Contacts of the strand formed by residues 166 - 171 (chain A) in PDB entry 1TUB


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 LYS 166 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  PHE*     3.4    19.1    -      -       +      +
    154A  MET*     1.4    77.3    +      -       +      +
    157A  LEU*     3.1    15.7    -      -       +      +
    158A  SER*     2.4    27.3    -      -       -      +
    164A  LYS      3.9     9.2    -      -       -      +
    165A  SER*     1.3    77.6    -      -       -      +
    167A  LEU*     1.2    62.6    +      -       -      +
    168A  GLU*     4.2     0.4    +      -       -      -
    197A  HIS*     1.7    23.1    +      -       +      -
    198A  SER*     3.8    11.7    -      -       -      +
    199A  ASP*     2.6    31.6    +      -       -      +
    200A  CYS      3.5     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  CYS*     5.6     0.2    -      -       -      -
    134A  GLY*     5.2     0.9    -      -       -      -
    135A  PHE      2.4    26.9    +      -       -      +
    136A  SER*     3.3     4.2    -      -       -      -
    137A  VAL*     2.9    14.1    +      -       -      +
    165A  SER      4.4     5.4    -      -       -      +
    166A  LYS*     1.2    83.6    -      -       -      +
    168A  GLU*     1.3    65.1    +      -       -      +
    169A  PHE*     5.6     4.7    -      -       +      -
    199A  ASP*     4.3     5.2    -      -       +      -
    200A  CYS*     3.3    28.9    -      -       +      +
    202A  PHE*     4.3    15.5    -      -       +      -
    238A  ILE*     5.3     3.8    -      -       +      -
    239A  THR*     5.8     0.2    -      -       -      +
    252A  LEU*     3.2    52.7    -      -       +      +
    255A  PHE*     4.4    15.0    -      -       +      -
    256A  GLN*     4.9     2.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  VAL*     3.0    20.6    -      -       +      +
    139A  HIS*     3.4     9.5    -      -       +      -
    154A  MET*     1.6    65.7    -      -       +      +
    166A  LYS*     4.4     1.1    -      -       +      -
    167A  LEU*     1.3    79.3    -      -       -      +
    169A  PHE*     1.3    69.3    +      -       -      +
    193A  THR*     3.0    27.3    -      -       -      +
    198A  SER*     4.2     8.7    -      -       -      -
    199A  ASP      5.9     0.2    -      -       -      +
    200A  CYS      3.6     5.0    +      -       -      +
    201A  ALA*     3.1    13.6    -      -       +      +
    202A  PHE*     3.0    26.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ILE*     4.2     9.6    -      -       +      -
    136A  SER*     5.0    10.8    -      -       -      -
    137A  VAL      2.4    20.4    +      -       -      +
    138A  PHE*     4.0    31.4    -      +       +      -
    139A  HIS*     2.9    29.5    +      -       -      +
    167A  LEU*     6.0     4.0    -      -       +      -
    168A  GLU*     1.3    80.6    -      -       -      +
    170A  SER*     1.2    62.9    +      -       -      +
    201A  ALA*     5.8     0.2    -      -       -      -
    202A  PHE*     3.1    30.5    -      +       +      -
    203A  MET*     5.2     0.9    -      -       -      -
    204A  VAL*     5.8     1.3    -      -       +      -
    231A  ILE*     5.1     8.3    -      -       +      -
    234A  ILE*     4.5     9.2    -      -       +      -
    235A  VAL*     2.8    46.2    -      -       +      -
    238A  ILE*     4.0    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  HIS*     3.2     6.1    -      -       -      -
    141A  PHE*     3.1    16.2    -      -       -      -
    169A  PHE*     1.2    80.0    -      -       -      +
    171A  ILE*     1.3    60.6    +      -       -      +
    201A  ALA*     5.8     1.8    -      -       -      -
    202A  PHE      2.3    14.1    +      -       -      -
    203A  MET*     0.5   171.5    -      -       -      +
    204A  VAL*     2.8    29.5    +      -       -      +
    231A  ILE*     5.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  ALA*     3.9    28.3    -      -       +      +
     16A  ILE*     4.6    18.2    -      -       +      -
    139A  HIS      3.1    10.8    +      -       -      +
    140A  SER*     3.5     3.1    -      -       -      -
    141A  PHE*     3.2    21.7    +      -       -      +
    170A  SER*     1.3    76.8    -      -       -      +
    172A  TYR*     1.3    59.7    -      -       -      +
    203A  MET*     2.2     8.6    -      -       -      +
    204A  VAL*     3.4    16.6    -      -       +      +
    206A  ASN*     3.3    32.3    -      -       +      +
    228A  ASN*     5.3     0.9    -      -       -      +
    231A  ILE*     5.0     5.6    -      -       +      -
    500A  GTP      3.5    41.7    -      -       +      +
----------------------------------------------------------
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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