Contacts of the strand formed by residues 22 - 28 (chain B) in PDB entry 1TK0


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 ALA 22 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  GLY*     1.3    70.8    -      -       -      -
     23B  ILE*     1.3    64.2    +      -       -      +
     52B  LYS      3.5    23.9    +      -       -      +
     53B  LEU*     3.6     9.7    -      -       +      +
     54B  THR*     2.9    25.7    +      -       -      -
     80B  LEU*     4.2    14.8    -      -       +      -
     81B  PHE      3.6     5.4    -      -       -      -
     82B  LYS*     4.7    10.4    -      -       +      +
    107B  LEU*     4.8     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  ILE*     5.8     0.7    -      -       +      -
     15B  ASP      4.4     6.3    -      -       -      +
     16B  VAL*     4.4    13.5    -      -       +      +
     19B  ALA*     3.5    33.4    -      -       +      -
     21B  GLY*     3.8     7.6    -      -       -      +
     22B  ALA*     1.3    77.5    -      -       -      +
     24B  LEU*     1.3    60.6    +      -       -      +
     25B  VAL*     3.7    19.4    +      -       +      -
     54B  THR*     3.2    37.9    -      -       +      +
     56B  ALA*     4.3    14.8    -      -       +      -
     79B  LEU      3.4     1.9    -      -       -      +
     80B  LEU*     3.4     4.1    -      -       -      +
     81B  PHE*     2.6    48.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  ALA      4.3     0.6    -      -       -      -
     23B  ILE*     1.3    72.3    -      -       -      +
     25B  VAL*     1.3    62.4    +      -       -      +
     26B  ASP*     4.0     0.6    +      -       +      -
     42B  LEU*     4.2    24.0    -      -       +      -
     45B  ILE*     5.1     0.4    -      -       +      -
     53B  LEU*     4.3    13.6    -      -       +      +
     54B  THR      2.8    12.9    +      -       -      +
     55B  VAL*     3.6    16.4    -      -       +      +
     56B  ALA      2.8    28.9    +      -       -      +
     78B  LEU*     4.2    22.4    -      -       +      -
     79B  LEU      3.4    19.3    -      -       -      +
     80B  LEU*     4.2    13.9    -      -       +      +
     99B  LEU*     4.2    13.2    -      -       +      -
    102B  PHE*     4.5     7.0    -      -       +      -
    103B  LEU*     4.1    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  LEU*     4.1    19.7    -      -       +      -
     12B  PHE*     4.2     3.1    -      -       +      -
     16B  VAL*     4.0    23.1    -      -       +      -
     23B  ILE*     4.0     9.0    -      -       +      -
     24B  LEU*     1.3    77.9    -      -       -      +
     26B  ASP*     1.3    64.6    +      -       -      +
     27B  PHE*     3.4    35.4    +      -       +      -
     56B  ALA*     3.2     3.8    -      -       +      +
     58B  LEU*     4.5     6.1    -      -       +      -
     77B  THR      3.3     4.5    -      -       -      +
     78B  LEU*     3.4     2.8    -      -       -      +
     79B  LEU      2.6    40.8    +      -       -      +
     81B  PHE*     3.7    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  LEU*     5.4     1.1    -      -       +      +
     25B  VAL*     1.3    72.8    -      -       -      +
     27B  PHE*     1.3    63.0    +      -       -      +
     28B  TRP*     3.2    18.8    -      -       -      +
     35B  CYS      5.6     0.9    -      -       -      +
     38B  ILE*     4.8     3.3    -      -       -      +
     39B  ALA*     5.7     0.5    -      -       -      -
     42B  LEU*     3.2    35.4    -      -       +      +
     55B  VAL*     5.8     0.9    -      -       +      -
     56B  ALA      2.8    14.9    +      -       -      +
     57B  LYS*     3.6    17.4    +      -       +      +
     58B  LEU      3.0    23.7    +      -       -      -
     76B  PRO*     3.6    24.6    -      -       -      +
     77B  THR      3.5     2.6    -      -       -      +
     78B  LEU*     3.8    14.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  PHE*     4.1    10.1    -      +       -      -
     25B  VAL*     3.4    28.0    -      -       +      -
     26B  ASP*     1.3    70.8    -      -       -      +
     28B  TRP*     1.3    59.5    +      -       -      +
     58B  LEU*     3.5    33.2    -      -       +      -
     60B  ILE*     4.1     9.4    -      -       +      -
     66B  THR*     4.0     2.2    -      -       +      -
     67B  ALA*     3.8    33.9    -      -       +      -
     70B  TYR*     4.0    19.5    -      +       -      -
     72B  ILE*     4.2     8.7    -      -       +      -
     75B  ILE*     3.6     8.4    -      -       +      +
     76B  PRO*     3.4     7.4    -      -       -      +
     77B  THR*     2.9    56.4    +      -       +      +
     79B  LEU*     3.6    22.9    -      -       +      -
     81B  PHE*     4.7     0.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with TRP 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  ASP*     3.2    34.1    -      -       -      +
     27B  PHE*     1.3    74.2    -      -       -      +
     29B  ALA*     1.3    80.8    +      -       -      +
     30B  GLU*     3.5    37.9    -      -       -      -
     35B  CYS*     3.6    26.9    -      -       +      +
     57B  LYS*     3.7    35.7    -      -       +      +
     58B  LEU      3.2     9.7    +      -       -      -
     59B  ASN*     3.4    36.0    -      -       +      +
     60B  ILE*     3.0    33.5    +      -       -      +
     62B  GLN*     5.8     0.7    -      -       -      -
     75B  ILE*     4.6     3.4    -      -       -      -
----------------------------------------------------------
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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