Contacts of the strand formed by residues 86 - 97 (chain D) in PDB entry 5FL6


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 ARG 86 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44D  ALA      5.6     1.8    +      -       -      -
     45D  LEU*     3.9    15.2    -      -       -      +
     81D  ALA*     3.3     3.5    -      -       -      -
     82D  LEU*     2.8    69.3    +      -       +      +
     83D  GLY*     3.0    21.6    +      -       -      +
     84D  PRO*     3.8     7.9    -      -       -      +
     85D  GLY*     1.3    79.6    -      -       -      +
     87D  GLU*     1.3    60.2    +      -       -      +
     88D  TYR*     3.4    16.6    +      -       +      +
    194D  GLN*     2.8    31.1    +      -       -      -
    209D  ILE*     4.3     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 87 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79D  GLU*     5.8     2.9    -      -       -      +
     80D  MET      3.7     3.4    -      -       -      +
     81D  ALA*     3.4    24.9    +      -       -      +
     83D  GLY      5.3     0.2    -      -       -      -
     85D  GLY*     3.8    12.9    +      -       -      -
     86D  ARG*     1.3    79.7    -      -       -      +
     88D  TYR*     1.3    69.8    +      -       -      +
    124D  SER*     3.7     4.3    +      -       -      -
    125D  THR*     3.1    42.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 88 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79D  GLU*     3.5     6.9    -      -       -      +
     80D  MET*     2.7    50.3    +      -       +      +
     82D  LEU*     3.7    17.8    -      -       +      +
     86D  ARG*     3.4    28.5    +      -       +      +
     87D  GLU*     1.3    77.9    +      -       -      +
     89D  ARG*     1.3    62.7    +      -       -      +
    122D  HIS*     3.7    14.1    -      -       +      -
    123D  LEU      3.3     7.6    -      -       -      +
    124D  SER*     3.3    29.8    -      -       -      -
    125D  THR*     4.2     8.7    -      -       -      +
    138D  GLY*     2.7    37.6    +      -       -      -
    140D  LEU      4.0     0.4    -      -       -      -
    141D  ALA*     3.5    29.6    -      -       +      -
    209D  ILE*     4.2     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 89 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  PRO*     3.6    33.2    -      -       -      +
     76D  PRO*     6.5     0.4    -      -       +      -
     77D  GLY      5.7     4.0    -      -       -      +
     78D  LEU      3.2    15.0    -      -       -      +
     79D  GLU*     4.9     3.8    -      -       +      -
     88D  TYR*     1.3    74.3    -      -       -      +
     90D  ALA*     1.3    68.2    +      -       -      +
     91D  LEU*     3.6     4.8    +      -       +      +
    122D  HIS*     3.1     5.9    -      -       -      -
    123D  LEU*     2.8    55.6    +      -       +      +
    124D  SER      3.0    26.9    +      -       -      -
    125D  THR*     3.5    21.2    -      -       +      +
    127D  PHE      2.9    19.6    +      -       -      -
    128D  ALA*     3.4    21.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 90 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  PHE*     4.1     5.8    -      -       +      -
     74D  LEU*     3.8    22.6    -      -       +      +
     75D  PRO      4.1    14.9    -      -       -      +
     76D  PRO*     5.6     1.0    -      -       -      +
     78D  LEU*     2.9    29.7    +      -       +      +
     89D  ARG*     1.3    78.1    -      -       -      +
     91D  LEU*     1.3    62.9    +      -       -      +
    120D  VAL*     4.5     0.7    -      -       +      -
    121D  VAL      3.7     2.7    -      -       -      +
    122D  HIS*     3.4    27.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 91 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73D  THR*     4.0     5.0    -      -       -      +
     74D  LEU*     3.0    28.0    +      -       -      +
     89D  ARG*     4.2    11.4    -      -       +      +
     90D  ALA*     1.3    79.5    -      -       -      +
     92D  GLN*     1.3    69.4    +      -       +      +
    121D  VAL*     2.7    29.5    +      -       +      +
    122D  HIS      4.5     0.9    -      -       -      -
    123D  LEU*     4.0    32.8    -      -       +      +
    130D  VAL*     3.3    33.0    -      -       +      -
    140D  LEU*     4.8     1.1    -      -       +      -
    266D  Y0R      5.3     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 92 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71D  GLN*     3.4    24.0    +      -       +      +
     72D  LEU      3.2    16.4    -      -       -      +
     73D  THR*     4.3     4.7    -      -       +      +
     74D  LEU*     3.8     9.9    -      -       -      +
     91D  LEU*     1.3    89.1    -      -       +      +
     93D  LEU*     1.3    64.4    +      -       -      +
     94D  HIS*     2.7    23.8    +      -       -      -
    120D  VAL*     3.6     1.9    -      -       -      +
    121D  VAL*     2.8    41.1    +      -       +      +
    266D  Y0R      3.4    21.0    +      -       -      +
   1261D  GOL      3.3    29.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 93 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70D  VAL      5.7     0.4    -      -       -      +
     71D  GLN*     3.3     1.4    -      -       -      -
     72D  LEU*     2.7    68.3    +      -       +      +
     74D  LEU*     4.2     6.5    -      -       +      +
     92D  GLN*     1.3    78.8    -      -       -      +
     94D  HIS*     1.3    67.5    +      -       -      +
     95D  LEU*     5.4     5.4    -      -       +      -
    118D  ILE*     4.2    14.8    -      -       +      -
    119D  HIS      3.1    14.8    -      -       -      +
    120D  VAL*     3.9    17.3    -      -       +      -
    160D  LEU*     4.6     8.1    -      -       +      -
    181D  ILE*     3.7    29.8    -      -       +      -
    184D  LEU*     3.7    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 94 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  SER*     3.5     8.7    -      -       -      +
     70D  VAL      3.1    17.9    -      -       -      +
     71D  GLN*     3.9     4.5    -      -       -      -
     92D  GLN*     2.7    25.9    +      -       -      +
     93D  LEU*     1.3    77.9    -      -       -      +
     95D  LEU*     1.3    67.7    +      -       -      +
     96D  HIS*     3.4    11.0    -      +       -      -
    118D  ILE*     3.6     4.5    -      -       -      +
    119D  HIS*     3.0    34.1    +      -       +      +
    121D  VAL*     3.7    13.0    -      -       +      -
    266D  Y0R      3.1    22.8    +      -       -      -
   1260D   ZN      2.2    31.6    -      -       -      -
   1261D  GOL      3.3    29.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  SER*     2.6    25.2    +      -       -      -
     70D  VAL*     3.5    14.7    +      -       +      +
     93D  LEU*     5.4     4.3    -      -       +      -
     94D  HIS*     1.3    81.5    -      -       -      +
     96D  HIS*     1.3    70.1    +      -       -      +
     97D  TRP*     3.4    16.1    -      -       +      -
    117D  GLU      3.4     5.2    -      -       -      +
    118D  ILE*     3.5    39.5    -      -       +      +
    147D  LEU*     4.4     5.2    -      -       +      -
    157D  TYR*     4.3    20.4    -      -       +      -
    160D  LEU*     5.9     7.9    -      -       +      -
    161D  LEU*     5.2     4.5    -      -       +      -
    164D  LEU*     6.4     0.2    -      -       +      -
    227D  LEU*     3.6    31.2    -      -       +      -
    242D  ASN*     3.4     9.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 96 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11D  TYR*     3.5    19.5    -      -       -      -
     69D  SER*     5.3     2.5    -      -       -      -
     94D  HIS*     3.4     6.7    -      +       -      -
     95D  LEU*     1.3    79.5    +      -       -      +
     97D  TRP*     1.3    62.8    +      -       -      +
    104D  GLY      3.5     8.7    -      -       -      +
    106D  GLU*     3.3    28.7    +      -       +      -
    116D  ALA*     3.1     5.9    -      -       -      +
    117D  GLU*     2.8    38.8    +      -       +      +
    119D  HIS*     3.3    20.2    -      +       -      -
    200D  THR*     4.3     0.4    -      -       -      -
    242D  ASN*     2.6    28.6    +      -       -      +
    266D  Y0R      3.9     4.7    -      -       -      -
   1260D   ZN      2.2    36.2    -      -       -      -
   1261D  GOL      4.0     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 97 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  SER*     4.0     2.0    -      -       -      -
     70D  VAL*     3.8    23.1    -      -       +      -
     95D  LEU*     3.4    36.8    -      -       +      -
     96D  HIS*     1.3    74.9    -      -       -      +
     98D  GLY*     1.3    72.3    +      -       -      +
    104D  GLY*     3.5    12.3    +      -       -      +
    115D  PRO      3.9     5.8    -      -       -      +
    116D  ALA*     3.9    12.1    -      -       +      -
    224D  LEU      6.0     0.2    -      -       -      +
    227D  LEU*     3.6    39.5    -      -       +      -
    228D  SER*     3.5    22.4    -      -       -      +
    231D  LEU*     3.8    21.3    -      -       +      -
    239D  LEU*     2.8    44.1    +      -       +      -
    240D  GLN*     3.7     2.6    -      -       -      +
    241D  LEU*     3.0    16.5    +      -       -      -
    242D  ASN*     2.9    33.2    +      -       -      +
----------------------------------------------------------
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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