Contacts of the strand formed by residues 190 - 199 (chain B) in PDB entry 1TCR


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 TYR 190 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  GLY      3.3    23.2    +      -       -      -
    152B  PHE*     3.0    45.2    +      -       +      +
    153B  PHE*     3.6    30.9    -      +       -      -
    155B  ASP*     3.6    36.7    +      -       +      -
    178B  ALA*     3.7    21.3    -      -       +      -
    179B  TYR      3.2    22.9    -      -       -      -
    180B  LYS*     3.9    31.9    -      -       +      -
    181B  GLU*     3.4     4.1    -      -       -      +
    189B  SER*     1.3    74.2    +      -       -      +
    191B  CYS*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  PHE*     4.3     7.2    -      -       -      -
    183A  TRP*     3.8    28.9    -      -       +      -
    149B  ALA      3.3    11.2    -      -       -      +
    150B  ARG*     4.1     6.1    -      -       +      -
    152B  PHE*     3.8     2.9    -      -       -      -
    178B  ALA*     3.3     4.9    -      -       -      +
    179B  TYR*     2.8    57.2    +      -       -      -
    181B  GLU*     3.8    25.6    -      -       -      +
    190B  TYR*     1.3    76.8    -      -       -      +
    192B  LEU*     1.3    64.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 192 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  TRP*     5.9     0.4    -      -       -      -
    147B  CYS      4.0     0.2    -      -       -      +
    148B  LEU*     3.6     4.4    -      -       -      +
    149B  ALA*     2.9    35.1    +      -       +      +
    152B  PHE*     4.1    11.4    -      -       +      -
    157B  VAL*     4.2    23.1    -      -       +      +
    159B  LEU*     4.0    33.5    -      -       +      +
    174B  THR*     4.4     4.5    -      -       -      +
    175B  ASP*     3.5    38.6    -      -       +      +
    177B  GLN      4.7     0.2    -      -       -      +
    178B  ALA*     3.7    26.0    -      -       +      +
    191B  CYS*     1.3    77.3    -      -       -      +
    193B  SER*     1.3    66.5    +      -       -      +
    214B  VAL*     6.0     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 193 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  THR*     3.8    14.2    +      -       -      +
    181A  ILE*     4.4    24.7    -      -       -      +
    183A  TRP*     5.0     0.2    -      -       -      -
    146B  VAL*     5.0     2.0    -      -       -      -
    147B  CYS      3.1    11.2    -      -       -      -
    148B  LEU*     4.2    13.0    -      -       -      -
    159B  LEU*     4.5     2.5    -      -       -      -
    174B  THR*     3.4     4.3    +      -       -      -
    175B  ASP*     2.8    51.9    +      -       -      +
    192B  LEU*     1.3    77.7    -      -       -      +
    194B  SER*     1.3    66.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  ILE*     5.3     0.6    -      -       -      +
    145B  LEU      3.7     0.2    -      -       -      +
    146B  VAL*     3.1     7.0    -      -       -      +
    147B  CYS      2.8    30.0    +      -       -      -
    159B  LEU*     3.7    15.7    -      -       -      -
    161B  TRP*     2.7    31.6    +      -       -      -
    173B  SER      3.5     6.7    -      -       -      -
    174B  THR*     3.1    25.1    -      -       -      +
    193B  SER*     1.3    81.4    -      -       -      +
    195B  ARG*     1.3    68.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  LEU*     3.7    22.9    -      -       +      -
    144A  THR*     3.5    22.0    +      -       -      -
    166A  THR*     3.0    43.9    +      -       -      -
    168A  LEU*     3.5    39.9    -      -       +      +
    177A  SER*     3.4    19.4    +      -       -      -
    178A  ASN      3.8     1.2    +      -       -      -
    179A  GLY*     3.5    15.1    -      -       -      +
    181A  ILE*     3.8    19.3    -      -       +      +
    144B  THR*     3.7    18.5    +      -       +      +
    145B  LEU      3.4     3.1    -      -       -      -
    146B  VAL*     4.5     2.2    -      -       +      -
    161B  TRP*     3.9     1.1    +      -       -      -
    171B  GLY      4.2     1.1    -      -       -      -
    172B  VAL*     3.2     9.0    -      -       -      +
    173B  SER      3.0    33.4    +      -       -      +
    194B  SER*     1.3    82.8    +      -       -      +
    196B  LEU*     1.3    61.1    +      -       -      +
    197B  ARG*     4.0     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143B  ALA      3.3     3.3    -      -       -      +
    144B  THR*     4.3     0.7    -      -       -      -
    145B  LEU*     2.8    41.5    +      -       +      +
    161B  TRP*     3.4    49.4    -      -       +      +
    163B  VAL*     4.2    22.4    -      -       +      -
    168B  VAL*     3.7    25.6    -      -       +      -
    170B  SER      4.2     4.0    -      -       -      +
    171B  GLY      3.6     5.8    -      -       -      +
    172B  VAL*     4.2    12.8    -      -       +      -
    195B  ARG*     1.3    74.5    -      -       -      +
    197B  ARG*     1.3    58.6    +      -       -      +
    198B  VAL*     4.2    17.3    -      -       +      -
    210B  PHE*     4.3    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  THR*     4.3     8.7    -      -       -      +
    145A  ASP*     2.7    43.6    +      -       -      -
    168A  LEU*     3.7    27.1    -      -       +      +
    170A  MET*     3.5    29.4    -      -       -      +
    177A  SER*     3.6    16.3    +      -       -      -
    136B  GLU*     2.6    42.4    +      -       -      +
    140B  LYS*     4.4     5.1    -      -       -      +
    142B  LYS*     3.7    33.7    -      -       +      +
    143B  ALA      3.2     4.5    -      -       -      -
    144B  THR*     3.0    22.8    +      -       -      +
    171B  GLY*     3.2    18.8    +      -       -      +
    195B  ARG*     4.0     1.7    -      -       -      +
    196B  LEU*     1.3    73.6    -      -       -      +
    198B  VAL*     1.3    66.6    +      -       -      +
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Residues in contact with VAL 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  MET*     4.1     9.3    -      -       -      +
    142B  LYS*     3.3     7.3    -      -       -      +
    143B  ALA*     2.7    39.9    +      -       +      +
    145B  LEU*     4.2     8.7    -      -       +      -
    163B  VAL*     5.9     1.3    -      -       +      -
    196B  LEU*     4.2    23.6    -      -       +      +
    197B  ARG*     1.3    81.2    -      -       -      +
    199B  SER*     1.3    68.6    +      -       -      +
    202B  PHE*     4.1    23.8    -      -       +      -
    203B  TRP*     4.1    22.7    -      -       +      +
    210B  PHE*     4.4     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  MET*     4.4     7.9    -      -       -      +
    141B  GLN      3.7     8.5    -      -       -      -
    142B  LYS*     4.3     2.2    -      -       -      +
    143B  ALA      4.5     0.7    -      -       -      -
    198B  VAL*     1.3    80.3    -      -       -      +
    200B  ALA*     1.3    66.5    +      -       -      +
    201B  THR*     4.0    12.5    -      -       -      +
    202B  PHE*     3.1    23.4    +      -       -      +
    203B  TRP*     3.1    18.5    +      -       -      +
----------------------------------------------------------
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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