Contacts of the strand formed by residues 54 - 68 (chain C) in PDB entry 1TNF


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 GLY 54 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PRO*     3.3    20.4    -      -       -      +
     53C  GLU*     1.3    76.9    -      -       -      +
     55C  LEU*     1.3    58.1    +      -       -      -
     56C  TYR*     3.7     7.1    +      -       -      -
    125C  GLN*     2.9    16.5    +      -       -      +
    126C  LEU*     2.8    31.7    +      -       -      -
    156C  ALA*     6.0     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 55 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ARG      4.4     1.6    -      -       -      +
      8A  PRO*     3.7    27.3    -      -       +      +
      9A  SER*     5.5     1.6    -      -       -      -
     11A  LYS*     5.9     2.0    -      -       +      -
     13A  VAL*     3.7    35.7    -      -       +      -
     36A  LEU*     4.3    17.0    -      -       +      -
    155A  ILE*     4.3    10.5    -      -       +      -
     54C  GLY*     1.3    70.0    -      -       -      -
     56C  TYR*     1.3    63.2    +      -       -      +
     57C  LEU      4.0     0.3    +      -       -      -
    123C  VAL*     4.9     8.5    -      -       +      -
    124C  PHE      3.4     6.7    -      -       -      +
    125C  GLN*     3.5    40.6    -      -       +      +
    156C  ALA*     3.8     2.0    -      -       -      +
    157C  LEU*     3.1    40.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 56 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12C  PRO*     3.5    27.5    -      -       +      +
     50C  VAL*     3.6    18.8    -      -       +      +
     51C  PRO*     3.4    26.7    +      -       +      +
     52C  SER*     3.6    12.0    -      -       -      -
     53C  GLU      3.9    18.6    -      -       -      -
     54C  GLY*     3.7    13.0    -      -       -      -
     55C  LEU*     1.3    74.8    -      -       -      +
     57C  LEU*     1.4    58.9    +      -       -      +
     58C  ILE*     3.4     5.1    -      -       +      +
    123C  VAL*     4.4     1.6    -      -       -      -
    124C  PHE      2.6    38.9    +      -       -      +
    126C  LEU*     3.6    29.2    -      -       +      -
    154C  ILE*     3.6    34.1    -      -       +      -
    155C  ILE      3.6     3.8    -      -       -      -
    156C  ALA*     3.8    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 57 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  LEU*     4.4    15.0    -      -       +      -
     59A  TYR*     5.5     3.4    -      -       +      -
    119A  TYR*     5.4     3.1    -      -       -      +
     57B  LEU*     4.4    27.4    -      -       +      -
    123B  VAL*     5.3     0.7    -      -       +      -
    157B  LEU*     5.2     1.6    -      -       +      -
     55C  LEU      4.0     1.4    +      -       -      -
     56C  TYR*     1.4    70.2    -      -       -      +
     58C  ILE*     1.3    65.1    +      -       -      +
     59C  TYR*     4.8    15.1    -      -       +      -
    121C  GLY*     5.1     1.8    -      -       -      -
    122C  GLY*     3.5    15.9    -      -       -      +
    123C  VAL*     3.5    28.0    -      -       +      +
    153C  GLY      3.9     0.2    -      -       -      +
    154C  ILE*     3.0     6.8    -      -       -      +
    155C  ILE*     3.0    54.8    +      -       +      +
    157C  LEU*     4.2    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 58 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56C  TYR*     3.4    14.4    -      -       +      +
     57C  LEU*     1.3    77.6    -      -       -      +
     59C  TYR*     1.3    65.5    +      -       -      +
     80C  ILE*     4.1    17.3    -      -       +      -
     93C  LEU*     4.2    15.5    -      -       +      -
     94C  LEU*     4.5     7.8    -      -       +      +
    121C  GLY*     3.3     2.9    -      -       -      -
    122C  GLY      2.8    35.4    +      -       -      +
    124C  PHE*     3.5    34.8    -      -       +      -
    126C  LEU*     4.5    15.7    -      -       +      -
    132C  LEU*     4.5     6.5    -      -       +      -
    152C  PHE*     4.0    19.7    -      -       +      -
    153C  GLY      3.3     2.9    -      -       -      -
    154C  ILE*     3.8    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 59 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  LEU*     5.8     2.9    -      -       +      -
    121B  GLY      3.7    11.9    -      -       -      -
    122B  GLY*     3.6    11.0    -      -       -      -
    123B  VAL*     2.7    47.2    +      -       +      +
     14C  ALA      3.7     2.4    +      -       -      -
     15C  HIS*     2.7    42.2    +      +       -      +
     57C  LEU*     4.8    17.0    -      -       +      -
     58C  ILE*     1.3    78.4    -      -       -      +
     60C  SER*     1.4    60.0    +      -       -      +
     80C  ILE*     4.4     4.5    -      -       -      -
    119C  TYR*     3.4    22.4    -      -       +      +
    120C  LEU      3.2     9.0    -      -       -      +
    121C  GLY*     4.4     1.8    -      -       -      -
    151C  TYR*     4.1     8.5    -      +       -      -
    152C  PHE*     3.1     9.6    -      -       -      -
    153C  GLY*     2.7    61.6    +      -       -      -
    154C  ILE*     4.2     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 60 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28C  TRP*     5.5     1.3    -      -       -      -
     59C  TYR*     1.4    74.3    -      -       -      +
     61C  GLN*     1.3    61.0    +      -       -      +
     78C  HIS*     2.8    33.3    +      -       -      -
     80C  ILE*     3.3    16.2    -      -       -      +
    118C  ILE      3.8     0.3    -      -       -      +
    119C  TYR*     3.2     8.8    -      -       -      -
    120C  LEU*     2.9    34.4    +      -       -      +
    134C  ALA*     4.3     1.9    -      -       -      +
    151C  TYR*     3.2    21.5    -      -       -      -
    152C  PHE*     3.8    15.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 61 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  SER      3.2    13.5    +      -       -      +
     96B  ALA*     4.0     8.0    -      -       -      +
    119B  TYR      3.9     7.1    +      -       -      -
    120B  LEU*     3.5    24.4    -      -       -      +
     28C  TRP*     5.1     0.2    -      -       -      -
     60C  SER*     1.3    75.6    -      -       -      +
     62C  VAL*     1.3    74.1    +      -       -      +
     63C  LEU*     5.0     1.8    -      -       -      +
     78C  HIS*     4.7     0.2    -      -       -      -
    117C  PRO*     4.9     6.5    -      -       +      +
    118C  ILE      3.0    16.6    -      -       -      +
    119C  TYR*     3.9     4.7    -      -       +      -
    148C  GLY      3.4     1.4    -      -       -      +
    149C  GLN*     2.5    31.6    -      -       -      +
    150C  VAL*     3.1     7.3    -      -       -      +
    151C  TYR*     2.9    67.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  LEU*     4.6     8.1    -      -       +      -
     28C  TRP*     5.4     1.6    -      -       +      -
     61C  GLN*     1.3    79.1    -      -       -      +
     63C  LEU*     1.3    61.0    +      -       -      +
     64C  PHE*     3.8    14.1    -      -       +      -
     78C  HIS*     3.4    54.3    -      -       +      +
    116C  GLU      3.8     1.0    -      -       -      +
    117C  PRO*     3.5     2.4    -      -       -      +
    118C  ILE*     2.8    43.6    +      -       +      +
    136C  ILE*     3.6    15.7    -      -       +      -
    142C  LEU*     4.9     4.7    -      -       +      -
    149C  GLN      4.0     2.0    -      -       -      -
    150C  VAL*     4.2    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ALA*     5.2     1.8    -      -       -      -
     97B  ILE*     4.1    30.3    -      -       +      +
     61C  GLN*     5.0     1.6    -      -       -      +
     62C  VAL*     1.3    73.2    -      -       -      +
     64C  PHE*     1.3    68.9    +      -       -      +
    115C  TYR*     4.3     7.0    -      -       +      -
    116C  GLU      3.7    17.3    -      -       -      +
    117C  PRO*     3.7    22.0    -      -       +      -
    141C  TYR      3.8     0.9    -      -       -      +
    142C  LEU*     3.9     9.2    -      -       -      +
    143C  LEU*     3.4    36.3    +      -       +      -
    149C  GLN*     3.5    52.9    +      -       +      +
    150C  VAL*     4.0     8.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 64 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62C  VAL*     3.8    12.3    -      -       +      -
     63C  LEU*     1.3    80.9    -      -       -      +
     65C  LYS*     1.3    59.9    +      -       -      +
     76C  LEU*     3.5    47.8    -      -       +      -
     77C  THR      3.6    22.9    -      -       -      -
    114C  TRP*     3.9     7.1    -      -       +      -
    115C  TYR*     3.5     4.0    -      -       -      -
    116C  GLU*     2.9    45.1    +      -       +      +
    118C  ILE*     3.4    33.4    -      -       +      -
    136C  ILE*     4.0    21.5    -      -       +      -
    137C  ASN*     4.8     3.1    -      -       -      -
    138C  ARG      4.1    15.0    -      -       -      -
    141C  TYR*     3.2    22.4    -      -       +      +
    142C  LEU*     5.2     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 65 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64C  PHE*     1.3    74.5    -      -       -      +
     66C  GLY*     1.3    60.5    +      -       -      +
     67C  GLN*     3.8    23.4    -      -       -      +
    113C  PRO*     5.8     2.7    -      -       +      -
    114C  TRP*     3.7     9.2    -      -       -      +
    115C  TYR*     4.2    15.9    -      -       +      +
    140C  ASP      5.8     1.1    -      -       -      -
    141C  TYR*     2.9    26.3    +      -       -      +
    142C  LEU      3.4    17.9    +      -       -      -
    143C  LEU*     3.3    52.8    -      -       +      +
    144C  PHE*     4.1    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 66 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  LYS*     1.3    75.3    -      -       -      +
     67C  GLN*     1.3    64.4    +      -       -      -
     68C  GLY      3.3     7.8    +      -       -      -
    113C  PRO*     3.2     3.2    -      -       -      +
    114C  TRP*     2.8    63.8    +      -       -      -
    141C  TYR*     4.2     8.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 67 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  LYS*     3.8    26.4    -      -       -      +
     66C  GLY*     1.3    77.8    -      -       -      -
     68C  GLY*     1.3    61.5    +      -       -      +
    111C  ALA*     3.5    30.2    -      -       +      +
    113C  PRO*     3.9    19.4    -      -       +      +
    141C  TYR*     5.5     2.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 68 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  GLN*     5.8     0.4    -      -       -      -
     66C  GLY*     3.3     5.3    +      -       -      +
     67C  GLN*     1.3    77.2    -      -       -      +
     69C  CYS*     1.3    61.6    +      -       -      -
     70C  PRO*     4.6     2.2    -      -       -      +
    106C  PRO*     3.6    24.7    -      -       -      -
    111C  ALA*     4.2     4.3    -      -       -      -
    112C  LYS      4.0    13.4    +      -       -      -
    114C  TRP*     2.7    29.6    +      -       -      -
    141C  TYR*     5.6     0.9    +      -       -      -
----------------------------------------------------------
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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