Contacts of the strand formed by residues 440 - 443 (chain A) in PDB entry 4FDI


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 LEU 440 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399A  LYS      3.5     1.7    -      -       -      +
    400A  ALA*     3.4     0.3    -      -       -      -
    401A  HIS*     2.7    49.1    +      -       +      +
    404A  THR*     4.2    11.9    -      -       +      -
    426A  GLY      3.5    24.9    -      -       -      +
    427A  VAL*     4.0    15.5    -      -       +      -
    435A  HIS*     3.5    40.1    -      -       +      +
    438A  LEU      3.5     5.8    +      -       -      +
    439A  PRO*     1.3    69.2    -      -       -      +
    441A  ILE*     1.3    59.7    +      -       -      +
    442A  PHE*     4.2     9.6    -      -       +      -
    453A  PRO*     4.7    15.9    -      -       +      -
    456A  PHE*     4.1    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 441 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398A  HIS*     4.1    12.6    -      -       +      -
    399A  LYS      3.1     7.9    -      -       -      +
    400A  ALA*     3.6    25.4    -      -       +      -
    439A  PRO      3.4     4.4    +      -       -      +
    440A  LEU*     1.3    74.8    -      -       -      +
    442A  PHE*     1.3    70.2    +      -       -      +
    453A  PRO*     3.6     4.2    -      -       -      +
    454A  LEU*     2.8    52.8    +      -       +      +
    456A  PHE*     5.6     0.2    -      -       -      -
    461A  TYR*     3.5    40.1    -      -       +      +
    464A  ALA*     4.1     7.6    -      -       +      -
    465A  LEU*     3.8    35.7    -      -       +      +
    468A  ILE*     5.0     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 442 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398A  HIS*     3.3     8.3    -      -       -      -
    399A  LYS*     2.8    33.9    +      -       +      +
    401A  HIS*     3.4    38.6    -      +       -      -
    427A  VAL*     3.8    30.3    -      -       +      -
    440A  LEU*     4.1    13.0    -      -       +      -
    441A  ILE*     1.3    73.4    -      -       -      +
    443A  HIS*     1.3    64.1    +      -       -      +
    444A  LEU*     3.7     7.4    +      -       +      -
    447A  ASP*     3.5    22.0    -      -       -      +
    450A  GLU*     3.4    44.2    -      -       +      -
    452A  PHE      3.8     1.1    -      -       -      -
    453A  PRO*     3.4    35.4    -      -       +      -
    454A  LEU*     4.0     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 443 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397A  GLN*     3.5    31.0    -      -       +      +
    398A  HIS*     3.5    18.6    -      +       +      -
    442A  PHE*     1.3    70.3    -      -       -      +
    444A  LEU*     1.3    58.7    +      -       -      +
    445A  GLY*     3.3     4.0    +      -       -      -
    446A  ARG*     3.1    52.7    +      -       +      +
    447A  ASP*     2.8    33.5    +      -       +      +
    454A  LEU*     3.6     8.3    -      -       +      +
    460A  GLU*     3.4    22.2    -      -       -      +
    250B  GLN*     3.2    29.4    +      -       -      -
----------------------------------------------------------
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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