Contacts of the strand formed by residues 164 - 173 (chain D) in PDB entry 1TW8


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 164 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84D  THR*     3.7    22.2    -      -       +      -
     85D  LEU*     4.2    11.2    -      -       +      -
     88D  LEU*     3.8    16.4    -      -       +      -
    122D  PHE*     4.2     2.0    -      -       -      -
    123D  TYR*     3.0    21.3    -      -       +      +
    125D  LEU*     4.3     4.9    -      -       +      -
    151D  THR*     3.5    25.4    -      -       +      -
    155D  MET*     3.7    22.2    -      -       +      -
    160D  GLU*     5.4     2.0    -      -       +      -
    161D  PHE*     6.4     0.4    -      -       -      -
    162D  ASP      3.8     0.6    -      -       -      -
    163D  LEU*     1.3   103.7    +      -       +      +
    165D  ASP*     1.3    79.2    +      -       -      +
    166D  ILE*     3.7    20.2    -      -       +      -
    191D  PHE*     3.5    24.8    -      +       -      -
    223D  ARG*     3.8     5.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 165 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2D  SER*     4.5     7.2    +      -       -      +
    122D  PHE*     2.9    26.2    -      -       +      -
    123D  TYR      2.9     8.9    +      -       -      +
    124D  GLU*     4.5     5.8    -      -       +      -
    125D  LEU*     2.7    37.4    +      -       -      +
    164D  PHE*     1.3    86.7    -      -       -      +
    166D  ILE*     1.3    61.0    +      -       -      +
    167D  ASN*     3.9    17.7    +      -       -      +
    189D  GLU*     5.1     8.3    -      -       -      +
    191D  PHE*     3.3     9.6    -      -       +      -
    223D  ARG*     3.0    26.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 166 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88D  LEU*     4.9     6.5    -      -       +      -
    112D  THR*     6.2     4.7    -      -       +      -
    125D  LEU*     3.3    20.9    -      -       +      +
    127D  ASP*     5.6     1.8    -      -       +      -
    143D  ILE*     4.8     7.9    -      -       +      -
    148D  LEU*     5.5     5.2    -      -       +      -
    151D  THR*     5.3     5.8    -      -       +      +
    164D  PHE*     3.7    27.4    -      -       +      -
    165D  ASP*     1.3    79.6    -      -       -      +
    167D  ASN*     1.3    66.1    +      -       -      +
    168D  TYR*     3.2    33.3    -      -       +      +
    190D  LEU*     3.1    43.8    +      -       +      +
    191D  PHE*     3.9    18.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 167 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2D  SER*     3.5    13.1    +      -       -      +
    124D  GLU*     2.9    35.9    +      -       +      +
    125D  LEU      3.0     8.1    +      -       -      +
    126D  LEU*     3.4     7.4    -      -       +      -
    127D  ASP*     2.8    30.1    +      -       -      +
    165D  ASP*     3.9     8.7    -      -       -      +
    166D  ILE*     1.3    85.6    +      -       -      +
    168D  TYR*     1.3    65.6    +      -       -      +
    187D  PHE*     3.2    25.3    -      -       +      -
    188D  ALA      3.4    13.2    -      -       -      +
    189D  GLU*     3.5    18.9    -      -       -      +
    191D  PHE*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 168 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126D  LEU*     3.9     5.4    -      -       -      -
    127D  ASP*     3.0    46.0    -      -       +      +
    129D  LYS*     3.7    14.1    -      -       +      -
    142D  ILE*     3.0    37.8    -      -       +      +
    143D  ILE*     3.1    24.2    -      -       +      +
    166D  ILE*     3.2    34.3    -      -       +      +
    167D  ASN*     1.3    77.1    -      -       -      +
    169D  LEU*     1.3    61.2    +      -       -      +
    170D  GLU      4.0     0.7    -      -       -      -
    186D  SER      3.7     0.2    -      -       -      +
    187D  PHE*     3.3    29.1    -      -       -      -
    188D  ALA*     3.3    11.8    +      -       +      +
    190D  LEU*     4.1    13.4    -      -       +      +
    210D  PHE*     4.4    12.6    -      +       -      -
    212D  VAL*     3.7    23.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 169 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  ILE*     5.9     4.9    -      -       +      -
      8D  TYR*     3.9    27.1    -      -       +      -
     11D  ILE*     4.8     5.4    -      -       +      -
     15D  LEU*     4.0    15.0    -      -       +      -
     41D  VAL*     3.4    46.2    -      -       +      -
     45D  LEU*     5.8     0.2    -      -       +      -
    126D  LEU*     4.0    14.3    -      -       +      +
    127D  ASP      3.1     8.5    +      -       -      -
    128D  VAL*     3.4    10.9    -      -       +      +
    129D  LYS      3.0    24.3    +      -       -      +
    168D  TYR*     1.3    74.0    -      -       -      +
    170D  GLU*     1.3    65.8    +      -       -      +
    171D  VAL*     4.3     3.8    -      -       +      -
    185D  THR*     4.4     6.5    -      -       -      -
    186D  SER      3.5    13.2    -      -       -      +
    187D  PHE*     4.6     6.7    -      -       +      -
    212D  VAL*     4.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 170 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129D  LYS*     3.2    11.0    -      -       +      +
    131D  ARG*     4.1    14.9    -      -       +      -
    169D  LEU*     1.3    73.9    -      -       -      +
    171D  VAL*     1.3    62.5    +      -       -      +
    172D  ASP*     2.8    34.8    -      -       -      +
    185D  THR*     3.0    28.2    -      -       -      -
    186D  SER*     2.9    15.4    +      -       -      +
    211D  HIS*     3.5     5.1    -      -       -      +
    212D  VAL*     3.0    32.1    +      -       +      +
    213D  ARG*     2.7    51.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 171 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15D  LEU*     4.9     4.9    -      -       +      -
     37D  PHE*     3.7    36.8    -      -       +      -
     41D  VAL*     4.5     7.4    -      -       +      -
    128D  VAL*     4.1    14.6    -      -       +      -
    129D  LYS      2.7    14.1    +      -       -      +
    130D  THR*     4.3     5.4    -      -       +      -
    131D  ARG      3.0    22.3    +      -       -      -
    169D  LEU*     3.8    21.5    -      -       +      +
    170D  GLU*     1.3    77.8    -      -       -      +
    172D  ASP*     1.3    61.8    +      -       -      +
    173D  TRP*     3.2     8.3    -      -       +      -
    182D  CYS*     4.1    17.5    -      -       -      -
    184D  SER      3.7     2.9    -      -       -      -
    185D  THR*     4.9     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 172 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131D  ARG*     3.5    16.6    -      -       -      +
    133D  ILE*     3.4    29.1    -      -       +      +
    170D  GLU*     2.8    28.8    -      -       -      +
    171D  VAL*     1.3    71.3    -      -       -      +
    173D  TRP*     1.3    53.6    +      -       -      +
    182D  CYS*     3.3     5.4    -      -       -      -
    183D  VAL*     2.7    42.8    +      -       +      -
    184D  SER*     2.7    40.7    +      -       -      +
    185D  THR*     4.0     1.2    +      -       -      -
    186D  SER*     4.4     2.9    +      -       -      -
    213D  ARG*     3.7    10.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 173 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28D  LEU*     4.6    19.3    -      -       +      -
     33D  ALA*     4.2    21.5    -      -       +      -
     37D  PHE*     3.8    29.8    -      +       +      -
    130D  THR*     3.5    17.2    +      -       -      -
    131D  ARG      2.7    36.7    +      -       -      +
    132D  ASN*     3.4    34.2    +      -       +      -
    133D  ILE*     3.7     8.6    +      -       -      +
    171D  VAL*     3.2    13.7    -      -       +      -
    172D  ASP*     1.3    74.3    -      -       -      +
    174D  GLU*     1.3    67.3    +      -       -      +
    175D  LEU*     4.3     5.6    -      -       +      -
    180D  LEU*     3.4    46.9    -      -       +      -
    181D  VAL      3.1    15.0    -      -       -      +
    182D  CYS*     4.2     0.7    -      -       -      -
    183D  VAL*     4.1     2.0    -      -       -      +
     10G    C      3.7    18.8    -      -       -      -
----------------------------------------------------------
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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