE*     3.3     8.6    -      -       +      -
    492A  ILE*     6.2     0.2    -      -       -      -
    493A  LYS      4.1     2.2    -      -       -      -
    494A  VAL*     4.5    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 433 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    431A  THR*     3.7    17.9    -      -       -      +
    432A  LEU*     1.3    73.5    -      -       -      +
    434A  LEU*     1.3    54.9    +      -       -      +
    435A  MET*     5.0     0.4    -      -       -      -
    443A  HIS*     3.3    37.9    -      -       +      +
    444A  LEU      3.0    10.8    -      -       -      +
    445A  GLY*     4.2     2.9    -      -       -      -
    473A  PHE*     3.9     4.0    -      -       -      -
    492A  ILE*     2.8    29.8    -      -       -      +
    493A  LYS*     3.0    71.7    +      -       +      +
    495A  ILE*     3.4    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 434 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    396A  LEU*     6.4     0.2    -      -       +      -
    407A  LEU*     5.7     7.9    -      -       +      -
    433A  MET*     1.3    72.1    -      -       -      +
    435A  MET*     1.3    66.5    +      -       -      +
    436A  ASP      3.7     2.1    +      -       -      -
    442A  ARG      4.2     2.4    -      -       -      +
    443A  HIS*     3.6    20.3    -      -       -      -
    444A  LEU*     2.5    16.8    +      -       +      +
    473A  PHE*     3.5    19.3    -      -       +      -
    474A  VAL*     4.1    24.7    -      -       +      -
    479A  LEU*     4.8     8.1    -      -       +      -
    484A  TYR*     3.8    42.6    -      -       +      -
    490A  ILE*     4.9    16.8    -      -       +      -
    491A  PHE      3.5    18.6    -      -       -      +
    492A  ILE*     4.6    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 435 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  ILE*     4.5     8.3    -      -       +      -
    433A  MET*     5.0     0.2    -      -       -      -
    434A  LEU*     1.3    78.0    -      -       -      +
    436A  ASP*     1.3    68.3    +      -       -      +
    437A  GLN*     4.1     1.0    +      -       -      +
    443A  HIS*     3.0    48.7    -      -       +      +
    484A  TYR*     4.6     4.7    -      -       -      +
    490A  ILE*     4.9     0.3    -      -       -      -
    491A  PHE*     2.6    51.4    +      -       +      +
    492A  ILE      4.3     1.8    -      -       -      -
    493A  LYS*     3.6    43.5    -      -       +      +
----------------------------------------------------------
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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