Contacts of the strand formed by residues 198 - 205 (chain F) in PDB entry 3STJ


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 LEU 198 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68F  VAL*     4.1    16.2    -      -       +      -
     70F  ILE*     5.3     0.7    -      -       +      -
     78F  LEU*     4.7    11.0    -      -       +      -
    127F  ILE*     3.8    17.5    -      -       +      +
    128F  ALA      2.8    16.6    +      -       -      +
    129F  ILE*     4.2    16.2    -      -       +      -
    130F  ALA*     2.9    24.3    +      -       -      +
    190F  ALA*     3.8    26.9    -      -       +      -
    191F  LEU      3.6     3.6    -      -       -      +
    192F  LEU*     4.0     5.6    -      -       +      +
    196F  GLY      4.1     0.4    +      -       -      -
    197F  GLU*     1.3    68.7    -      -       -      +
    199F  ILE*     1.3    60.0    +      -       -      +
    200F  GLY      3.4    25.1    -      -       -      +
    201F  ILE*     4.3    19.1    -      -       +      -
    221F  SER*     3.4    18.7    +      -       -      +
    224F  ALA*     5.5     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 199 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130F  ALA*     3.9    17.7    -      -       +      -
    131F  ASP      5.7     0.4    -      -       -      +
    132F  SER*     3.8     4.7    -      -       -      -
    135F  LEU*     3.9    39.9    -      -       +      -
    140F  PHE      4.9     1.8    -      -       -      +
    141F  ALA*     4.1    17.0    -      -       +      -
    159F  VAL*     4.2     8.1    -      -       +      -
    176F  ILE*     3.2    15.1    -      -       -      +
    191F  LEU*     2.8    45.6    +      -       +      +
    192F  LEU      3.9     7.4    -      -       -      +
    193F  ASN*     4.0    21.1    -      -       +      +
    197F  GLU      3.4     0.8    +      -       -      +
    198F  LEU*     1.3    76.6    -      -       -      +
    200F  GLY*     1.3    57.4    +      -       -      +
    220F  PRO*     3.6     0.2    -      -       -      +
    221F  SER*     2.9    25.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 200 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176F  ILE*     4.3     4.5    -      -       -      -
    190F  ALA      3.8     0.2    -      -       -      -
    191F  LEU*     2.8    39.9    +      -       -      +
    198F  LEU*     3.4    11.9    -      -       -      +
    199F  ILE*     1.3    82.1    -      -       -      +
    201F  ILE*     1.3    61.3    +      -       -      -
    218F  ALA*     4.3     1.6    -      -       -      -
    219F  ILE      3.1    14.1    -      -       -      -
    221F  SER*     3.7     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 201 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68F  VAL*     3.5    35.9    -      -       +      -
     78F  LEU*     4.2    20.2    -      -       +      -
     79F  THR      4.6     7.6    -      -       -      +
     80F  ASN*     4.0    14.4    -      -       -      +
    113F  ILE*     5.3     2.7    -      -       +      -
    188F  GLY*     3.6    29.2    -      -       -      +
    189F  GLY      3.4     2.0    -      -       -      +
    198F  LEU*     4.3    12.3    -      -       +      -
    200F  GLY*     1.3    73.7    -      -       -      +
    202F  ASN*     1.3    61.8    +      -       -      +
    203F  THR*     2.9    10.3    +      -       -      +
    218F  ALA*     3.1     2.1    -      -       -      -
    219F  ILE*     2.7    44.1    +      -       +      +
    224F  ALA*     4.2    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 202 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80F  ASN*     2.8     3.1    -      -       -      +
    143F  ALA*     4.0     7.8    -      -       -      +
    144F  VAL      4.1     3.5    -      -       -      +
    182F  ILE*     3.6    40.5    -      -       +      +
    186F  ASN*     3.8    17.9    -      -       -      +
    187F  SER*     3.5     2.8    -      -       -      -
    188F  GLY*     2.8    27.8    +      -       -      -
    189F  GLY      3.0     9.5    +      -       -      +
    190F  ALA      3.0    25.3    +      -       -      +
    191F  LEU*     3.4    26.5    -      -       -      +
    201F  ILE*     1.3    69.2    -      -       -      +
    203F  THR*     1.3    58.2    +      -       -      +
    217F  PHE      3.8     4.2    +      -       -      -
    218F  ALA*     3.8     7.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 203 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80F  ASN*     3.2    28.5    +      -       -      +
     82F  HIS*     3.3    20.1    +      -       -      -
    112F  ASP*     3.5    17.9    -      -       -      +
    170F  GLU*     3.6    14.6    -      -       -      +
    175F  PHE*     4.0    15.0    -      -       +      -
    182F  ILE*     5.7     1.7    -      -       -      +
    187F  SER*     4.2     6.0    -      -       -      -
    201F  ILE      2.9    15.9    +      -       -      -
    202F  ASN*     1.3    71.9    -      -       -      +
    204F  ALA*     1.3    59.2    +      -       +      +
    217F  PHE      2.9    14.0    +      -       -      -
    219F  ILE*     3.2    18.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 204 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169F  LEU*     3.9    37.9    -      -       +      -
    170F  GLU*     5.3     1.3    -      -       -      +
    175F  PHE*     5.0     1.8    -      -       +      -
    182F  ILE*     4.7     2.0    -      -       -      +
    203F  THR*     1.3    85.4    -      -       +      +
    205F  ILE*     1.3    67.5    +      -       -      +
    217F  PHE*     2.8    37.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 205 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169F  LEU*     5.1     5.2    -      -       -      +
    182F  ILE*     3.4    50.0    -      -       +      +
    183F  ASN*     4.6    10.5    -      -       -      -
    184F  ARG*     5.2     3.8    -      -       +      +
    204F  ALA*     1.3    84.7    -      -       -      +
    206F  LEU*     1.4    68.3    +      -       -      +
    207F  ALA*     3.6    26.7    +      -       +      -
    210F  GLY      4.6     7.6    -      -       -      +
    211F  GLY      4.3     1.6    -      -       -      -
    212F  SER*     4.1    14.1    -      -       -      +
    215F  ILE      3.4    13.9    -      -       -      +
    216F  GLY*     4.2     2.0    -      -       -      -
    217F  PHE*     4.2     4.5    -      -       -      -
----------------------------------------------------------
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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