Contacts of the strand formed by residues 83 - 90 (chain D) in PDB entry 6F8F


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 TYR 83 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74D  LYS*     3.5     3.3    -      -       -      -
     75D  GLY*     2.7    31.7    +      -       -      -
     79D  GLU      4.2     9.6    -      -       -      -
     80D  SER      2.6    19.5    +      -       -      +
     81D  LYS      3.3     0.6    -      -       -      -
     82D  ASP*     1.3    79.8    -      -       +      +
     84D  LEU*     1.3    59.4    +      -       -      +
    134D  LYS      4.2     2.9    -      -       -      +
    135D  LYS*     3.7    62.4    -      -       +      -
    137D  ILE      3.3     6.1    -      -       -      +
    138D  ARG*     3.0    55.3    +      -       +      -
    139D  ARG*     4.1     5.2    -      -       -      -
    223G  PRO*     2.3    45.6    +      -       +      +
    224G  GLU      3.7     9.0    -      -       -      -
    225G  GLN*     4.7     1.3    -      -       -      -
    226G  ASP      5.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 84 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  PHE*     3.7    35.7    -      -       +      -
     71D  VAL*     3.9    20.0    -      -       +      -
     72D  ASN      3.5     5.8    -      -       -      +
     73D  PRO*     3.7     8.7    -      -       +      +
     83D  TYR*     1.3    72.5    -      -       -      +
     85D  SER*     1.3    75.0    +      -       -      +
     86D  LEU*     4.1     5.4    -      -       +      -
    106D  ILE*     6.4     0.2    -      -       +      -
    134D  LYS      4.3     0.2    -      -       -      -
    136D  PHE*     2.9    51.5    +      -       +      +
    137D  ILE*     2.8    26.5    +      -       +      +
    139D  ARG*     4.0     4.2    -      -       +      +
    142D  LEU*     4.2     8.7    -      -       +      -
    155D  LEU*     3.8    14.6    -      -       +      -
    157D  LEU*     5.0     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 85 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71D  VAL*     3.1     9.9    -      -       -      +
     72D  ASN*     3.0    51.8    +      -       -      +
     75D  GLY*     3.7    17.8    -      -       -      -
     76D  LEU      4.9     0.5    +      -       -      -
     83D  TYR      3.7     0.4    +      -       -      -
     84D  LEU*     1.3    74.6    -      -       -      +
     86D  LEU*     1.3    61.4    +      -       -      +
     87D  TYR*     3.7    11.4    -      -       -      -
    133D  PHE      3.4     9.2    -      -       -      -
    134D  LYS*     2.5    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 86 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  LEU*     4.6    15.3    -      -       +      -
     70D  ARG      3.6     3.8    -      -       -      +
     71D  VAL*     3.5    24.5    -      -       +      -
     84D  LEU*     4.1     4.3    -      -       +      -
     85D  SER*     1.3    74.9    -      -       -      +
     87D  TYR*     1.3    66.8    +      -       -      +
    104D  PHE*     3.5    47.8    -      -       +      -
    132D  GLY*     3.4     2.1    -      -       -      -
    133D  PHE*     2.8    36.3    +      -       -      +
    136D  PHE*     3.9    33.0    -      -       +      +
    157D  LEU*     3.9    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 87 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  LEU*     3.3     9.5    -      -       -      +
     70D  ARG*     2.9    88.3    +      -       +      +
     72D  ASN*     3.8     1.1    -      -       -      -
     85D  SER*     3.7    20.5    -      -       -      -
     86D  LEU*     1.3    77.5    -      -       -      +
     88D  LEU*     1.3    59.1    +      -       -      +
    104D  PHE*     3.8     6.5    -      -       -      -
    130D  ASP*     4.0    18.8    -      -       +      -
    131D  TRP      3.5     7.2    -      -       -      +
    132D  GLY*     3.3    26.0    -      -       -      -
    133D  PHE      4.4     0.2    -      -       -      -
    134D  LYS*     3.4    36.0    -      -       -      +
    230G  THR*     3.7    21.4    +      -       -      -
    231G  SER      5.0     0.5    +      -       -      -
    232G  GLY*     4.3    10.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 88 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57D  PHE*     4.0    22.0    -      -       +      -
     67D  TRP*     3.6    39.5    -      -       +      -
     68D  CYS      3.8     9.6    -      -       -      +
     69D  LEU*     4.1     6.7    -      -       +      -
     87D  TYR*     1.3    71.0    -      -       -      +
     89D  LEU*     1.3    60.6    +      -       -      +
    100D  ALA*     5.3     0.4    -      -       +      -
    102D  PHE*     4.0    17.3    -      -       +      -
    104D  PHE*     3.6    16.4    -      -       +      -
    125D  PHE*     3.4    18.8    -      -       +      -
    130D  ASP*     3.1     3.1    -      -       -      -
    131D  TRP      2.9    35.0    +      -       -      +
    159D  CYS*     4.4     0.9    -      -       -      -
    161D  VAL*     3.9    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 89 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  LYS*     3.6    34.3    -      -       +      +
     67D  TRP*     3.2     9.2    -      -       -      +
     68D  CYS*     2.8    56.7    +      -       -      +
     70D  ARG*     5.1     9.4    -      -       +      -
     87D  TYR      4.0     0.2    -      -       -      -
     88D  LEU*     1.3    73.6    -      -       -      +
     90D  LEU*     1.3    76.6    +      -       -      +
     91D  VAL*     4.3     5.4    -      -       +      -
    128D  GLY*     3.5    36.1    -      -       -      +
    129D  LYS      3.5     6.3    -      -       -      +
    130D  ASP*     3.8    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 90 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65D  LEU*     4.2    12.1    -      -       +      -
     66D  LYS      3.8    13.2    -      -       -      +
     67D  TRP*     3.8    34.4    -      -       +      -
     89D  LEU*     1.3    73.6    -      -       -      +
     91D  VAL*     1.3    59.3    +      -       -      +
     92D  SER*     3.8    14.4    -      -       -      +
     94D  PRO*     3.9    22.4    -      -       +      -
     98D  VAL*     4.2     3.1    -      -       +      -
    125D  PHE*     3.9    23.8    -      -       +      +
    126D  VAL*     3.4    36.3    -      -       -      +
    127D  GLN      3.7     3.8    -      -       -      +
    128D  GLY      2.9    28.1    +      -       -      -
    129D  LYS      3.1     7.9    +      -       -      -
----------------------------------------------------------
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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