Contacts of the strand formed by residues 198 - 205 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68E  VAL*     4.1    16.2    -      -       +      -
     70E  ILE*     5.3     0.7    -      -       +      -
     78E  LEU*     4.7    10.5    -      -       +      -
    127E  ILE*     3.8    17.4    -      -       +      +
    128E  ALA      2.8    16.6    +      -       -      +
    129E  ILE*     4.3    15.0    -      -       +      -
    130E  ALA*     3.0    23.9    +      -       -      +
    190E  ALA*     3.7    27.6    -      -       +      -
    191E  LEU      3.6     3.4    -      -       -      +
    192E  LEU*     4.1     6.2    -      -       +      +
    196E  GLY      4.1     0.2    +      -       -      -
    197E  GLU*     1.4    68.1    -      -       -      +
    199E  ILE*     1.3    59.8    +      -       -      +
    200E  GLY      3.5    24.2    -      -       -      +
    201E  ILE*     4.0    20.6    -      -       +      -
    221E  SER*     3.3    19.6    +      -       -      +
    224E  ALA*     5.5     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 199 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130E  ALA*     3.9     8.3    -      -       +      -
    131E  ASP      5.6     0.2    -      -       -      +
    132E  SER*     3.7     5.1    -      -       -      -
    135E  LEU*     3.9    40.8    -      -       +      -
    140E  PHE      4.9     1.6    -      -       -      +
    141E  ALA*     4.1    16.8    -      -       +      -
    159E  VAL*     4.3     6.7    -      -       +      -
    176E  ILE*     3.2    16.1    -      -       -      +
    191E  LEU*     2.8    46.5    +      -       +      +
    192E  LEU      3.9     7.2    -      -       -      +
    193E  ASN*     3.9    29.2    -      -       +      +
    197E  GLU      3.4     2.4    +      -       -      +
    198E  LEU*     1.3    76.7    -      -       -      +
    200E  GLY*     1.3    58.3    +      -       -      +
    221E  SER*     3.0    25.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 200 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176E  ILE*     4.4     0.9    -      -       -      -
    191E  LEU*     2.8    42.1    +      -       -      +
    198E  LEU*     3.5    10.4    -      -       -      +
    199E  ILE*     1.3    80.8    -      -       -      +
    201E  ILE*     1.4    62.3    +      -       -      -
    218E  ALA*     4.2     5.6    -      -       -      -
    219E  ILE      3.1    14.1    -      -       -      -
    220E  PRO*     4.3     0.2    -      -       -      -
    221E  SER*     3.7     6.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 201 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68E  VAL*     3.6    31.0    -      -       +      -
     78E  LEU*     4.0    23.6    -      -       +      -
     79E  THR      4.5    10.1    -      -       -      +
     80E  ASN*     4.0    15.0    -      -       -      +
    113E  ILE*     5.2     2.2    -      -       +      -
    188E  GLY*     3.9    28.5    -      -       -      +
    189E  GLY      3.4     2.5    -      -       -      +
    198E  LEU*     4.0    17.9    -      -       +      -
    200E  GLY*     1.4    71.6    -      -       -      -
    202E  ASN*     1.4    51.5    +      -       -      +
    203E  THR*     2.9    23.5    +      -       -      +
    218E  ALA*     3.9     1.1    -      -       -      -
    219E  ILE*     2.9    37.4    +      -       +      +
    224E  ALA*     4.0    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 202 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80E  ASN*     3.1     1.6    -      -       -      +
    143E  ALA*     3.9     9.5    -      -       -      +
    144E  VAL      4.2     3.3    -      -       -      +
    182E  ILE*     3.7    35.6    -      -       +      +
    186E  ASN*     4.2    13.7    -      -       -      +
    187E  SER*     3.4     3.0    -      -       -      -
    188E  GLY      2.9    29.3    +      -       -      -
    189E  GLY*     3.0    13.2    +      -       -      +
    190E  ALA      3.2    20.9    -      -       -      +
    191E  LEU*     3.3    34.6    -      -       -      +
    201E  ILE*     1.4    67.0    -      -       -      +
    203E  THR*     1.3    58.4    +      -       -      +
    217E  PHE      3.7     5.8    -      -       -      +
    218E  ALA*     3.9     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 203 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80E  ASN*     3.0    22.2    +      -       -      +
     82E  HIS*     3.3    20.3    +      -       +      -
    112E  ASP*     3.6    23.6    -      -       -      +
    170E  GLU*     3.6    15.0    -      -       -      +
    175E  PHE*     4.1    19.1    -      -       +      -
    182E  ILE*     5.6     1.8    -      -       -      +
    187E  SER*     4.1     6.9    +      -       -      -
    201E  ILE      2.9    16.2    +      -       -      -
    202E  ASN*     1.3    70.3    -      -       -      +
    204E  ALA*     1.3    61.4    +      -       +      +
    217E  PHE      2.8    13.6    +      -       -      -
    219E  ILE*     3.1    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 204 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169E  LEU*     3.9    37.7    -      -       +      -
    170E  GLU*     5.2     1.1    -      -       -      +
    175E  PHE*     5.0     1.1    -      -       +      -
    182E  ILE*     4.7     2.2    -      -       -      +
    203E  THR*     1.3    87.9    -      -       +      +
    205E  ILE*     1.3    65.6    +      -       -      +
    217E  PHE*     2.7    38.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 205 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169E  LEU*     5.0     6.5    -      -       -      +
    182E  ILE*     3.4    48.9    -      -       +      +
    183E  ASN*     4.5    10.5    -      -       -      -
    184E  ARG*     5.2     3.6    -      -       +      +
    204E  ALA*     1.3    83.8    -      -       -      +
    206E  LEU*     1.3    68.2    +      -       -      +
    207E  ALA*     3.8    26.4    +      -       +      -
    210E  GLY      4.6     7.9    -      -       -      +
    211E  GLY      4.3     1.1    -      -       -      -
    212E  SER*     4.1    14.8    -      -       -      +
    215E  ILE      3.4    13.2    -      -       -      +
    216E  GLY*     4.1     2.2    -      -       -      -
    217E  PHE*     4.2     4.7    -      -       -      -
----------------------------------------------------------
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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