Contacts of the strand formed by residues 84 - 90 (chain C) in PDB entry 1F11


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 84 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37C  GLN*     3.9    20.0    -      -       +      -
     38C  GLN      3.3    21.1    -      -       -      +
     39C  LYS*     4.0     9.6    -      -       +      +
     40C  PRO*     4.9     0.2    -      -       -      -
     82C  ASP      2.9    11.2    +      -       -      +
     83C  ALA*     1.3    77.3    -      -       -      +
     85C  THR*     1.3    61.5    +      -       -      +
     86C  TYR*     3.7     3.3    -      -       +      -
    102C  THR      3.6     1.0    -      -       -      +
    103C  LYS*     3.4    16.9    -      -       -      +
    104C  LEU*     2.9    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 85 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37C  GLN*     3.7     1.7    -      -       -      -
     38C  GLN*     2.8    37.3    +      -       -      +
     84C  ALA*     1.3    75.8    -      -       -      +
     86C  TYR*     1.3    63.4    +      -       -      +
     87C  TYR*     3.4    39.1    -      -       +      +
    101C  GLY*     4.2     2.0    -      -       -      -
    102C  THR      3.3    19.7    -      -       -      +
    103C  LYS*     3.3    27.5    +      -       -      +
     43D  LYS*     4.0    14.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 86 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  GLN*     2.6    25.9    +      -       -      +
     21C  ILE*     4.4    20.2    -      -       +      -
     35C  TRP*     5.1     1.6    -      -       +      -
     36C  TYR      3.4    13.0    -      -       -      +
     37C  GLN*     3.1    38.8    +      -       +      -
     47C  LEU*     3.6    17.7    -      -       +      -
     62C  PHE*     3.9    11.1    -      +       -      -
     73C  LEU*     4.0    14.6    -      -       +      -
     75C  ILE*     4.0     9.1    -      -       +      +
     82C  ASP*     2.9    38.4    +      -       -      +
     84C  ALA      3.7    16.8    -      -       -      -
     85C  THR*     1.3    72.3    -      -       -      +
     87C  TYR*     1.3    58.8    +      -       -      +
    101C  GLY*     3.1     5.2    -      -       -      -
    102C  THR*     2.8    27.8    +      -       -      +
    104C  LEU*     3.8    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 87 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  GLN*     3.5     3.8    -      -       -      +
     35C  TRP*     3.1    10.2    -      -       -      -
     36C  TYR*     2.7    50.6    +      -       +      +
     38C  GLN*     3.3    38.6    +      -       +      -
     44C  PRO*     5.3     0.7    -      -       +      -
     85C  THR*     3.4    25.0    -      -       +      +
     86C  TYR*     1.3    76.4    -      -       -      +
     88C  CYS*     1.3    64.7    +      -       -      +
     98C  PHE*     4.5    13.2    -      -       +      -
     99C  GLY      3.7    15.7    -      -       -      +
    100C  SER      4.6     2.0    -      -       -      -
    101C  GLY*     3.5    27.6    -      -       -      -
     39D  GLN*     3.6     8.7    +      -       -      -
     43D  LYS*     4.0    17.0    +      -       -      +
     44D  SER*     5.0     9.4    -      -       -      -
     45D  LEU*     3.9    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 88 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  LEU*     3.7     6.0    -      -       -      +
      6C  GLN*     3.7    19.1    +      -       -      -
     23C  CYS*     2.0    54.3    -      -       +      -
     33C  MET*     4.1     5.6    -      -       -      -
     34C  ASN      3.1     8.1    -      -       -      +
     35C  TRP*     3.6    19.0    -      -       +      -
     87C  TYR*     1.3    75.0    -      -       -      +
     89C  GLN*     1.3    58.9    +      -       -      +
     98C  PHE*     3.6     0.5    -      -       -      -
     99C  GLY*     2.7    33.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 89 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  LEU*     3.9     0.7    -      -       -      -
     33C  MET*     3.5     5.1    -      -       -      -
     34C  ASN*     2.7    44.6    +      -       -      +
     36C  TYR*     2.6    39.0    +      -       +      -
     88C  CYS*     1.3    76.4    -      -       -      +
     90C  GLN*     1.3    82.0    +      -       -      +
     91C  SER*     3.1    21.2    +      -       -      -
     96C  PHE*     4.3     4.6    -      -       -      +
     97C  THR      3.0    22.4    -      -       -      +
     98C  PHE*     3.7    26.2    -      -       +      -
    100D  PHE*     3.3    20.7    +      -       -      +
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Residues in contact with GLN 90 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  MET*     3.9    23.0    -      -       -      +
      4C  LEU*     3.7    14.3    -      -       +      +
     27C  VAL*     3.7    28.9    -      -       -      -
     32C  TYR      3.5     6.1    -      -       -      +
     33C  MET*     4.2     3.8    -      -       -      -
     89C  GLN*     1.3    85.8    +      -       -      +
     91C  SER*     1.3    60.3    +      -       -      +
     92C  ASN*     3.3    11.2    -      -       +      +
     93C  GLU*     2.6    43.2    +      -       -      +
     95C  PRO      3.7     4.8    +      -       -      +
     96C  PHE*     3.7     4.2    -      -       -      +
     97C  THR*     2.9    41.3    +      -       -      +
----------------------------------------------------------
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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