Contacts of the strand formed by residues 176 - 183 (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 ARG 176 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  PHE*     3.4    33.2    +      -       +      -
    145A  ALA*     3.8    18.6    -      -       -      +
    146A  MET      5.4     1.0    +      -       -      -
    172A  THR*     2.7    28.1    +      -       -      -
    173A  ASP*     2.8    33.0    +      -       -      +
    175A  HIS*     1.3    77.9    -      -       -      +
    177A  LEU*     1.3    59.3    +      -       -      +
    323A  SER*     5.6     0.2    +      -       -      -
    324A  TYR*     3.5    45.1    +      -       +      +
    327A  ASP*     2.8    33.3    +      -       -      +
    361A  VAL*     3.3    15.3    -      -       -      +
    362A  VAL*     4.4    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  PHE*     5.4     1.9    -      -       -      -
    145A  ALA*     4.2     3.1    -      -       -      -
    170A  VAL*     3.8    19.3    -      -       +      -
    171A  ALA      3.3    11.0    -      -       -      +
    172A  THR*     3.9    16.4    -      -       +      +
    176A  ARG*     1.3    76.8    -      -       -      +
    178A  ALA*     1.3    76.9    +      -       -      +
    179A  MET*     4.1    12.6    -      -       +      -
    245A  TYR*     3.8    21.8    -      -       +      -
    248A  VAL*     4.6    15.5    -      -       +      -
    249A  LEU*     4.0    22.9    -      -       +      -
    328A  VAL*     5.7     1.0    -      -       -      +
    359A  ALA      4.5     1.1    -      -       -      +
    360A  TYR*     3.3     5.7    -      -       -      +
    361A  VAL*     2.9    46.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  THR*     3.7    32.1    -      -       -      +
    144A  PHE*     3.9     4.3    -      -       +      -
    145A  ALA*     3.8     7.8    -      -       +      +
    170A  VAL*     3.4     4.2    -      -       -      +
    171A  ALA      2.9    31.8    +      -       -      +
    177A  LEU*     1.3    76.5    -      -       -      +
    179A  MET*     1.3    60.2    +      -       -      +
    359A  ALA      3.6     6.1    -      -       -      -
    360A  TYR*     3.5    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  THR*     3.6     5.0    -      -       -      +
    168A  ARG*     3.4    45.3    -      -       -      +
    169A  SER      3.1    12.8    -      -       -      +
    170A  VAL*     4.0     7.9    -      -       +      -
    177A  LEU*     4.1     6.3    -      -       +      -
    178A  ALA*     1.3    77.2    -      -       -      +
    180A  CYS*     1.3    61.1    +      -       -      +
    181A  SER*     4.4     4.5    -      -       -      +
    245A  TYR*     4.2     8.7    -      -       +      -
    249A  LEU*     3.7    38.1    -      -       +      -
    357A  ASP      4.6     1.1    -      -       -      +
    358A  SER*     3.4     4.3    -      -       -      -
    359A  ALA*     2.9    56.1    +      -       +      +
    360A  TYR*     4.7     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  ARG*     4.7     7.6    -      -       -      -
    138A  LEU*     3.4    20.5    -      -       +      +
    141A  ARG*     4.1    20.9    -      -       +      -
    142A  THR*     3.7     8.3    -      -       +      +
    168A  ARG*     3.2     3.5    -      -       -      +
    169A  SER*     2.8    44.1    +      -       -      +
    179A  MET*     1.3    75.9    -      -       -      +
    181A  SER*     1.3    68.9    +      -       -      +
    182A  LEU*     4.9     4.3    -      -       -      -
    357A  ASP*     3.4    10.1    -      -       -      -
    358A  SER*     3.5    20.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  LEU*     4.2     0.2    -      -       -      -
    166A  THR*     4.0    16.8    -      -       -      -
    167A  LEU      3.5     4.5    -      -       -      -
    168A  ARG*     2.8    35.7    +      -       -      +
    179A  MET*     4.4     4.3    -      -       -      +
    180A  CYS*     1.3    75.0    -      -       -      +
    182A  LEU*     1.3    74.8    +      -       -      +
    357A  ASP*     2.9    32.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  ILE*     5.7     2.2    -      -       +      -
    134A  LYS*     3.4    49.1    -      -       +      +
    137A  ARG*     4.6    14.8    -      -       +      +
    138A  LEU*     3.8    19.1    -      -       +      -
    166A  THR*     3.3     5.0    -      -       -      +
    167A  LEU*     2.9    37.3    +      -       +      +
    180A  CYS*     4.9     4.9    -      -       -      -
    181A  SER*     1.3    82.6    -      -       -      +
    183A  ASP*     1.3    63.7    +      -       -      +
    184A  ALA*     3.0     6.3    +      -       +      +
    357A  ASP*     5.0    11.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  GLY      5.7     0.7    -      -       -      -
    166A  THR*     4.4    13.9    -      -       -      +
    182A  LEU*     1.3    71.4    -      -       -      +
    184A  ALA*     1.3    59.2    +      -       -      +
    185A  GLN*     3.5     4.3    -      -       -      +
----------------------------------------------------------
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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