Contacts of the strand formed by residues 84 - 92 (chain E) in PDB entry 1FPY


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 84 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189D  GLN*     5.1     3.4    -      -       -      +
    193D  SER*     5.7     0.9    -      -       -      +
     14E  VAL*     4.1     1.3    -      -       -      -
     16E  PHE*     3.3    29.4    -      -       +      -
     18E  ASP*     4.1     7.2    -      -       -      +
     32E  THR*     5.6     0.9    -      -       -      -
     76E  ILE*     3.6     9.4    -      -       -      +
     77E  ASP*     2.9    33.2    +      -       -      +
     80E  PHE*     3.4    42.5    -      -       +      -
     82E  ASP*     2.7    20.8    +      -       +      +
     83E  SER*     1.3    75.0    +      -       -      +
     85E  LEU*     1.4    65.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 85 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5E  VAL*     4.1    22.7    -      -       +      +
      8E  MET*     3.6    22.0    -      -       +      -
      9E  LEU*     3.9    20.4    -      -       +      -
     14E  VAL*     3.6    16.5    -      -       +      +
     16E  PHE      2.8     9.9    +      -       -      +
     17E  VAL*     3.0    12.0    -      -       +      +
     18E  ASP      2.6    31.3    +      -       -      -
     74E  ALA*     4.1     9.6    -      -       +      -
     75E  VAL*     3.3    37.7    -      -       -      +
     76E  ILE*     3.5    11.2    -      -       +      +
     84E  THR*     1.4    71.9    -      -       -      +
     86E  ILE*     1.3    61.8    +      -       -      +
     87E  ILE*     4.4     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 86 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18E  ASP*     3.3    11.4    -      -       +      +
     20E  ARG*     3.5    62.1    -      -       +      +
     73E  THR      4.0     1.5    -      -       -      +
     74E  ALA*     3.2     1.9    -      -       -      -
     75E  VAL*     2.9    46.8    +      -       +      +
     77E  ASP*     3.5    30.7    -      -       +      +
     85E  LEU*     1.3    73.2    -      -       -      +
     87E  ILE*     1.3    76.5    +      -       -      +
     88E  ARG*     4.8     7.9    -      -       -      +
    202E  MET*     3.8    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 87 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5E  VAL*     4.5    15.5    -      -       +      -
     17E  VAL*     3.8    22.4    -      -       +      -
     18E  ASP      2.8    10.7    +      -       -      +
     19E  LEU*     3.4    11.3    -      -       +      -
     20E  ARG      2.9    23.1    +      -       -      -
     38E  VAL*     5.8     0.9    -      -       +      -
     42E  PHE*     4.9     8.3    -      -       +      -
     43E  PHE*     4.6    11.7    -      -       +      -
     69E  PRO*     3.9    12.6    -      -       +      -
     70E  ASP      3.7    20.4    -      -       -      +
     71E  ALA*     4.9     0.9    -      -       -      +
     73E  THR*     3.8     7.9    -      -       -      +
     74E  ALA*     4.1    12.1    -      -       +      +
     85E  LEU*     4.4    14.1    -      -       +      -
     86E  ILE*     1.3    85.1    -      -       -      +
     88E  ARG*     1.3    74.1    +      -       -      +
     89E  CYS*     3.6     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 88 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20E  ARG*     3.2    21.0    +      -       -      +
     21E  PHE*     5.0     1.5    -      -       -      +
     22E  THR*     4.4     6.1    +      -       -      -
     28E  GLU*     2.6    45.8    +      -       -      +
     70E  ASP*     3.1    27.0    +      -       -      +
     73E  THR*     2.8    28.5    +      -       +      +
     86E  ILE*     4.3     7.9    -      -       -      +
     87E  ILE*     1.3    73.6    -      -       -      +
     89E  CYS*     1.3    64.4    +      -       -      +
    105E  ARG*     3.8    17.5    -      -       -      +
    233E  ASP*     3.4    32.7    +      -       -      +
    236E  GLN*     3.6    16.3    -      -       -      +
    237E  ILE*     4.0    25.9    -      -       -      +
    368E  TYR*     3.7    10.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 89 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19E  LEU*     3.6    35.7    -      -       -      -
     20E  ARG      2.6    13.7    +      -       -      +
     21E  PHE*     3.8    15.5    -      -       +      +
     67E  LEU*     3.7    27.1    -      -       +      -
     68E  MET      3.3    10.5    -      -       -      +
     69E  PRO*     3.8    22.0    -      -       -      -
     87E  ILE      3.7     9.4    -      -       -      -
     88E  ARG*     1.3    77.7    -      -       -      +
     90E  ASP*     1.3    64.4    +      -       -      +
     91E  ILE*     5.4     0.2    -      -       -      +
    103E  ASP*     5.5     0.3    -      -       -      +
    105E  ARG*     4.0    14.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 90 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66E  VAL      3.2     2.6    -      -       -      +
     67E  LEU*     3.6     1.6    -      -       -      -
     68E  MET*     2.7    44.8    +      -       +      +
     69E  PRO      5.2     0.2    -      -       -      +
     70E  ASP*     4.3     6.1    -      -       -      +
     89E  CYS*     1.3    74.4    -      -       -      +
     91E  ILE*     1.3    63.6    +      -       -      +
     92E  LEU*     3.6    19.3    +      -       +      -
    103E  ASP*     3.8     8.3    -      -       -      +
    105E  ARG*     3.1    31.0    +      -       -      +
    106E  SER*     4.6     3.9    +      -       -      +
    109E  LYS*     3.1    36.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 91 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21E  PHE*     4.1    16.8    -      -       +      -
     22E  THR      5.6     0.2    -      -       -      +
     49E  PHE*     3.8    17.5    -      -       +      -
     57E  TRP*     3.8    25.4    -      -       +      -
     65E  MET*     3.8    30.7    -      -       +      -
     66E  VAL      3.4     1.8    -      -       -      +
     67E  LEU*     3.5    32.1    -      -       +      -
     90E  ASP*     1.3    71.9    -      -       -      +
     92E  LEU*     1.3    62.0    +      -       -      +
     99E  GLY*     3.8     2.6    -      -       -      -
    100E  TYR*     2.9    38.4    +      -       +      +
    103E  ASP*     2.9    30.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 92 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65E  MET*     3.3    10.2    -      -       -      +
     66E  VAL*     3.0    38.3    +      -       +      -
     68E  MET*     3.5    48.5    -      -       +      -
     90E  ASP*     4.1    15.9    -      -       +      -
     91E  ILE*     1.3    78.1    -      -       -      +
     93E  GLU*     1.3    61.7    +      -       -      +
     97E  LEU*     3.6    31.6    -      -       +      +
     98E  GLN      4.3     3.4    -      -       -      -
     99E  GLY*     3.8    21.5    -      -       -      +
    100E  TYR      4.0     3.4    -      -       -      +
    106E  SER*     4.8     1.6    -      -       -      +
----------------------------------------------------------
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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