Contacts of the strand formed by residues 434 - 442 (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 ALA 434 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364B  PHE*     3.7     4.6    -      -       -      -
    366B  LYS*     3.1    10.8    -      -       +      +
    368B  GLY*     3.8    25.1    -      -       -      -
    369B  LYS      5.1     0.2    -      -       -      +
    431B  HIS*     2.6    31.8    +      -       +      +
    432B  THR      3.3     0.2    -      -       -      -
    433B  ASN*     1.3    74.9    -      -       -      +
    435B  ALA*     1.3    60.3    +      -       -      +
    436B  CYS      3.9     7.9    -      -       -      +
    477B  LYS*     2.7    33.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 435 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361B  ASN      4.5     1.4    -      -       -      +
    362B  MET*     3.6    42.3    -      -       +      +
    364B  PHE*     3.6    26.7    -      -       +      +
    366B  LYS      3.0    13.6    +      -       -      +
    367B  LEU*     3.2    12.1    +      -       +      +
    434B  ALA*     1.3    72.8    -      -       -      +
    436B  CYS*     1.3    63.9    +      -       -      +
    477B  LYS*     3.6    17.0    -      -       -      +
    478B  PRO*     3.7     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 436 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362B  MET*     5.1     1.1    -      -       +      -
    367B  LEU*     2.9    29.2    +      -       -      +
    368B  GLY*     3.4    11.8    -      -       -      -
    369B  LYS      4.1     0.9    +      -       -      -
    406B  PHE*     3.5    31.4    -      -       -      -
    431B  HIS*     4.8     0.9    +      -       -      -
    434B  ALA*     3.3     8.6    -      -       -      +
    435B  ALA*     1.3    81.0    -      -       +      +
    437B  PHE*     1.3    67.6    +      -       -      +
    474B  LEU*     3.9    11.9    -      -       -      +
    477B  LYS*     4.4     0.9    -      -       -      -
    478B  PRO*     3.3    31.0    -      -       +      +
    480B  LEU*     5.0     2.9    -      -       -      -
    599B  LEU*     5.2     1.8    -      -       -      -
    601B  PHE*     4.4     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 437 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369B  LYS*     3.7    37.9    -      -       +      -
    371B  ILE*     4.2    17.0    -      -       +      -
    423B  LEU*     4.7     0.4    -      -       +      -
    426B  ALA*     4.4     4.5    -      -       +      -
    431B  HIS*     3.9    12.6    -      +       -      +
    436B  CYS*     1.3    82.0    -      -       -      +
    438B  ALA*     1.3    96.3    +      -       -      +
    439B  CYS*     3.9    14.4    -      -       +      -
    466B  PHE*     3.6    42.0    -      +       -      -
    474B  LEU*     3.6    22.2    -      -       +      -
    478B  PRO      3.1     7.2    +      -       -      +
    479B  LYS*     4.7     7.0    -      -       +      -
    480B  LEU*     3.0    30.7    +      -       -      +
    481B  PHE*     4.3    10.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with ALA 438 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369B  LYS      3.1     6.1    +      -       -      +
    370B  CYS*     3.2    17.4    -      -       -      -
    371B  ILE      3.1    20.8    +      -       -      -
    401B  PHE*     4.5    10.1    -      -       +      -
    406B  PHE*     4.0    22.7    -      -       +      -
    437B  PHE*     1.3    90.5    -      -       -      +
    439B  CYS*     1.3    61.9    +      -       -      +
    440B  ILE*     5.5     0.2    -      -       +      -
    480B  LEU*     3.2    19.7    -      -       +      +
    482B  PHE*     4.8     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 439 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371B  ILE*     3.2    18.6    -      -       +      +
    373B  ILE*     4.9     0.7    -      -       -      -
    423B  LEU*     4.0    22.0    -      -       +      -
    437B  PHE*     3.9     9.2    -      -       +      -
    438B  ALA*     1.3    76.7    -      -       -      +
    440B  ILE*     1.3    68.5    +      -       -      +
    441B  LEU*     3.7    30.0    -      -       -      +
    480B  LEU      3.1     5.5    +      -       -      -
    481B  PHE*     3.2    30.9    -      -       +      +
    482B  PHE*     2.8    25.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 440 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370B  CYS*     4.0     5.6    -      -       -      -
    371B  ILE      2.9     9.7    +      -       -      +
    372B  ILE*     3.4    22.5    -      -       +      +
    373B  ILE      2.9    28.1    +      -       -      +
    397B  LEU*     3.5    32.3    -      -       +      -
    401B  PHE*     3.8    41.3    -      -       +      -
    439B  CYS*     1.3    81.2    -      -       -      +
    441B  LEU*     1.3    63.7    +      -       -      +
    442B  LEU*     4.0    13.2    -      -       +      -
    482B  PHE*     3.1    29.4    -      -       +      +
    484B  GLN      5.9     0.2    -      -       -      +
    542B  VAL*     5.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 441 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373B  ILE*     3.7    30.1    -      -       +      -
    419B  MET*     5.4     3.4    -      -       -      -
    423B  LEU*     5.0     1.8    -      -       +      -
    439B  CYS*     3.7    26.0    -      -       -      +
    440B  ILE*     1.3    71.7    -      -       -      +
    442B  LEU*     1.3    62.1    +      -       -      +
    443B  SER*     4.0     1.8    -      -       -      -
    450B  ILE*     4.6    19.3    -      -       +      -
    459B  ILE*     4.9     7.6    -      -       +      -
    462B  LEU*     4.2    27.8    -      -       +      -
    463B  THR*     5.9     0.4    -      -       +      -
    481B  PHE*     5.4     7.4    -      -       +      -
    482B  PHE      2.8     9.2    +      -       -      +
    483B  ILE*     3.6    29.7    -      -       +      -
    484B  GLN*     2.8    30.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 442 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372B  ILE*     4.2     6.7    -      -       +      -
    373B  ILE      3.0    16.3    +      -       -      +
    374B  ASN*     3.5    20.6    -      -       -      +
    375B  ASN*     3.1    21.8    +      -       -      +
    387B  ARG*     3.2    16.3    +      -       -      +
    390B  THR*     4.0     4.7    -      -       -      +
    393B  ASP*     4.3     4.9    -      -       +      +
    394B  ALA*     4.0    27.4    -      -       +      +
    397B  LEU*     3.8    23.8    -      -       +      -
    440B  ILE*     4.0     9.4    -      -       +      +
    441B  LEU*     1.3    78.6    -      -       -      +
    443B  SER*     1.3    65.2    +      -       -      +
    484B  GLN*     3.5    22.0    -      -       +      -
    542B  VAL*     4.0    10.1    -      -       +      -
----------------------------------------------------------
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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