Contacts of the strand formed by residues 24 - 28 (chain I) in PDB entry 3EXG


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 THR 24 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6I  THR*     3.8    20.6    -      -       -      +
      7I  PHE      3.3     6.4    +      -       -      -
      8I  GLU*     6.1     0.4    -      -       -      +
      9I  ILE*     4.3     0.4    -      -       -      -
     22I  PRO*     3.2    25.3    +      -       +      +
     23I  VAL*     1.3    83.4    -      -       +      +
     25I  THR*     1.3    66.3    +      -       -      +
    235I  GLU*     4.6     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 25 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5I  ALA      4.0     0.2    -      -       -      +
      6I  THR*     3.3     7.9    -      -       -      +
      7I  PHE*     2.9    35.9    +      -       +      +
      9I  ILE*     3.8    29.6    -      -       +      -
     24I  THR*     1.3    78.3    +      -       -      +
     26I  VAL*     1.3    69.9    +      -       -      +
     27I  LEU      4.2     0.4    +      -       -      -
    231I  LEU*     4.2    18.4    -      -       +      -
    234I  ARG*     2.8    27.2    +      -       -      +
    235I  GLU*     3.3    22.5    +      -       +      -
    238I  ARG*     5.2     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 26 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4I  ASP*     4.3    17.7    -      -       +      +
      5I  ALA      3.5    14.1    -      -       -      +
      6I  THR*     3.7    17.5    -      -       -      +
     25I  THR*     1.3    76.6    +      -       -      +
     27I  LEU*     1.3    66.4    +      -       -      +
     28I  THR*     4.2    14.5    +      -       +      +
     31I  ASP*     5.5     0.3    -      -       -      +
    234I  ARG*     3.1    20.8    +      -       -      -
    238I  ARG*     5.3     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 27 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4I  ASP*     3.1    21.6    -      -       -      -
      5I  ALA      3.2     9.4    +      -       -      -
      7I  PHE*     3.7    25.5    -      -       +      -
     25I  THR      4.2     0.4    -      -       -      -
     26I  VAL*     1.3    71.2    -      -       -      +
     28I  THR*     1.3    67.0    +      -       -      +
     29I  ARG      3.7     0.2    +      -       -      -
     31I  ASP*     3.7     7.4    -      -       +      -
     32I  GLY*     3.2    36.1    -      -       -      +
     35I  TYR*     4.3    10.1    -      -       +      -
    231I  LEU*     4.2    19.5    -      -       +      -
    234I  ARG*     4.4     4.0    -      -       -      +
    291I  LEU*     4.0    26.9    -      -       +      -
    295I  MET*     4.3     3.4    -      -       +      -
    300I  LEU*     3.7    24.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 28 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3I  ASN      3.4    10.5    -      -       -      -
      4I  ASP*     3.6     5.2    -      -       +      -
     26I  VAL*     4.5    15.0    -      -       +      +
     27I  LEU*     1.3    79.3    -      -       -      +
     29I  ARG*     1.3    65.9    +      -       -      +
     30I  GLU*     3.6     7.8    +      -       -      +
     31I  ASP*     3.0    42.7    +      -       -      +
     32I  GLY      3.2    10.0    +      -       -      -
    300I  LEU*     4.3     0.4    -      -       -      -
----------------------------------------------------------
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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