Contacts of the strand formed by residues 479 - 484 (chain B) in PDB entry 1F1J


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 LYS 479 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    437B  PHE*     3.7     9.2    -      -       +      -
    466B  PHE*     3.0    39.9    -      -       +      +
    468B  GLY*     4.9     5.7    -      -       -      +
    474B  LEU*     3.0    39.8    +      -       +      -
    475B  LEU*     4.4     2.2    -      -       -      +
    476B  GLU      4.4     3.0    -      -       -      +
    477B  LYS      2.6    28.2    +      -       -      +
    478B  PRO*     1.3    74.0    -      -       -      +
    480B  LEU*     1.3    62.1    +      -       -      +
    481B  PHE*     3.3    27.4    -      -       +      -
    517B  ALA      3.9    10.7    +      -       -      -
    518B  ASP*     3.0    16.7    +      -       -      +
    519B  PHE*     3.6    24.9    -      -       +      -
    520B  LEU      3.3    16.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 480 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401B  PHE*     5.8     0.2    -      -       +      -
    406B  PHE*     4.9     2.0    -      -       +      -
    436B  CYS*     5.0     2.0    -      -       -      -
    437B  PHE*     3.0    15.3    +      -       -      +
    438B  ALA*     3.2    10.8    -      -       +      -
    439B  CYS      3.1    22.3    +      -       -      -
    478B  PRO*     4.0    14.6    -      -       +      -
    479B  LYS*     1.3    75.5    -      -       -      +
    481B  PHE*     1.3    66.9    +      -       -      +
    482B  PHE*     3.8    28.3    -      -       +      -
    520B  LEU*     3.6    26.9    -      -       +      +
    558B  ILE*     5.1     4.3    -      -       +      -
    595B  LEU*     4.8     3.1    -      -       +      -
    599B  LEU*     3.7    24.0    -      -       +      -
    601B  PHE*     3.5    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 481 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    423B  LEU*     5.2     2.0    -      -       +      -
    437B  PHE*     4.3     7.0    -      +       -      -
    439B  CYS*     3.2    36.8    -      -       +      +
    441B  LEU*     5.4     6.1    -      -       +      -
    462B  LEU*     5.1     1.1    -      -       +      -
    463B  THR*     3.6    29.2    -      -       +      -
    466B  PHE*     3.7    35.0    -      +       -      -
    479B  LYS*     3.3    35.4    -      -       +      -
    480B  LEU*     1.3    73.3    -      -       -      +
    482B  PHE*     1.3    63.5    +      -       -      +
    483B  ILE*     4.1     8.7    -      -       +      -
    519B  PHE*     3.7    18.8    -      +       -      -
    520B  LEU*     2.9     7.1    +      -       -      +
    521B  PHE*     3.4    29.7    -      +       +      -
    522B  ALA*     2.9    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 482 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401B  PHE*     3.9    23.3    -      +       -      -
    438B  ALA*     4.8     1.8    -      -       +      -
    439B  CYS      2.8     8.7    +      -       -      +
    440B  ILE*     3.1    32.7    -      -       +      +
    441B  LEU      2.8    25.8    +      -       -      +
    480B  LEU*     3.8    36.1    -      -       +      -
    481B  PHE*     1.3    75.5    -      -       -      +
    483B  ILE*     1.3    63.8    +      -       -      +
    484B  GLN      4.2     0.4    -      -       -      -
    520B  LEU*     5.1     3.8    -      -       +      -
    522B  ALA*     3.4    28.9    -      -       +      +
    541B  PHE*     4.5     8.3    -      +       +      -
    545B  LEU*     3.8    39.3    -      -       +      -
    549B  LEU*     5.8     1.3    -      -       +      -
    558B  ILE*     4.7    12.3    -      -       +      -
    562B  LEU*     4.2     9.9    -      -       +      -
    601B  PHE*     5.7     1.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 483 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    441B  LEU*     3.6    30.1    -      -       +      -
    450B  ILE*     4.4     2.5    -      -       +      -
    459B  ILE*     4.3    21.1    -      -       +      -
    481B  PHE*     4.3     9.0    -      -       +      +
    482B  PHE*     1.3    79.9    -      -       -      +
    484B  GLN*     1.3    60.9    +      -       -      +
    485B  ALA*     3.9    21.9    +      -       +      +
    487B  ARG*     6.5     0.2    -      -       +      -
    521B  PHE*     4.2    22.7    -      -       +      -
    522B  ALA      2.9     9.9    +      -       -      +
    523B  TYR*     3.4    45.1    -      -       +      +
    524B  SER*     2.9    29.5    +      -       -      -
    541B  PHE*     3.9     4.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 484 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387B  ARG*     3.8    14.8    -      -       -      +
    393B  ASP*     4.9     0.4    -      -       -      +
    440B  ILE*     6.1     0.2    -      -       +      -
    441B  LEU      2.8    14.2    +      -       -      +
    442B  LEU*     3.8    16.4    -      -       +      -
    443B  SER      2.9    26.2    +      -       -      +
    482B  PHE      4.2     0.4    -      -       -      -
    483B  ILE*     1.3    71.6    -      -       -      +
    485B  ALA*     1.3    58.8    +      -       -      +
    524B  SER*     3.2    21.2    -      -       -      -
    531B  SER*     3.4    19.4    +      -       -      -
    532B  TRP      4.1     5.4    +      -       -      +
    539B  SER*     3.4    28.4    -      -       -      +
    541B  PHE*     3.5    17.3    +      -       +      +
    542B  VAL*     4.4     6.7    -      -       +      -
    587B  GLN*     4.9     0.2    +      -       -      -
    805D  ASJ      2.6    28.1    +      -       -      -
----------------------------------------------------------
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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