Contacts of the strand formed by residues 231 - 236 (chain A) in PDB entry 4TR8


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 PHE 231 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  LEU*     5.9     5.4    -      -       +      -
     53A  LEU*     3.8    23.6    -      -       +      -
     54A  VAL      3.1    13.2    -      -       -      +
     55A  GLY*     4.6     2.0    -      -       -      -
     56A  ARG*     3.2    10.9    +      -       -      +
    132A  GLN*     5.2     0.2    -      -       -      -
    204A  LEU*     4.5     5.6    -      -       +      -
    207A  LEU*     3.2    57.7    -      -       +      -
    208A  LEU*     4.3     9.6    -      -       +      -
    210A  GLU*     5.1     4.0    -      -       -      -
    226A  ALA*     4.1     8.1    -      -       +      -
    227A  THR*     3.5     0.2    -      -       -      -
    228A  THR*     2.9    70.0    +      -       +      -
    229A  GLY      3.5     0.6    -      -       -      -
    230A  GLU*     1.4    84.9    -      -       +      +
    232A  THR*     1.3    59.7    +      -       -      +
    233A  PHE*     3.9    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  GLU*     3.7     3.3    -      -       -      +
     53A  LEU*     3.6     2.3    -      -       -      -
     54A  VAL*     2.8    49.1    +      -       +      +
     56A  ARG*     2.8    35.7    +      -       -      +
    225A  ARG*     3.8    24.5    -      -       +      +
    226A  ALA      3.5     2.2    -      -       -      -
    227A  THR*     3.7    23.4    -      -       +      +
    231A  PHE*     1.3    70.9    +      -       -      +
    233A  PHE*     1.3    60.1    +      -       -      +
    234A  THR*     4.2     4.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  VAL*     4.2    14.4    -      -       +      -
     52A  GLU      3.5     7.4    -      -       -      -
     53A  LEU*     4.2     7.9    -      -       +      -
    196A  VAL*     5.3     1.8    -      -       +      -
    200A  GLY*     3.2    30.7    -      -       -      -
    203A  GLU*     4.0    17.9    -      -       +      -
    204A  LEU*     3.9    30.3    -      -       +      -
    207A  LEU*     3.8    16.6    -      -       +      -
    224A  ILE*     4.7     9.0    -      -       +      -
    225A  ARG*     3.3     5.4    -      -       -      +
    226A  ALA*     2.8    48.9    +      -       +      +
    231A  PHE*     3.9    18.6    -      -       +      -
    232A  THR*     1.3    71.6    -      -       -      +
    234A  THR*     1.3    64.5    +      -       -      +
    235A  SER*     3.8    30.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLU      4.1     0.3    -      -       -      +
     51A  VAL*     3.2     5.4    -      -       -      +
     52A  GLU*     2.8    58.2    +      -       +      +
    119A  VAL*     4.0    18.2    -      -       +      -
    121A  GLU*     5.1     4.5    -      -       +      -
    223A  HIS*     3.7    26.5    -      -       +      -
    224A  ILE      3.4     8.7    -      -       -      +
    225A  ARG*     3.7    20.5    -      -       +      +
    232A  THR*     4.5     4.9    +      -       -      +
    233A  PHE*     1.3    79.2    +      -       -      +
    235A  SER*     1.3    63.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLU*     3.5     5.3    +      -       -      +
     51A  VAL*     3.6    13.4    -      -       -      +
    196A  VAL*     4.2     4.8    -      -       -      +
    197A  PRO*     3.8    12.5    -      -       -      +
    200A  GLY*     4.4     1.6    -      -       -      -
    223A  HIS*     3.2     9.3    -      -       -      -
    224A  ILE*     3.0    41.8    +      -       -      +
    233A  PHE*     3.8    25.1    -      -       -      -
    234A  THR*     1.3    75.5    -      -       -      +
    236A  LYS*     1.3    79.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  LEU      3.4    24.7    +      -       -      +
     50A  GLU*     3.0    27.6    +      -       +      +
    197A  PRO*     3.1    14.2    -      -       +      +
    222A  HIS      3.5     8.1    -      -       -      +
    223A  HIS*     3.7    23.4    +      -       +      +
    235A  SER*     1.3    88.4    +      -       -      +
    237A  LEU*     1.3    68.1    +      -       -      +
----------------------------------------------------------
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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