Contacts of the strand formed by residues 660 - 664 (chain A) in PDB entry 6DBT


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 660 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    600A  ARG*     5.0    23.3    -      -       +      +
    602A  LEU*     5.6     4.9    -      -       +      -
    650A  SER*     3.1     5.5    -      -       -      -
    651A  ILE*     2.9    57.8    +      -       +      +
    653A  LEU      4.8     2.0    -      -       -      +
    657A  ASP*     3.7    30.7    -      -       +      -
    658A  ASP*     5.0     1.8    -      -       -      +
    659A  GLY*     1.3    83.0    -      -       -      +
    661A  THR*     1.3    61.7    +      -       -      +
    662A  ILE*     3.0    14.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 661 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    600A  ARG*     4.4    25.0    +      -       -      +
    648A  SER*     5.7     2.1    -      -       -      -
    649A  ILE      3.9     4.4    +      -       -      -
    650A  SER*     4.0     6.3    -      -       -      -
    659A  GLY      3.9     2.9    -      -       -      +
    660A  ILE*     1.3    70.4    -      -       -      +
    662A  ILE*     1.3    64.2    +      -       -      +
    663A  PHE*     3.8     2.4    +      -       -      -
    664A  GLN*     3.7    29.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 662 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    593A  ILE*     4.3    26.2    -      -       +      +
    596A  GLY*     4.3    18.3    -      -       -      -
    597A  LEU*     4.0    24.2    -      -       +      +
    600A  ARG*     5.9     7.6    -      -       +      -
    602A  LEU*     5.5     2.9    -      -       +      -
    611A  PHE*     5.1     3.8    -      -       +      -
    649A  ILE*     2.8    37.9    +      -       +      +
    650A  SER      4.5     1.6    -      -       -      -
    651A  ILE*     3.4    36.1    -      -       +      +
    660A  ILE*     3.0    26.9    +      -       +      +
    661A  THR*     1.3    74.9    -      -       -      +
    663A  PHE*     1.3    63.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 663 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    589A  LEU*     3.6    31.2    -      -       +      -
    592A  ASP*     5.1    26.9    -      -       +      +
    593A  ILE*     5.3     5.2    -      -       +      -
    646A  ILE*     4.2    12.6    -      -       +      -
    647A  MET      4.8     1.1    -      -       -      -
    648A  SER*     3.3     2.1    -      -       -      -
    649A  ILE*     2.9    50.9    +      -       +      +
    661A  THR*     3.4     4.4    -      -       -      -
    662A  ILE*     1.3    84.9    -      -       +      +
    664A  GLN*     1.3    78.5    +      -       -      +
    665A  GLU*     3.4    32.1    -      -       +      -
    666A  GLN*     4.7     1.8    -      -       +      -
   1019A  LYS*     5.6     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 664 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    647A  MET*     4.1    15.4    -      -       +      +
    648A  SER*     4.4     8.5    -      -       -      -
    661A  THR*     3.7    14.7    +      -       -      +
    663A  PHE*     1.3    84.6    -      -       -      +
    665A  GLU*     1.3    76.7    +      -       -      +
    666A  GLN*     3.6    17.2    +      -       -      +
    918A  THR*     5.2    15.4    +      -       -      +
    919A  CYS*     5.5     6.3    -      -       -      +
    977A  ALA*     5.9     4.6    -      -       -      +
----------------------------------------------------------
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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