Contacts of the strand formed by residues 46 - 51 (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 46 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  ARG*     2.9    37.4    +      -       -      -
      6D  ILE      3.6     2.8    +      -       -      -
      7D  ILE*     3.3    23.8    -      -       +      +
      8D  ALA      3.2    10.9    +      -       -      -
     44D  ILE*     3.0    20.4    -      -       -      +
     45D  ASP*     1.3    87.2    -      -       +      +
     47D  LEU*     1.3    66.4    +      -       -      +
     75D  ILE*     4.0     2.7    -      -       -      -
     76D  PRO*     3.3    31.7    -      -       +      +
     77D  PHE      5.9     0.2    -      -       -      -
     78D  THR*     4.7     5.0    +      -       -      -
     99D  LYS*     2.9    29.5    +      -       -      +
    199D  ILE*     5.7     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 47 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  ILE*     4.0     0.8    -      -       -      +
      8D  ALA*     3.4    14.1    -      -       +      +
     10D  LEU*     4.3    11.7    -      -       +      -
     36D  GLY*     3.6    26.2    -      -       -      +
     39D  TYR*     3.9    26.7    -      -       +      -
     44D  ILE*     4.0     6.7    -      -       +      -
     46D  GLU*     1.3    85.4    -      -       -      +
     48D  VAL*     1.3    68.5    +      -       -      +
     49D  PHE*     3.9    18.6    -      -       +      -
     73D  ILE*     3.5    29.2    -      -       +      -
     75D  ILE*     3.9     9.9    -      -       +      -
     76D  PRO      3.0     5.7    +      -       -      -
     77D  PHE*     3.2    10.3    -      -       +      -
     78D  THR*     2.9    25.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 48 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  ILE*     3.8     8.1    -      -       +      -
      8D  ALA      2.9     6.7    +      -       -      +
      9D  CYS*     3.5    15.7    -      -       -      -
     10D  LEU*     2.7    35.3    +      -       -      +
     47D  LEU*     1.3    79.2    -      -       -      +
     49D  PHE*     1.3    66.7    +      -       -      +
     50D  LEU*     3.9     7.1    +      -       +      +
     78D  THR*     3.4    27.8    -      -       +      +
     80D  GLY*     5.1     3.1    -      -       -      +
    101D  SER*     5.9     1.3    -      -       -      -
    169D  LEU*     4.7    15.3    -      -       +      -
    199D  ILE*     6.0     3.6    -      -       +      -
    222D  LEU*     3.7    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 49 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  LEU*     3.4    34.1    -      -       +      -
     12D  VAL*     3.9    24.2    -      -       +      -
     17D  VAL*     4.5     1.3    -      -       +      -
     32D  PRO*     3.7    27.6    -      -       +      -
     47D  LEU*     3.9    22.0    -      -       +      -
     48D  VAL*     1.3    74.5    -      -       -      +
     50D  LEU*     1.3    59.2    +      -       -      +
     51D  ASP      3.9     0.6    +      -       -      -
     62D  MET*     4.8     4.7    -      -       -      +
     65D  LEU*     4.1    14.4    -      -       +      -
     69D  VAL*     3.9    33.7    -      -       +      -
     77D  PHE*     3.7    25.6    -      +       +      -
     78D  THR      2.8    11.1    +      -       -      +
     79D  VAL*     3.4    12.2    -      -       +      +
     80D  GLY      2.9    25.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 50 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9D  CYS*     4.0    18.2    -      -       -      -
     10D  LEU      3.0     7.3    +      -       -      -
     11D  ASP*     3.4    24.2    -      -       -      +
     12D  VAL*     2.8    25.8    +      -       -      -
     48D  VAL*     3.8     6.2    -      -       +      -
     49D  PHE*     1.3    73.1    -      -       -      +
     51D  ASP*     1.3    66.0    +      -       -      +
     52D  ILE*     3.2    15.4    +      -       +      +
     80D  GLY*     3.4    23.3    -      -       -      +
     81D  GLY*     3.8     9.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 51 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12D  VAL*     3.5    17.3    -      -       -      +
     14D  ASP      4.6     7.1    +      -       -      -
     49D  PHE      3.9     1.6    +      -       -      -
     50D  LEU*     1.3    72.7    -      -       -      +
     52D  ILE*     1.3    57.9    +      -       -      +
     53D  THR*     2.7    14.8    +      -       -      -
     54D  ALA*     2.3    56.2    +      -       -      +
     58D  LYS*     4.1    17.8    -      -       +      +
     61D  THR*     4.6     3.1    +      -       -      -
     62D  MET*     4.1    24.8    -      -       +      +
     80D  GLY      2.9    16.6    +      -       -      +
     81D  GLY*     3.6    14.1    -      -       -      +
----------------------------------------------------------
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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