Contacts of the strand formed by residues 198 - 205 (chain I) 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 I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68I  VAL*     4.1    17.5    -      -       +      -
     70I  ILE*     5.2     1.6    -      -       +      -
     78I  LEU*     4.8     8.3    -      -       +      -
    127I  ILE*     3.7    18.4    -      -       +      +
    128I  ALA      2.7    17.8    +      -       -      +
    129I  ILE*     4.3    14.4    -      -       +      -
    130I  ALA*     2.9    26.9    +      -       -      +
    190I  ALA*     3.7    27.1    -      -       +      -
    191I  LEU      3.6     3.6    -      -       -      +
    192I  LEU*     4.0     6.0    -      -       +      +
    196I  GLY      4.1     0.4    +      -       -      -
    197I  GLU*     1.3    68.2    -      -       -      +
    199I  ILE*     1.3    59.8    +      -       -      +
    200I  GLY      3.4    24.0    -      -       -      +
    201I  ILE*     3.7    22.0    -      -       +      -
    221I  SER*     3.3    19.5    +      -       -      +
    224I  ALA*     5.5     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 199 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130I  ALA*     3.9    18.6    -      -       +      -
    131I  ASP      5.7     0.4    -      -       -      +
    132I  SER*     3.8     4.3    -      -       -      -
    135I  LEU*     3.9    40.2    -      -       +      -
    140I  PHE      4.9     1.3    -      -       -      +
    141I  ALA*     4.1    10.5    -      -       +      -
    159I  VAL*     4.2     7.4    -      -       +      -
    176I  ILE*     3.2    15.6    -      -       -      +
    191I  LEU*     2.8    46.7    +      -       +      +
    192I  LEU      3.9    13.5    -      -       -      +
    193I  ASN*     4.0    15.7    -      -       +      +
    197I  GLU      3.4     6.0    +      -       -      +
    198I  LEU*     1.3    77.7    -      -       -      +
    200I  GLY*     1.3    58.7    +      -       -      +
    221I  SER*     3.0    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 200 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176I  ILE*     4.5     0.7    -      -       -      -
    191I  LEU*     2.9    35.5    +      -       -      -
    198I  LEU*     3.4    11.9    -      -       -      +
    199I  ILE*     1.3    82.1    -      -       -      +
    201I  ILE*     1.4    66.0    +      -       -      -
    218I  ALA*     4.2     5.4    -      -       -      -
    219I  ILE      3.1    13.9    -      -       -      -
    220I  PRO*     4.3     0.2    -      -       -      -
    221I  SER*     3.8     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 201 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68I  VAL*     4.0     9.0    -      -       +      -
     78I  LEU*     3.6    38.6    -      -       +      -
     79I  THR      4.7     7.6    -      -       -      +
     80I  ASN*     3.9    18.4    -      -       -      +
    113I  ILE*     5.3     2.9    -      -       +      -
    188I  GLY*     3.6    22.4    -      -       -      +
    189I  GLY      3.2    12.3    -      -       -      +
    198I  LEU*     3.7    24.5    -      -       +      -
    200I  GLY*     1.4    71.4    -      -       -      +
    202I  ASN*     1.3    62.5    +      -       -      +
    203I  THR*     2.6    24.5    +      -       -      +
    218I  ALA*     3.8     1.5    -      -       -      +
    219I  ILE*     2.9    31.3    +      -       +      +
    224I  ALA*     4.4     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 202 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80I  ASN*     3.0     1.6    -      -       -      +
    143I  ALA*     3.6    12.6    -      -       -      +
    144I  VAL      4.3     2.1    +      -       -      +
    178I  THR*     4.7     0.2    -      -       -      +
    182I  ILE*     3.5    40.0    -      -       +      +
    186I  ASN*     3.7    18.4    -      -       -      +
    187I  SER*     3.5     3.0    -      -       -      -
    188I  GLY*     2.9    28.2    +      -       -      -
    189I  GLY      3.1     6.1    +      -       -      +
    190I  ALA      3.0    28.1    +      -       -      +
    191I  LEU*     3.6    22.6    -      -       -      +
    201I  ILE*     1.3    68.2    -      -       -      +
    203I  THR*     1.3    58.3    +      -       -      +
    217I  PHE      3.8     4.4    +      -       -      -
    218I  ALA*     3.7     9.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 203 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80I  ASN*     3.3    21.9    +      -       -      +
     82I  HIS*     3.3    13.3    +      -       -      -
    112I  ASP*     3.8     5.4    -      -       -      +
    170I  GLU*     3.7    22.7    -      -       -      +
    175I  PHE*     3.9    20.4    -      -       +      -
    182I  ILE*     5.5     2.1    -      -       -      +
    187I  SER*     3.1    18.5    +      -       -      -
    201I  ILE      2.6    21.3    +      -       -      -
    202I  ASN*     1.3    71.1    -      -       -      +
    204I  ALA*     1.3    60.9    +      -       +      +
    217I  PHE      2.8    13.5    +      -       -      -
    219I  ILE*     3.2    21.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 204 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169I  LEU*     3.9    37.0    -      -       +      -
    170I  GLU*     5.3     1.6    -      -       -      +
    175I  PHE*     5.0     1.6    -      -       +      -
    182I  ILE*     4.8     1.9    -      -       -      +
    203I  THR*     1.3    86.7    -      -       +      +
    205I  ILE*     1.3    66.8    +      -       -      +
    217I  PHE*     2.8    37.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 205 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169I  LEU*     5.0     5.4    -      -       -      +
    182I  ILE*     3.5    50.0    -      -       +      +
    183I  ASN*     4.6    10.1    -      -       -      -
    184I  ARG*     5.2     3.6    -      -       +      +
    204I  ALA*     1.3    82.9    -      -       -      +
    206I  LEU*     1.3    67.4    +      -       -      +
    207I  ALA*     3.7    26.3    +      -       +      -
    210I  GLY      4.4     8.5    -      -       -      +
    211I  GLY      4.3     1.3    -      -       -      -
    212I  SER*     4.3    12.6    -      -       -      +
    215I  ILE      3.4    10.1    -      -       -      +
    216I  GLY*     4.1     6.1    -      -       -      -
    217I  PHE*     4.2     4.9    -      -       -      -
----------------------------------------------------------
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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