Contacts of the strand formed by residues 99 - 108 (chain J) 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 GLU 99 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30J  ARG*     6.2     2.2    -      -       -      -
     91J  SER*     5.8     5.2    -      -       -      -
     92J  ILE      3.3     6.5    -      -       -      +
     93J  GLN*     3.3    29.4    -      -       +      +
     97J  GLY      3.5     6.9    +      -       -      +
     98J  ARG*     1.3    76.4    -      -       -      +
    100J  PHE*     1.3    67.8    +      -       -      +
    250K  SER*     5.5     1.9    -      -       -      -
    251K  ALA*     3.8    23.9    +      -       +      +
    252K  ASP*     3.9    23.5    -      -       -      +
    255K  LYS*     2.7    31.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 100 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91J  SER*     3.3     6.6    -      -       -      -
     92J  ILE*     2.8    43.0    +      -       +      +
     94J  LEU*     3.7    35.0    -      -       +      -
     98J  ARG*     3.5    39.7    -      -       +      -
     99J  GLU*     1.3    79.4    -      -       -      +
    101J  ASP*     1.3    62.1    +      -       -      +
    118J  ILE*     3.5    29.6    -      -       +      -
    119J  GLN      3.8     4.7    -      -       -      +
    120J  ASN      3.5    22.0    -      -       -      -
    121J  PRO*     4.1     1.6    -      -       +      -
    122J  SER*     4.0    17.7    -      -       -      -
    124J  LEU*     4.0     6.3    -      -       +      -
    255K  LYS*     6.2     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 101 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89J  LYS*     5.4     6.2    -      -       -      +
     90J  ILE      3.3    18.8    +      -       -      +
     91J  SER*     5.1     5.0    -      -       -      -
    100J  PHE*     1.3    77.0    -      -       -      +
    102J  ALA*     1.3    62.1    +      -       -      +
    118J  ILE*     3.5     4.9    -      -       -      -
    119J  GLN*     2.8    43.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 102 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90J  ILE*     2.9    39.0    +      -       +      +
     92J  ILE*     3.6    30.7    -      -       +      -
    101J  ASP*     1.3    78.6    -      -       -      +
    103J  LYS*     1.3    65.7    -      -       -      +
    116J  LEU*     4.4     8.5    -      -       +      -
    117J  GLN      3.3    14.4    -      -       -      +
    118J  ILE*     4.5     2.9    -      -       +      -
    119J  GLN*     4.4     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 103 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90J  ILE*     5.2     0.4    -      -       -      -
    102J  ALA*     1.3    77.4    -      -       -      +
    104J  LEU*     1.3    66.5    +      -       -      +
    105J  ILE*     3.3     8.2    +      -       +      +
    116J  LEU*     3.4     5.0    -      -       -      -
    117J  GLN*     2.9    30.9    +      -       -      -
    119J  GLN*     3.5    38.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 104 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84J  ILE*     3.9    26.5    -      -       +      +
     90J  ILE*     4.5    13.0    -      -       +      +
    103J  LYS*     1.3    72.0    -      -       -      +
    105J  ILE*     1.3    63.8    +      -       -      +
    106J  GLY*     3.5    29.6    -      -       -      +
    107J  SER*     4.4    12.3    -      -       -      +
    114J  ALA*     4.2     4.7    -      -       +      -
    115J  LEU      3.5     9.2    -      -       -      +
    116J  LEU*     3.8    18.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 105 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76J  TYR*     4.6     6.7    -      -       +      -
    103J  LYS*     3.3     6.5    +      -       +      +
    104J  LEU*     1.3    77.9    -      -       -      +
    106J  GLY*     1.3    58.7    +      -       -      +
    115J  LEU*     2.8    35.8    +      -       +      +
    116J  LEU      4.1     2.5    -      -       -      -
    117J  GLN*     3.5    48.7    -      -       +      +
    231J  LEU      3.4    22.9    -      -       -      +
    232J  ILE*     4.0     8.1    -      -       +      +
    235J  GLY*     3.9    15.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 106 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104J  LEU*     3.5    11.5    -      -       -      +
    105J  ILE*     1.3    81.8    -      -       -      +
    107J  SER*     1.3    60.5    +      -       -      -
    115J  LEU*     2.8    30.4    +      -       -      +
    231J  LEU*     3.6    19.5    -      -       -      +
    235J  GLY      3.8     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 107 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81J  ASN*     3.3    25.2    +      -       -      -
     84J  ILE*     5.0     0.4    -      -       -      -
    104J  LEU*     4.4    14.2    -      -       -      +
    106J  GLY*     1.3    75.3    -      -       -      -
    108J  ASP*     1.3    61.3    +      -       -      +
    109J  ASP*     4.2     8.6    +      -       -      +
    113J  ILE      3.3    10.5    -      -       -      -
    114J  ALA*     4.0     9.2    -      -       -      -
    231J  LEU*     3.4    14.7    -      -       -      +
    235J  GLY      4.8     1.0    +      -       -      +
    236J  GLU*     5.3     2.4    -      -       -      -
    237J  ILE*     4.8     5.2    -      -       -      +
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Residues in contact with ASP 108 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81J  ASN*     3.9     4.4    -      -       -      +
    107J  SER*     1.3    72.7    -      -       -      +
    109J  ASP*     1.3    58.7    +      -       -      +
    110J  GLN*     3.2    11.6    +      -       -      +
    111J  SER*     2.6    29.9    +      -       -      +
    112J  ASP*     2.9    26.2    +      -       -      -
    113J  ILE*     2.7    20.0    +      -       +      +
    227J  LEU*     4.0     3.4    -      -       +      +
    231J  LEU*     5.5     0.2    -      -       +      -
    237J  ILE*     3.7    26.5    -      -       +      +
    239J  ARG*     2.8    43.9    +      -       -      -
----------------------------------------------------------
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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