Contacts of the strand formed by residues 79 - 83 (chain A) in PDB entry 2FQ6


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 GLY 79 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  CYS*     3.4     9.9    -      -       -      -
     77A  GLY      3.5     1.0    -      -       -      -
     78A  ALA*     1.3    79.7    -      -       -      +
     80A  CYS*     1.3    60.0    +      -       -      -
     81A  VAL      4.2     0.2    -      -       -      -
    223A  ALA      4.5     0.2    -      -       -      -
    224A  VAL*     3.4     7.1    -      -       -      +
    225A  CYS      2.9    27.6    +      -       -      -
    230A  TRP*     3.4    32.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  GLN*     2.9    53.5    -      -       -      +
     71A  MET*     3.5    30.7    -      -       +      -
     72A  CYS*     3.7     3.6    -      -       -      -
     79A  GLY*     1.3    73.9    -      -       -      +
     81A  VAL*     1.3    67.6    +      -       -      +
     82A  LEU*     3.7    23.3    -      -       -      -
    222A  THR*     4.1     7.0    -      -       -      -
    223A  ALA      3.4     4.3    -      -       -      -
    224A  VAL*     4.1    11.4    -      -       +      +
    230A  TRP*     3.9     4.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  GLN*     4.8     0.7    -      -       -      -
     80A  CYS*     1.3    75.9    -      -       -      +
     82A  LEU*     1.3    68.5    +      -       -      +
     83A  PHE*     3.5    29.0    -      -       +      -
    222A  THR*     3.4     4.9    -      -       -      -
    223A  ALA*     2.9    38.9    +      -       +      +
    225A  CYS*     4.4     1.3    -      -       -      -
    230A  TRP*     4.1    13.0    -      -       +      +
    233A  LEU*     4.2    11.2    -      -       +      +
    234A  ARG*     3.8    38.8    -      -       +      +
    237A  ALA*     3.9    17.9    -      -       +      -
    242A  GLN      5.8     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  HIS*     4.1    22.7    -      -       +      +
     67A  LEU*     4.0    23.3    -      -       +      -
     68A  GLN*     4.0    27.2    +      -       +      +
     80A  CYS*     3.7    26.0    -      -       -      -
     81A  VAL*     1.3    77.0    -      -       -      +
     83A  PHE*     1.3    70.0    +      -       -      +
    220A  ILE*     4.7     1.6    -      -       +      -
    221A  GLY      3.6     2.5    -      -       -      +
    222A  THR*     3.9    16.2    -      -       +      -
    242A  GLN*     3.8     7.1    -      -       -      +
    243A  MET*     3.7    19.1    +      -       -      -
    244A  VAL*     3.8    30.5    -      -       +      +
    249A  ALA*     5.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  VAL*     3.5    36.8    -      -       +      -
     82A  LEU*     1.3    74.7    -      -       -      +
     84A  PRO*     1.3    71.4    -      -       +      +
     85A  CYS      3.3    16.2    -      -       -      +
     88A  ALA*     3.6    13.5    -      -       +      -
     89A  ALA*     3.3    20.4    -      -       +      +
     92A  ASN*     3.5    22.2    -      -       +      -
     93A  SER*     4.1    13.5    -      -       -      -
    220A  ILE*     3.5     4.0    -      -       -      -
    221A  GLY      2.9    28.3    +      -       -      +
    223A  ALA*     3.7    17.3    -      -       +      -
    233A  LEU*     4.1     7.0    -      -       +      -
    237A  ALA*     3.8    18.2    -      -       +      -
    242A  GLN*     3.6    20.0    -      -       +      -
    243A  MET      3.7     4.7    -      -       -      -
    244A  VAL*     3.6     8.5    -      -       -      +
----------------------------------------------------------
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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