Contacts of the strand formed by residues 167 - 172 (chain D) in PDB entry 1THF


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 GLU 167 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  ARG*     2.9    34.8    +      -       -      -
     99D  LYS*     2.7    39.1    +      -       -      +
    123D  GLN*     4.9     3.4    -      -       -      +
    125D  VAL      3.4     3.1    +      -       -      +
    126D  VAL*     3.5    15.3    -      -       +      +
    127D  VAL      3.0    24.7    +      -       -      -
    165D  ALA*     3.6     4.8    -      -       -      +
    166D  GLY*     1.3    81.8    -      -       -      +
    168D  ILE*     1.3    66.1    +      -       -      +
    196D  LEU*     4.5     3.4    -      -       -      -
    197D  PRO*     3.5    23.0    -      -       +      +
    199D  ILE*     3.5    21.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 168 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126D  VAL*     4.7     0.9    -      -       -      -
    127D  VAL      3.4     5.8    -      -       -      +
    129D  ILE*     3.8    24.7    -      -       +      -
    157D  VAL*     4.0    29.6    -      -       +      +
    160D  VAL*     3.9    26.5    -      -       +      -
    167D  GLU*     1.3    77.9    -      -       -      +
    169D  LEU*     1.3    65.1    +      -       -      +
    170D  LEU*     3.6    15.1    +      -       +      +
    190D  VAL*     5.2     4.0    -      -       +      -
    194D  THR*     4.1    21.1    -      -       +      +
    196D  LEU*     4.3     8.9    -      -       +      +
    197D  PRO      3.0    10.3    +      -       -      +
    198D  ILE*     3.5     9.1    -      -       +      +
    199D  ILE*     2.8    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 169 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48D  VAL*     4.7    17.5    -      -       +      -
     78D  THR*     5.6     1.8    -      -       +      -
    101D  SER*     4.3    14.4    -      -       -      +
    126D  VAL*     3.7    25.0    -      -       +      +
    127D  VAL      2.9     8.3    +      -       -      -
    128D  ALA*     3.3    13.2    -      -       +      +
    129D  ILE      2.8    32.2    +      -       -      +
    168D  ILE*     1.3    70.1    -      -       -      +
    170D  LEU*     1.3    54.7    +      -       -      +
    171D  THR*     3.4    21.7    +      -       -      +
    199D  ILE*     3.5    22.9    -      -       +      -
    201D  SER*     3.8    18.2    -      -       -      +
    222D  LEU*     4.0    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 170 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129D  ILE*     3.6    16.8    -      -       +      +
    131D  ALA*     5.1     0.7    -      -       +      -
    153D  LEU*     4.2    15.7    -      -       +      -
    168D  ILE*     3.6    10.5    +      -       +      -
    169D  LEU*     1.3    69.8    -      -       -      +
    171D  THR*     1.3    59.8    +      -       -      +
    172D  SER      4.0     0.5    +      -       -      -
    186D  MET*     3.9    34.7    -      -       +      +
    187D  ILE*     4.1    17.6    -      -       +      +
    190D  VAL*     3.8    38.4    -      -       +      -
    198D  ILE*     4.2    19.5    -      -       +      -
    199D  ILE      2.8    14.5    +      -       -      +
    200D  ALA*     3.8     2.0    -      -       -      -
    201D  SER*     3.0    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 171 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128D  ALA*     5.7     0.2    -      -       -      +
    129D  ILE      2.9     9.5    +      -       -      +
    130D  ASP*     3.4    24.6    +      -       -      +
    131D  ALA      3.1    26.0    +      -       -      +
    169D  LEU*     3.4    24.1    +      -       -      +
    170D  LEU*     1.3    72.4    -      -       -      +
    172D  SER*     1.3    70.7    +      -       -      +
    173D  ILE*     3.5     7.0    +      -       +      +
    176D  ASP*     3.9    21.8    -      -       -      +
    186D  MET*     4.2     4.9    -      -       -      +
    201D  SER*     3.3    18.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 172 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131D  ALA      3.8     5.7    +      -       -      -
    132D  LYS*     5.9     0.3    -      -       -      -
    170D  LEU      4.0     1.0    +      -       -      -
    171D  THR*     1.3    73.6    -      -       -      +
    173D  ILE*     1.3    63.9    +      -       -      +
    174D  ASP*     4.0     6.2    +      -       -      +
    175D  ARG*     3.1    18.4    +      -       -      +
    176D  ASP*     3.0    21.1    +      -       -      +
    183D  ASP*     2.8    45.7    +      -       -      +
    186D  MET*     3.7    11.7    -      -       -      +
    201D  SER      3.2    10.6    +      -       -      -
    202D  GLY*     4.4     1.8    -      -       -      -
----------------------------------------------------------
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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