Contacts of the strand formed by residues 198 - 205 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68D  VAL*     4.1    11.7    -      -       +      -
     70D  ILE*     5.3     1.3    -      -       +      -
     78D  LEU*     4.8    11.0    -      -       +      -
    127D  ILE*     3.8    17.9    -      -       +      +
    128D  ALA      2.7    17.0    +      -       -      +
    129D  ILE*     4.2    15.7    -      -       +      -
    130D  ALA*     2.9    24.3    +      -       -      +
    190D  ALA*     3.8    26.7    -      -       +      -
    191D  LEU      3.6     3.6    -      -       -      +
    192D  LEU*     4.1     5.4    -      -       +      +
    196D  GLY      4.1     0.2    +      -       -      -
    197D  GLU*     1.4    67.9    -      -       -      +
    199D  ILE*     1.3    58.2    +      -       -      +
    200D  GLY      3.4    24.2    -      -       -      +
    201D  ILE*     3.9    24.5    -      -       +      -
    221D  SER*     3.4    19.2    +      -       -      +
    224D  ALA*     5.5     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 199 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130D  ALA*     3.9    17.7    -      -       +      -
    131D  ASP      5.7     0.2    -      -       -      +
    132D  SER*     3.8     4.2    -      -       -      -
    135D  LEU*     3.8    41.3    -      -       +      -
    140D  PHE      4.9     1.8    -      -       -      +
    141D  ALA*     4.0    17.7    -      -       +      -
    159D  VAL*     4.3     6.7    -      -       +      -
    176D  ILE*     3.1    16.0    -      -       +      +
    191D  LEU*     2.8    44.5    +      -       +      +
    192D  LEU      3.9     8.1    -      -       -      +
    193D  ASN*     3.9    20.0    -      -       +      +
    197D  GLU      4.0     2.2    -      -       -      +
    198D  LEU*     1.3    78.5    -      -       -      +
    200D  GLY*     1.3    58.4    +      -       -      +
    220D  PRO*     3.7     0.2    -      -       -      +
    221D  SER*     3.0    25.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 200 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176D  ILE*     4.4     1.1    -      -       -      -
    190D  ALA      3.8     0.2    -      -       -      -
    191D  LEU*     2.8    38.0    +      -       -      -
    198D  LEU*     3.4    13.8    -      -       -      +
    199D  ILE*     1.3    81.2    -      -       -      +
    201D  ILE*     1.3    63.3    +      -       -      -
    218D  ALA*     4.3     5.2    -      -       -      -
    219D  ILE      3.1    13.5    -      -       -      -
    220D  PRO*     4.3     0.2    -      -       -      -
    221D  SER*     3.8     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 201 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68D  VAL*     3.6    33.7    -      -       +      -
     78D  LEU*     4.3    17.7    -      -       +      -
     79D  THR      4.8     6.3    -      -       -      +
     80D  ASN*     3.8    16.6    -      -       -      +
    113D  ILE*     5.6     2.5    -      -       +      -
    188D  GLY*     3.7    30.1    -      -       -      +
    189D  GLY      3.4     3.1    -      -       -      +
    198D  LEU*     3.9    18.6    -      -       +      -
    200D  GLY*     1.3    73.4    -      -       -      +
    202D  ASN*     1.3    56.0    +      -       -      +
    203D  THR*     2.8    14.6    +      -       -      -
    218D  ALA*     3.7     2.5    -      -       -      -
    219D  ILE*     2.8    43.9    +      -       +      +
    224D  ALA*     4.1    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 202 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80D  ASN*     3.0     1.9    -      -       -      +
    143D  ALA*     3.6    12.5    -      -       -      +
    144D  VAL      4.1     3.8    -      -       -      +
    182D  ILE*     3.7    36.7    -      -       +      +
    186D  ASN*     3.6    21.3    -      -       -      +
    187D  SER*     3.4     3.3    -      -       -      -
    188D  GLY      2.9    29.1    +      -       -      -
    189D  GLY      2.9    13.0    +      -       -      +
    190D  ALA      3.2    21.0    +      -       -      +
    191D  LEU*     3.5    25.7    -      -       -      +
    200D  GLY      4.1     0.2    -      -       -      -
    201D  ILE*     1.3    67.6    -      -       -      +
    203D  THR*     1.3    58.5    +      -       -      +
    217D  PHE      3.8     4.3    -      -       -      -
    218D  ALA*     3.8     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 203 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80D  ASN*     3.2    22.8    +      -       -      +
     82D  HIS*     3.3    18.2    -      -       -      -
    112D  ASP*     3.5    23.3    -      -       -      +
    170D  GLU*     3.6    14.6    -      -       -      +
    175D  PHE*     4.0    15.3    -      -       +      -
    182D  ILE*     5.6     2.1    -      -       -      +
    187D  SER*     3.5     7.9    +      -       -      -
    201D  ILE      2.8    16.1    +      -       -      -
    202D  ASN*     1.3    71.0    -      -       -      +
    204D  ALA*     1.4    59.7    +      -       +      +
    217D  PHE      2.9    13.8    +      -       -      -
    219D  ILE*     3.2    17.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 204 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169D  LEU*     3.9    37.5    -      -       +      -
    170D  GLU*     5.3     1.1    -      -       -      +
    175D  PHE*     5.0     2.2    -      -       +      -
    182D  ILE*     4.7     2.0    -      -       -      +
    203D  THR*     1.4    85.4    -      -       +      +
    205D  ILE*     1.3    66.8    +      -       -      +
    217D  PHE*     2.8    38.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 205 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169D  LEU*     5.0     5.5    -      -       -      +
    182D  ILE*     3.4    48.9    -      -       +      +
    183D  ASN*     4.6     9.6    -      -       -      -
    184D  ARG*     5.2     3.1    -      -       +      +
    204D  ALA*     1.3    83.7    -      -       -      +
    206D  LEU*     1.3    67.2    +      -       -      +
    207D  ALA*     3.7    26.8    +      -       +      -
    210D  GLY      4.5     8.7    -      -       -      +
    211D  GLY      4.3     1.3    -      -       -      -
    212D  SER*     4.1    13.2    -      -       -      +
    215D  ILE      3.4     9.6    -      -       -      +
    216D  GLY*     4.0     6.5    -      -       -      -
    217D  PHE*     4.2     5.4    -      -       -      -
----------------------------------------------------------
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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