Contacts of the strand formed by residues 142 - 146 (chain C) in PDB entry 5TXN


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 ILE 142 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  VAL*     6.2     4.3    -      -       +      -
     49C  LYS*     4.2    18.6    -      -       +      -
    131C  THR*     3.5     0.5    -      -       -      -
    132C  ILE*     2.8    35.2    +      -       +      +
    139C  THR*     5.5     7.2    -      -       +      -
    141C  GLY*     1.3    77.7    -      -       -      -
    143C  ARG*     1.3    67.4    +      -       -      +
    144C  TYR*     3.4    44.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 143 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  LYS*     3.6     6.4    -      -       -      +
     50C  ILE*     3.2    59.9    +      -       +      +
     51C  GLY      3.9     8.3    +      -       -      -
     52C  PRO*     5.1     4.4    -      -       -      +
     54C  ASN*     2.8    29.9    +      -       -      +
     55C  PRO      3.6     3.7    +      -       -      -
     56C  TYR      2.4    33.7    +      -       -      -
     57C  ASN*     4.5     2.4    +      -       -      +
    129C  ALA*     3.5    11.1    -      -       -      +
    130C  PHE      3.1     5.4    -      -       -      +
    131C  THR*     3.1    33.0    +      -       +      +
    141C  GLY      4.4     4.7    -      -       -      +
    142C  ILE*     1.3    77.2    -      -       -      +
    144C  TYR*     1.3    62.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 144 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  VAL*     5.3     5.7    -      -       +      +
     38C  CYS*     3.5    23.1    -      -       -      +
     39C  THR*     4.9     1.9    +      -       -      -
     42C  GLU*     2.4    40.9    +      -       +      -
     47C  ILE*     3.6    21.3    -      -       +      -
     48C  SER      3.5    12.3    -      -       -      -
     49C  LYS*     3.8    15.5    -      -       +      -
     50C  ILE*     3.7     4.0    -      -       -      -
    129C  ALA*     3.2     2.1    -      -       -      -
    130C  PHE*     2.8    57.6    +      +       +      -
    132C  ILE*     3.9    20.4    -      -       +      -
    142C  ILE*     3.4    42.2    -      -       +      +
    143C  ARG*     1.3    77.5    -      -       -      +
    145C  GLN*     1.3    59.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 145 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47C  ILE*     3.7     3.3    -      -       -      +
     48C  SER*     3.0    41.4    +      -       -      +
     50C  ILE*     3.5    23.2    -      -       +      +
     54C  ASN*     3.6    13.9    +      -       -      +
    125C  ARG*     3.9    24.7    -      -       -      +
    126C  LYS*     3.3    23.4    -      -       -      +
    128C  THR*     3.6    13.0    -      -       -      +
    129C  ALA*     4.4     3.6    -      -       -      +
    144C  TYR*     1.3    74.7    -      -       -      +
    146C  TYR*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 146 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  MET*     4.7     5.8    -      -       -      -
     46C  LYS*     3.8    24.7    -      -       +      -
     47C  ILE*     4.2    12.1    -      -       +      -
     48C  SER*     5.4     0.4    -      -       -      -
     73C  LYS*     4.3    17.7    -      -       +      -
     75C  VAL*     3.5    33.7    -      -       +      -
     77C  PHE*     5.0     5.2    -      +       -      -
    116C  PHE*     3.8    33.2    -      +       -      -
    120C  LEU*     3.8    13.6    -      -       +      +
    125C  ARG*     3.3    33.7    -      -       -      +
    128C  THR*     3.1    33.6    +      -       +      +
    130C  PHE*     3.6    26.0    -      +       -      -
    145C  GLN*     1.3    80.2    -      -       -      +
----------------------------------------------------------
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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