Contacts of the strand formed by residues 82 - 90 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81E  GLY*     1.3    79.5    -      -       -      +
     83E  SER*     1.3    62.2    +      -       -      +
     84E  VAL*     3.8     0.2    -      -       -      +
    136E  LYS*     3.2     5.0    -      -       -      -
    137E  HIS*     2.8    55.2    +      -       +      +
    149E  UOC      3.8     6.7    -      -       +      -
    150E  COA      3.9    39.7    -      -       +      +
     52F  ILE*     4.1    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 83 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65E  ASP*     3.5    12.8    +      -       -      -
     82E  VAL*     1.3    72.0    -      -       -      +
     84E  VAL*     1.3    60.2    +      -       -      +
    134E  HIS*     2.7    36.5    +      -       -      -
    135E  THR      3.9     1.8    -      -       -      -
    136E  LYS*     3.5     4.3    -      -       -      +
    149E  UOC      4.3     0.2    +      -       -      -
    150E  COA      3.1    51.2    +      -       -      +
     90F  TYR*     3.3    28.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 84 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82E  VAL      3.8     0.2    -      -       -      +
     83E  SER*     1.3    75.1    -      -       -      +
     85E  ASP*     1.3    76.6    +      -       -      +
    113E  LEU*     4.6     3.8    -      -       +      -
    135E  THR*     2.8    22.4    +      -       +      +
    136E  LYS      4.0     1.8    -      -       -      -
    137E  HIS*     3.5    41.5    -      -       +      +
    150E  COA      4.1     5.4    -      -       +      -
     89F  THR*     3.4     1.4    -      -       -      +
     90F  TYR*     2.9    31.8    +      -       -      -
     84G  VAL*     6.0     0.9    -      -       +      -
    113G  LEU*     3.9    19.7    -      -       +      -
    115G  PHE*     3.6    22.7    -      -       +      -
    135G  THR*     4.0     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 85 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84E  VAL*     1.3    92.4    -      -       -      +
     86E  MET*     1.3    62.9    +      -       -      +
     87E  ASN*     6.0     1.1    -      -       -      +
    133E  ARG      4.6     0.3    -      -       -      -
    134E  HIS*     3.4     4.2    -      -       -      -
    135E  THR*     2.9    30.0    +      -       -      +
     88F  ILE      3.5     5.2    -      -       -      +
     89F  THR*     2.6    27.0    +      -       -      +
     90F  TYR*     4.8     0.9    -      -       -      -
     85G  ASP*     3.7    35.3    -      -       +      +
     87G  ASN*     4.8     6.9    +      -       -      -
    133G  ARG*     4.7     0.9    +      -       -      +
    135G  THR*     2.7    32.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 86 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61E  ALA*     3.7    37.2    -      -       +      +
     64E  VAL*     3.7    25.4    -      -       +      -
     65E  ASP*     3.9    20.4    -      -       +      +
     85E  ASP*     1.3    77.3    -      -       -      +
     87E  ASN*     1.3    71.2    +      -       -      +
     88E  ILE*     4.2     9.2    -      -       +      -
    133E  ARG      3.3    12.1    -      -       -      +
    134E  HIS*     4.0    14.1    -      -       +      -
     57F  GLY      4.6     1.1    -      -       -      +
     61F  ALA*     4.3     3.1    -      -       +      -
     87F  ASN*     3.3     3.1    -      -       -      +
     88F  ILE*     2.8    41.5    +      -       +      +
     90F  TYR*     3.6    30.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 87 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85E  ASP*     6.0     1.6    -      -       -      +
     86E  MET*     1.3    76.9    -      -       -      +
     88E  ILE*     1.3    67.5    +      -       -      +
    132E  GLY*     3.0    22.5    -      -       -      -
    133E  ARG*     2.9    43.0    +      -       -      +
     86F  MET      3.3    11.2    -      -       -      +
     87F  ASN*     4.0    11.4    -      -       +      -
     85G  ASP*     4.8     5.9    +      -       -      -
     87G  ASN*     6.3     0.2    -      -       +      -
     87H  ASN*     3.4    27.3    -      -       +      +
     89H  THR*     4.8     2.4    +      -       -      -
    133H  ARG*     2.8    36.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 88 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60E  THR*     4.0    15.0    -      -       +      -
     61E  ALA*     3.7    33.4    -      -       +      -
     64E  VAL*     4.4    11.9    -      -       +      -
     86E  MET*     4.2    17.5    -      -       +      -
     87E  ASN*     1.3    81.9    -      -       -      +
     89E  THR*     1.3    70.7    +      -       -      +
     90E  TYR*     3.7    30.3    -      -       +      +
    130E  ALA*     4.2     3.6    -      -       +      -
    131E  GLN      3.5    11.7    -      -       -      +
     85F  ASP*     3.5     3.1    -      -       -      +
     86F  MET*     2.9    54.9    +      -       +      +
     88F  ILE*     4.3     4.7    -      -       +      -
    133H  ARG*     4.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 89 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88E  ILE*     1.3    71.7    -      -       -      +
     90E  TYR*     1.3    62.4    +      -       -      +
     91E  MET*     3.3     9.8    -      -       +      +
    130E  ALA*     3.1     7.0    -      -       -      +
    131E  GLN      2.7    33.9    +      -       -      -
     84F  VAL      3.5     4.0    -      -       -      +
     85F  ASP*     2.6    24.7    +      -       -      +
    115H  PHE*     3.3    37.9    -      -       +      -
    133H  ARG*     2.8    43.4    +      -       -      +
    135H  THR*     3.9     3.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 90 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57E  GLY*     2.8    42.0    +      -       -      -
     60E  THR*     3.7    24.9    -      -       +      -
     88E  ILE*     3.7    29.3    -      -       +      +
     89E  THR*     1.3    71.6    -      -       -      +
     91E  MET*     1.3    60.3    +      -       -      +
     92E  SER      3.8     0.4    -      -       -      -
    129E  ILE*     3.9     6.3    -      -       +      +
    130E  ALA*     4.4     5.2    -      -       +      -
     83F  SER*     3.3    37.9    -      -       -      +
     84F  VAL*     2.9    23.9    +      -       -      +
     86F  MET*     3.6    28.9    -      -       +      +
    150F  COA      3.1    42.2    +      -       -      +
    115H  PHE*     3.8    10.2    -      -       -      -
----------------------------------------------------------
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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