Contacts of the strand formed by residues 99 - 108 (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 GLU 99 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250D  SER*     5.5     1.6    -      -       -      -
    251D  ALA*     3.6    27.5    +      -       +      +
    252D  ASP*     4.0    20.4    -      -       -      +
    255D  LYS*     2.8    37.2    +      -       -      +
     30F  ARG*     6.2     1.8    -      -       -      -
     91F  SER*     5.8     5.6    -      -       -      -
     92F  ILE      3.3     6.5    -      -       -      +
     93F  GLN*     3.3    28.6    -      -       +      +
     97F  GLY      3.5     4.1    +      -       -      +
     98F  ARG*     1.3    76.7    -      -       -      +
    100F  PHE*     1.3    67.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 100 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255D  LYS*     5.1     1.1    -      -       -      +
     91F  SER*     3.3     6.5    -      -       -      -
     92F  ILE*     2.8    41.0    +      -       +      +
     94F  LEU*     3.7    34.5    -      -       +      -
     98F  ARG*     3.5    40.6    -      -       +      -
     99F  GLU*     1.3    79.1    -      -       -      +
    101F  ASP*     1.3    63.2    +      -       -      +
    118F  ILE*     3.5    29.6    -      -       +      -
    119F  GLN      3.8     4.5    -      -       -      -
    120F  ASN      3.5    22.4    -      -       -      -
    121F  PRO*     4.1     1.6    -      -       +      -
    122F  SER*     3.9    17.0    -      -       -      -
    124F  LEU*     4.0     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 101 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89F  LYS*     5.4     6.2    -      -       -      +
     90F  ILE      3.3    19.2    +      -       -      +
     91F  SER*     5.1     4.4    -      -       -      -
    100F  PHE*     1.3    78.6    -      -       -      +
    102F  ALA*     1.3    60.9    +      -       -      +
    118F  ILE*     3.5     4.5    -      -       -      -
    119F  GLN*     2.8    43.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 102 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90F  ILE*     2.9    38.1    +      -       +      +
     92F  ILE*     3.6    31.2    -      -       +      -
    101F  ASP*     1.3    79.2    -      -       -      +
    103F  LYS*     1.3    65.7    +      -       -      +
    116F  LEU*     4.4     9.0    -      -       +      -
    117F  GLN      3.3    14.8    -      -       -      +
    118F  ILE*     4.5     2.9    -      -       +      -
    119F  GLN*     4.4     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 103 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90F  ILE*     5.2     0.7    -      -       -      -
    102F  ALA*     1.3    78.5    -      -       -      +
    104F  LEU*     1.3    67.4    +      -       -      +
    105F  ILE*     3.3     7.8    +      -       +      +
    116F  LEU*     3.3     5.1    -      -       -      -
    117F  GLN*     2.9    31.0    +      -       -      -
    119F  GLN*     3.5    39.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 104 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84F  ILE*     4.0    25.6    -      -       +      +
     90F  ILE*     4.5    11.6    -      -       +      +
    103F  LYS*     1.3    72.7    -      -       -      +
    105F  ILE*     1.3    63.3    +      -       -      +
    106F  GLY*     3.4    30.5    -      -       -      +
    107F  SER*     4.4    11.9    -      -       -      +
    114F  ALA*     4.1     5.2    -      -       +      -
    115F  LEU      3.5     8.7    -      -       -      +
    116F  LEU*     3.8    19.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 105 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76F  TYR*     4.3    11.7    -      -       +      -
    103F  LYS*     4.2     6.1    -      -       +      +
    104F  LEU*     1.3    78.6    -      -       -      +
    106F  GLY*     1.3    59.2    +      -       -      +
    115F  LEU*     2.8    29.1    +      -       +      +
    116F  LEU      4.1     2.5    -      -       -      -
    117F  GLN*     3.5    49.6    -      -       +      +
    231F  LEU      3.5    24.7    -      -       -      +
    232F  ILE*     4.6     3.8    -      -       -      +
    235F  GLY*     3.8    14.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 106 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104F  LEU*     3.4    11.6    -      -       -      +
    105F  ILE*     1.3    81.9    -      -       -      +
    107F  SER*     1.3    59.1    +      -       -      -
    115F  LEU*     2.8    30.9    +      -       -      +
    231F  LEU*     3.6    20.5    -      -       -      +
    235F  GLY      3.9     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 107 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81F  ASN*     3.3    24.8    +      -       -      -
     84F  ILE*     5.1     0.4    -      -       -      -
    104F  LEU*     4.4    14.3    -      -       -      +
    106F  GLY*     1.3    74.6    -      -       -      -
    108F  ASP*     1.3    60.1    +      -       -      +
    109F  ASP*     4.2     8.7    +      -       -      +
    113F  ILE      3.3    11.0    -      -       -      -
    114F  ALA*     4.0     9.2    -      -       -      +
    231F  LEU*     3.6    14.1    -      -       -      +
    235F  GLY      5.0     0.4    +      -       -      -
    236F  GLU*     5.5     1.2    -      -       -      -
    237F  ILE*     5.2     4.5    +      -       -      +
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Residues in contact with ASP 108 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81F  ASN*     3.9     4.0    -      -       -      +
    107F  SER*     1.3    71.6    -      -       -      +
    109F  ASP*     1.3    58.2    +      -       -      +
    110F  GLN*     3.2    13.2    +      -       -      +
    111F  SER*     2.6    30.0    +      -       -      +
    112F  ASP*     3.0    26.0    +      -       -      -
    113F  ILE*     2.7    22.4    +      -       +      +
    227F  LEU*     3.7     4.9    -      -       +      +
    231F  LEU*     5.6     0.2    -      -       +      -
    237F  ILE*     4.0    23.3    -      -       +      +
    239F  ARG*     3.2    39.0    +      -       -      -
----------------------------------------------------------
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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