Contacts of the strand formed by residues 166 - 172 (chain B) 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 THR 166 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161B  GLU      3.6     1.2    -      -       -      +
    162B  VAL*     3.5     7.4    -      -       -      +
    163B  ASN*     3.2    35.8    +      -       -      -
    164B  GLY      3.4     0.6    -      -       -      +
    165B  GLY*     1.4    81.5    +      -       -      +
    167B  LEU*     1.3    65.1    +      -       -      +
    168B  ARG*     4.1     7.2    -      -       +      +
    181B  SER*     3.9    18.2    -      -       -      +
    182B  LEU      3.4    25.1    -      -       -      +
    183B  ASP*     4.2     5.6    -      -       -      +
    184B  ALA*     4.8     0.9    -      -       -      -
    186B  ILE*     5.0     1.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  PHE*     3.8    24.0    -      -       +      -
    130B  ILE*     3.7    21.5    -      -       +      -
    135B  LEU*     4.3    12.3    -      -       +      -
    138B  LEU*     3.6    31.6    -      -       +      +
    160B  LEU*     4.8    12.1    -      -       +      -
    161B  GLU      3.6    20.6    -      -       -      +
    162B  VAL*     3.8    18.4    -      -       +      -
    165B  GLY      4.3     0.6    +      -       -      -
    166B  THR*     1.3    73.4    -      -       -      +
    168B  ARG*     1.3    62.0    +      -       -      +
    181B  SER*     3.5     1.9    -      -       -      -
    182B  LEU*     2.8    37.6    +      -       +      +
    184B  ALA*     4.2    13.2    -      -       +      +
    186B  ILE*     4.4     3.1    -      -       +      -
    219B  LEU*     6.0     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138B  LEU*     5.0     0.9    -      -       -      -
    159B  LEU      3.6     0.7    -      -       -      +
    160B  LEU*     3.4     7.5    -      -       -      +
    161B  GLU*     2.8    57.4    +      -       +      +
    166B  THR*     4.1     8.0    -      -       +      +
    167B  LEU*     1.3    76.6    -      -       -      +
    169B  SER*     1.3    68.6    +      -       -      +
    170B  VAL*     3.8     9.1    +      -       +      -
    179B  MET*     3.5    24.1    -      -       +      +
    180B  CYS      3.2    11.2    -      -       -      +
    181B  SER*     2.8    25.2    +      -       -      +
    245B  TYR*     2.9    39.3    +      -       -      -
    246B  GLU*     4.9     5.5    +      -       -      +
    249B  LEU*     6.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138B  LEU*     2.8    41.2    +      -       -      +
    142B  THR*     3.4    15.4    -      -       -      +
    158B  MET*     3.9     5.8    -      -       -      -
    159B  LEU      3.1     6.7    -      -       -      -
    160B  LEU*     3.9    13.7    -      -       -      -
    168B  ARG*     1.3    71.6    -      -       -      +
    170B  VAL*     1.3    66.0    +      -       -      +
    179B  MET*     3.2     5.3    -      -       -      +
    180B  CYS*     2.9    33.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  THR*     5.1     0.2    -      -       -      -
    158B  MET*     3.7     3.3    -      -       -      +
    159B  LEU*     2.9    51.9    +      -       +      +
    168B  ARG*     3.8    24.2    -      -       +      -
    169B  SER*     1.3    80.6    -      -       -      +
    171B  ALA*     1.3    64.8    +      -       -      +
    177B  LEU*     3.9    22.7    -      -       +      -
    178B  ALA      3.4     9.6    -      -       -      +
    179B  MET*     4.1     7.6    -      -       +      -
    242B  PHE*     3.7    27.9    -      -       +      -
    245B  TYR*     4.0    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  THR*     3.3    31.9    -      -       -      +
    145B  ALA*     3.4     2.9    -      -       -      +
    146B  MET*     3.6    28.5    -      -       +      +
    157B  GLY      4.6     3.6    -      -       -      +
    158B  MET*     4.6     3.1    -      -       +      -
    170B  VAL*     1.3    76.4    -      -       -      +
    172B  THR*     1.3    64.1    +      -       -      +
    177B  LEU*     3.3     2.8    -      -       -      +
    178B  ALA      2.9    33.3    +      -       -      +
    242B  PHE*     4.4     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  ALA      3.0    12.2    +      -       -      +
    146B  MET*     4.4     1.0    -      -       -      +
    147B  ALA      3.6     6.6    +      -       -      -
    152B  ARG*     6.3     0.2    -      -       -      +
    155B  LEU*     3.6    43.0    +      -       +      +
    157B  GLY      5.2     0.2    +      -       -      -
    171B  ALA*     1.3    75.2    -      -       -      +
    173B  ASP*     1.3    57.5    +      -       -      +
    174B  GLY*     3.4    12.7    +      -       -      +
    176B  ARG      2.7    21.5    +      -       -      -
    177B  LEU*     3.7    20.6    -      -       +      +
    242B  PHE*     3.9    18.8    -      -       +      -
    243B  PRO*     5.1     4.9    -      -       +      -
    245B  TYR*     5.9     0.9    -      -       +      -
    248B  VAL*     5.8     2.3    -      -       -      +
----------------------------------------------------------
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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