Contacts of the strand formed by residues 2 - 8 (chain A) in PDB entry 1TKD


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 2 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     1.3    81.5    -      -       -      +
      3A  VAL*     1.3    58.9    +      -       -      +
      4A  SER*     5.3     0.7    -      -       -      -
     23A  ILE*     4.0    17.5    -      -       +      -
     24A  TYR      3.1     8.3    -      -       -      +
     25A  ASP*     3.7    25.6    -      -       +      +
     45A  ALA*     4.4     5.8    -      -       +      +
     46A  LEU*     3.8    28.7    -      -       +      -
     49A  GLU*     3.4    36.1    -      -       +      +
     52A  ARG*     5.2     0.4    -      -       -      +
     55A  LEU      2.9    15.9    +      -       -      +
     56A  ILE*     3.5    12.7    -      -       +      -
     57A  VAL*     2.7    35.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 3 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     1.3    77.2    -      -       -      +
      4A  SER*     1.3    66.2    +      -       -      +
     23A  ILE*     3.4     3.1    -      -       -      -
     24A  TYR*     2.7    46.3    +      -       +      +
     26A  TYR*     3.9    25.1    -      -       +      -
     57A  VAL*     3.5     9.9    -      -       +      +
    175A  VAL*     3.5    28.9    -      -       +      +
    178A  THR*     3.8    30.1    -      -       +      -
    179A  LYS*     4.2     9.0    -      -       +      +
    182A  LEU*     4.2    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 4 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     4.2     0.8    +      -       -      -
      3A  VAL*     1.3    80.0    -      -       -      +
      5A  ASP*     1.3    65.3    +      -       -      +
     22A  VAL      2.7    19.9    +      -       -      -
     23A  ILE*     3.5     8.9    -      -       -      +
     42A  TYR*     2.6    35.6    +      -       -      -
     46A  LEU*     4.5     7.0    -      -       -      -
     56A  ILE*     4.7     3.6    -      -       -      -
     57A  VAL      2.8    12.4    +      -       -      +
     58A  PHE*     3.2    31.7    -      -       -      -
     59A  HIS      4.6     1.2    +      -       -      -
    175A  VAL*     4.1     4.4    -      -       -      +
    178A  THR*     5.2     3.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 5 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  SER*     1.3    80.6    +      -       -      +
      6A  ILE*     1.3    73.9    +      -       -      +
      7A  GLU*     4.0     1.0    -      -       -      +
     21A  GLY*     3.4     2.3    -      -       -      -
     22A  VAL      3.2    18.3    +      -       -      -
     58A  PHE*     3.9     1.5    -      -       -      -
     59A  HIS*     4.9     5.7    +      -       -      +
     65A  ASP*     3.5    11.2    -      -       -      +
    171A  ASN*     3.0    29.7    +      -       -      +
    174A  ASP*     2.9    32.4    -      -       +      +
    175A  VAL*     4.0    12.1    -      -       +      +
    178A  THR*     5.6     2.7    -      -       -      +
    903A   MG      2.2    30.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 6 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ASP*     1.3    88.9    -      -       -      +
      7A  GLU*     1.3    70.9    +      -       -      +
      8A  ALA*     4.4     9.1    +      -       +      -
     18A  PHE*     3.9    14.4    -      -       +      -
     20A  CYS      3.3     8.7    -      -       -      +
     42A  TYR*     3.3    38.4    -      -       +      +
     58A  PHE*     4.8     0.7    -      -       +      -
     64A  TYR*     4.1    24.6    -      -       +      -
     65A  ASP*     3.1    19.5    +      -       -      +
     68A  ALA*     4.2    13.5    -      -       +      -
     69A  LEU*     4.0    28.7    -      -       +      -
     72A  LEU*     4.8     2.5    -      -       +      -
    171A  ASN*     4.1     0.7    -      -       -      +
    903A   MG      4.1     5.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 7 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ASP*     4.0     1.1    -      -       -      +
      6A  ILE*     1.3    80.7    -      -       -      +
      8A  ALA*     1.3    55.5    +      -       -      +
     18A  PHE*     3.8     3.1    -      -       -      -
     19A  HIS*     2.7    31.5    +      -       -      -
     20A  CYS*     2.8    27.0    +      -       -      +
    160A  TRP*     3.5    24.1    -      -       +      -
    167A  MET*     3.8    25.2    -      -       +      +
    170A  TYR*     4.1     5.2    -      -       -      +
    171A  ASN*     3.4    47.1    +      -       +      -
    174A  ASP*     3.5    13.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 8 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ILE*     4.4     5.5    +      -       +      +
      7A  GLU*     1.3    75.1    +      -       -      +
      9A  ASN*     1.3    63.7    +      -       -      +
     10A  ALA      3.4     1.6    +      -       -      -
     15A  VAL*     3.3    20.0    -      -       +      -
     17A  LYS      3.3    10.3    -      -       -      +
     19A  HIS*     3.4     7.4    -      -       -      -
     64A  TYR*     3.0    28.1    +      -       +      +
     72A  LEU*     4.3     9.9    -      -       +      -
    160A  TRP*     3.5    22.0    -      -       -      -
    992A  1PE      3.8     5.8    -      -       -      +
----------------------------------------------------------
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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