Contacts of the strand formed by residues 273 - 279 (chain J) in PDB entry 5DST


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 CYS 273 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222J  TYR*     3.2     6.9    -      -       -      -
    223J  VAL*     3.0    35.9    +      -       +      +
    272J  ALA*     1.3    75.8    -      -       -      +
    274J  LEU*     1.3    76.4    +      -       -      +
    275J  ILE*     3.6     0.6    +      -       -      -
    293J  ALA      4.4     0.7    -      -       -      -
    294J  PHE*     3.7    13.7    -      -       -      -
    295J  CYS      3.4    34.5    -      -       -      +
    296J  LEU*     3.8    10.5    -      -       +      -
    297O  GLN*     4.7     1.8    -      -       -      +
    353O  GLU*     3.3    29.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 274 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218J  ARG*     6.0     0.2    -      -       -      +
    220J  ALA*     3.9    10.1    -      -       +      -
    221J  LEU      3.6    15.5    -      -       -      +
    222J  TYR*     3.5    35.6    -      -       +      +
    272J  ALA      4.3     0.2    -      -       -      -
    273J  CYS*     1.3    82.5    -      -       -      +
    275J  ILE*     1.3    63.3    +      -       -      +
    276J  LYS      3.6    21.1    -      -       -      +
    277J  GLU*     3.6    29.4    -      -       +      +
    293J  ALA      4.5     3.6    -      -       -      +
    297O  GLN*     5.6     0.4    +      -       -      -
    349O  ARG*     6.1     0.2    -      -       -      +
    350O  ARG      5.8     1.3    -      -       -      +
    351O  GLY*     4.5    27.0    +      -       -      +
    352O  GLU*     6.0     4.0    -      -       +      -
    353O  GLU*     5.3     0.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 275 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221J  LEU*     2.9    48.0    +      -       +      +
    222J  TYR*     4.1     4.9    -      -       -      +
    223J  VAL*     3.5    35.7    -      -       +      -
    273J  CYS      4.0     0.4    -      -       -      +
    274J  LEU*     1.3    78.5    -      -       -      +
    276J  LYS*     1.3    66.9    +      -       -      +
    290J  PHE*     3.9     6.5    -      -       +      -
    292J  SER*     2.5    34.2    +      -       -      +
    293J  ALA      4.4     4.3    -      -       -      +
    294J  PHE*     3.9    16.4    -      -       +      -
    309J  THR*     4.6     2.7    -      -       +      -
    358J  ILE*     4.0    35.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 276 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191J  LEU*     5.5     0.5    -      -       -      +
    192J  PHE*     3.9    22.0    -      -       +      -
    219J  ALA      4.6     0.2    -      -       -      -
    220J  ALA*     3.3     3.5    -      -       -      -
    221J  LEU*     2.8    46.1    +      -       +      -
    274J  LEU*     3.6     5.9    -      -       -      +
    275J  ILE*     1.3    82.2    -      -       -      +
    277J  GLU*     1.3    74.8    +      -       -      +
    278J  VAL*     4.2     8.6    -      -       +      +
    283J  VAL*     5.7     3.1    -      -       -      -
    287J  GLU*     2.8    40.1    +      -       -      +
    288J  LEU*     4.8     6.7    -      -       -      -
    290J  PHE*     3.7    37.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 277 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218J  ARG*     3.2    35.6    +      -       -      +
    219J  ALA      3.6     3.4    -      -       -      +
    220J  ALA*     4.5     1.8    -      -       +      +
    274J  LEU*     3.6    26.5    -      -       +      +
    276J  LYS*     1.3    86.2    -      -       -      +
    278J  VAL*     1.3    72.6    +      -       -      +
    279J  ASP      4.2     1.0    +      -       -      +
    283J  VAL*     4.9     2.6    -      -       -      +
    349O  ARG*     3.5    35.3    +      -       -      -
    381O  GLN*     4.2     8.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 278 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186J  TRP*     5.3     0.7    -      -       +      -
    191J  LEU*     4.9     2.0    -      -       +      -
    192J  PHE*     4.0    29.8    -      -       +      -
    197J  LEU*     4.2    11.4    -      -       +      -
    218J  ARG*     3.5    10.6    -      -       -      +
    219J  ALA*     2.9    45.2    +      -       +      +
    276J  LYS*     4.2    11.0    -      -       +      -
    277J  GLU*     1.3    83.3    -      -       -      +
    279J  ASP*     1.3    59.0    +      -       -      +
    280J  ILE*     3.5    18.6    +      -       +      -
    283J  VAL*     3.9    28.9    -      -       +      -
    288J  LEU*     4.9     2.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 279 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217J  ASP      3.9     5.6    -      -       -      +
    218J  ARG*     5.1     7.2    -      -       +      +
    277J  GLU*     4.2     1.2    -      -       -      +
    278J  VAL*     1.3    70.9    -      -       -      +
    280J  ILE*     1.3    60.5    +      -       -      +
    281J  TYR*     3.0    29.3    -      -       -      +
    282J  THR*     2.8    51.7    +      -       -      +
    283J  VAL*     3.1    16.8    +      -       +      +
----------------------------------------------------------
 Back to top of page


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