Contacts of the strand formed by residues 82 - 90 (chain D) in PDB entry 3F5O


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 VAL 82 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  ILE*     4.7    12.3    -      -       +      -
     81D  GLY*     1.3    79.7    -      -       -      +
     83D  SER*     1.3    63.5    +      -       -      +
     84D  VAL*     3.9     0.2    -      -       -      +
    136D  LYS*     3.2     5.3    -      -       -      +
    137D  HIS*     2.8    57.5    +      -       +      +
    139D  GLY      5.8     2.7    -      -       -      -
    149D  UOC      3.7    17.3    -      -       +      -
    150D  COA      3.9    41.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 83 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  GLY*     5.3     0.4    -      -       -      -
     90C  TYR*     3.3    32.5    -      -       -      +
     65D  ASP*     3.7    12.1    +      -       -      -
     82D  VAL*     1.3    71.9    -      -       -      +
     84D  VAL*     1.3    61.0    +      -       -      +
    134D  HIS*     2.7    35.9    +      -       -      -
    135D  THR      3.9     1.3    -      -       -      -
    136D  LYS*     3.5     4.2    -      -       -      +
    150D  COA      3.2    44.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 84 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  VAL*     6.1     0.9    -      -       +      -
    113B  LEU*     3.9    16.8    -      -       +      -
    115B  PHE*     3.5    26.2    -      -       +      -
    135B  THR*     4.0     5.8    -      -       +      -
     89C  THR*     3.4     5.4    -      -       -      +
     90C  TYR*     2.9    31.0    +      -       -      -
     83D  SER*     1.3    75.8    -      -       -      +
     85D  ASP*     1.3    72.8    +      -       -      +
    113D  LEU*     4.5     3.1    -      -       +      -
    135D  THR*     2.8    21.9    +      -       +      +
    136D  LYS      4.1     2.0    -      -       -      -
    137D  HIS*     3.6    39.7    -      -       +      +
    150D  COA      4.1     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 85 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  ASP*     3.7    34.8    -      -       -      +
     87B  ASN*     4.8     7.1    +      -       -      -
    133B  ARG*     4.7     1.2    +      -       -      -
    135B  THR*     2.7    32.6    +      -       -      -
     88C  ILE      3.4     4.9    -      -       -      +
     89C  THR*     2.6    25.8    +      -       -      -
     90C  TYR*     4.8     1.1    -      -       -      -
     84D  VAL*     1.3    93.3    -      -       -      +
     86D  MET*     1.3    62.1    +      -       -      +
     87D  ASN*     6.0     1.3    -      -       -      +
    133D  ARG      4.0     0.5    -      -       -      +
    134D  HIS*     3.5     3.9    -      -       -      -
    135D  THR*     2.9    31.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 86 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  GLY      4.5     2.2    -      -       -      +
     61C  ALA*     4.3     2.2    -      -       +      -
     87C  ASN*     3.2     2.8    -      -       -      +
     88C  ILE*     2.8    50.2    +      -       +      +
     90C  TYR*     3.5    29.3    -      -       +      +
     61D  ALA*     3.8    32.8    -      -       +      +
     64D  VAL*     3.7    26.2    -      -       +      -
     65D  ASP*     4.0    19.1    -      -       +      +
     85D  ASP*     1.3    77.0    -      -       -      +
     87D  ASN*     1.3    70.6    +      -       -      +
     88D  ILE*     4.1     5.4    -      -       +      -
    133D  ARG      3.3    11.9    -      -       -      +
    134D  HIS*     4.1    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 87 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  ASN*     3.4    36.5    -      -       +      +
     89A  THR*     4.8     2.2    +      -       -      -
    133A  ARG*     2.9    35.2    +      -       -      +
     85B  ASP*     4.8     5.9    +      -       -      -
     87B  ASN*     6.2     0.2    -      -       +      -
     86C  MET      3.3    10.5    -      -       -      +
     87C  ASN*     4.0    11.4    -      -       +      -
     85D  ASP*     6.0     1.4    -      -       -      +
     86D  MET*     1.3    76.3    -      -       -      +
     88D  ILE*     1.3    68.4    +      -       -      +
    132D  GLY*     3.0    22.9    -      -       -      -
    133D  ARG*     3.0    31.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 88 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  ARG*     4.2     0.4    -      -       -      -
     85C  ASP*     3.5     3.6    -      -       -      +
     86C  MET*     2.8    48.4    +      -       +      +
     88C  ILE*     4.2     4.7    -      -       +      -
     60D  THR*     4.0    14.1    -      -       +      -
     61D  ALA*     3.8    32.5    -      -       +      -
     64D  VAL*     4.4    13.0    -      -       +      -
     86D  MET*     4.1    19.1    -      -       +      -
     87D  ASN*     1.3    81.2    -      -       -      +
     89D  THR*     1.3    71.9    +      -       -      +
     90D  TYR*     3.5    38.1    -      -       +      +
    130D  ALA*     4.2     2.5    -      -       +      -
    131D  GLN      3.4    12.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 89 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  ASN*     4.7     0.2    +      -       -      -
    115A  PHE*     3.3    37.2    -      -       +      -
    133A  ARG*     2.8    40.2    +      -       -      +
    135A  THR*     3.9     3.3    +      -       -      +
     84C  VAL      3.4     4.3    -      -       -      +
     85C  ASP*     2.6    24.6    +      -       -      +
     88D  ILE*     1.3    71.9    -      -       -      +
     90D  TYR*     1.3    63.0    +      -       -      +
     91D  MET*     3.6    13.1    +      -       +      +
    130D  ALA*     3.1     7.3    -      -       -      +
    131D  GLN      2.8    31.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 90 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  PHE*     3.8     8.9    -      -       -      -
     65C  ASP*     5.0     0.4    +      -       -      -
     83C  SER*     3.3    38.2    -      -       -      +
     84C  VAL*     2.9    24.2    +      -       -      +
     86C  MET*     3.5    30.6    -      -       +      +
    150C  COA      3.1    39.9    +      -       -      +
     57D  GLY*     2.8    42.1    +      -       -      -
     60D  THR*     3.7    22.7    -      -       +      -
     61D  ALA      4.4     0.2    +      -       -      -
     88D  ILE*     3.5    31.8    -      -       +      +
     89D  THR*     1.3    72.0    -      -       -      +
     91D  MET*     1.3    60.4    +      -       -      +
     92D  SER      3.8     0.7    -      -       -      +
    129D  ILE*     3.8     5.6    -      -       +      +
    130D  ALA*     4.4     3.1    -      -       +      -
----------------------------------------------------------
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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