Contacts of the strand formed by residues 84 - 92 (chain I) in PDB entry 1F1H


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 I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14I  VAL*     4.1     0.7    -      -       -      -
     16I  PHE*     3.0    13.0    +      -       -      +
     18I  ASP*     4.0    17.0    +      -       -      +
     32I  THR*     5.5     0.2    -      -       -      +
     76I  ILE*     3.6    10.8    -      -       -      +
     77I  ASP*     3.0    32.4    +      -       +      +
     80I  PHE*     3.4    26.5    -      -       +      -
     82I  ASP      2.6    30.7    +      -       -      +
     83I  SER*     1.3    73.4    +      -       -      +
     85I  LEU*     1.3    60.2    +      -       -      +
   1491I  MPD      2.9    38.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 85 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5I  VAL*     4.0    21.3    -      -       +      -
      8I  MET*     4.1    26.0    -      -       +      -
      9I  LEU*     3.8    22.2    -      -       +      -
     14I  VAL*     3.8    16.3    -      -       +      +
     16I  PHE      2.8     8.6    +      -       -      +
     17I  VAL*     3.1    11.1    -      -       +      +
     18I  ASP      2.7    28.7    +      -       -      -
     74I  ALA*     4.2     8.1    -      -       +      -
     75I  VAL*     3.6    30.5    -      -       -      +
     76I  ILE*     3.8    14.6    -      -       +      +
     84I  THR*     1.3    73.4    -      -       -      +
     86I  ILE*     1.3    63.7    +      -       -      +
     87I  ILE*     4.3     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 86 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18I  ASP*     3.4    11.2    -      -       +      +
     20I  ARG*     3.5    59.2    -      -       +      +
     73I  THR      3.9     1.9    -      -       -      +
     74I  ALA*     3.3     1.7    -      -       -      -
     75I  VAL*     2.6    46.6    +      -       +      +
     77I  ASP*     3.5    31.2    -      -       +      +
     84I  THR*     5.1     0.2    -      -       -      +
     85I  LEU*     1.3    73.2    -      -       -      +
     87I  ILE*     1.3    72.5    +      -       -      +
     88I  ARG*     4.7     9.4    -      -       -      +
    202I  MET*     3.6    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 87 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5I  VAL*     4.2    26.5    -      -       +      -
     17I  VAL*     3.9    23.3    -      -       +      -
     18I  ASP      2.9     9.0    +      -       -      +
     19I  LEU*     3.5    12.4    -      -       +      -
     20I  ARG      3.0    20.6    +      -       -      -
     38I  VAL*     5.7     0.7    -      -       +      -
     42I  PHE*     4.8     7.6    -      -       +      -
     43I  PHE*     4.6    10.3    -      -       +      -
     69I  PRO*     3.9    20.4    -      -       +      -
     70I  ASP      3.7    17.5    -      -       -      +
     71I  ALA*     4.7     2.2    -      -       -      +
     73I  THR*     3.9     3.1    -      -       -      +
     74I  ALA*     4.2    11.2    -      -       +      +
     85I  LEU*     3.9     7.8    +      -       +      -
     86I  ILE*     1.3    81.9    -      -       -      +
     88I  ARG*     1.3    74.1    +      -       -      +
     89I  CYS*     3.7     2.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 88 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20I  ARG*     3.3    22.2    +      -       -      +
     21I  PHE*     5.1     2.5    -      -       -      +
     22I  THR*     4.9     3.4    +      -       -      -
     28I  GLU*     2.5    46.2    +      -       -      +
     70I  ASP*     3.0    25.6    +      -       -      +
     73I  THR*     2.9    29.8    +      -       +      +
     75I  VAL*     6.2     1.0    -      -       -      +
     86I  ILE*     4.7    10.9    -      -       -      +
     87I  ILE*     1.3    74.2    -      -       -      +
     89I  CYS*     1.3    64.2    +      -       -      +
    105I  ARG*     3.8    18.4    -      -       -      +
    233I  ASP*     3.4    34.5    +      -       -      +
    236I  GLN*     3.7    14.9    -      -       -      +
    237I  ILE*     3.8    29.5    -      -       -      +
    368I  TYR*     3.8    10.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 89 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19I  LEU*     3.8    26.7    -      -       -      -
     20I  ARG      2.7    15.9    +      -       -      +
     21I  PHE*     4.0    10.0    -      -       -      +
     67I  LEU*     3.6    31.4    -      -       +      -
     68I  MET      3.3    10.3    -      -       -      +
     69I  PRO*     3.8    19.3    -      -       -      -
     70I  ASP*     4.4     0.4    -      -       -      +
     87I  ILE      3.7    12.1    -      -       -      -
     88I  ARG*     1.3    80.0    -      -       -      +
     90I  ASP*     1.3    64.9    +      -       -      +
    103I  ASP*     5.6     0.2    -      -       -      +
    105I  ARG*     3.8    17.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 90 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66I  VAL      3.4     1.7    -      -       -      +
     67I  LEU*     3.7     2.6    -      -       -      -
     68I  MET*     2.8    45.8    +      -       +      +
     70I  ASP*     4.3     5.0    -      -       -      +
     89I  CYS*     1.3    73.7    -      -       -      +
     91I  ILE*     1.3    62.9    +      -       -      +
     92I  LEU*     3.9    17.9    -      -       +      -
    103I  ASP*     3.7     8.3    -      -       -      +
    105I  ARG*     3.0    40.6    +      -       -      +
    106I  SER*     4.4     4.5    +      -       -      +
    109I  LYS*     3.1    29.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 91 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21I  PHE*     3.9    23.6    -      -       +      -
     49I  PHE*     4.0    16.4    -      -       +      -
     57I  TRP*     3.7    24.2    -      -       +      -
     65I  MET*     3.7    31.9    -      -       +      -
     66I  VAL      3.4     2.0    -      -       -      +
     67I  LEU*     3.6    29.6    -      -       +      -
     90I  ASP*     1.3    71.8    -      -       -      +
     92I  LEU*     1.3    61.9    +      -       -      +
     99I  GLY*     3.7     3.3    -      -       -      -
    100I  TYR*     3.0    33.5    +      -       +      +
    103I  ASP*     2.8    32.4    +      -       +      +
    106I  SER*     3.9     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 92 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65I  MET*     3.4     7.5    -      -       -      +
     66I  VAL*     2.9    39.7    +      -       +      +
     68I  MET*     3.3    50.7    -      -       +      -
     90I  ASP*     4.1    15.7    -      -       +      +
     91I  ILE*     1.3    78.3    -      -       -      +
     93I  GLU*     1.3    62.2    +      -       -      +
     97I  LEU*     3.8    30.5    -      -       +      +
     98I  GLN      4.1     5.2    -      -       -      +
     99I  GLY*     3.5    24.7    -      -       -      +
    100I  TYR      4.4     0.7    -      -       -      -
    106I  SER*     4.6     2.0    -      -       -      +
----------------------------------------------------------
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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