Contacts of the strand formed by residues 204 - 212 (chain A) in PDB entry 6K0X


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 204 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  GLU*     5.9     0.2    -      -       -      +
     28A  ASP*     5.2     1.0    +      -       -      +
    125A  TYR*     2.8    40.6    +      -       -      -
    126A  VAL*     5.1     4.2    -      -       -      +
    174A  ILE*     4.0    22.6    -      -       +      +
    176A  GLU*     5.2     5.4    -      -       -      +
    200A  GLN*     3.3     7.2    +      -       -      -
    201A  ALA*     2.8    55.0    +      -       +      +
    202A  GLY      3.4     0.2    -      -       -      -
    203A  GLN*     1.3    82.5    -      -       -      +
    205A  THR*     1.3    59.8    +      -       -      +
    206A  LEU*     3.8    12.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  ILE*     3.3     4.3    -      -       -      +
    175A  LYS*     3.1    42.9    +      -       +      +
    176A  GLU*     5.3     1.2    +      -       -      -
    198A  SER*     5.5     5.6    -      -       -      -
    199A  ARG      3.7     6.7    -      -       -      +
    200A  GLN*     2.6    24.8    +      -       -      +
    204A  GLU*     1.3    69.7    -      -       -      +
    206A  LEU*     1.3    64.1    +      -       -      +
    207A  SER*     4.0     4.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  GLU*     4.2     4.3    -      -       +      +
     28A  ASP*     3.8    32.8    -      -       +      +
     31A  LEU*     3.5    16.4    -      -       +      -
    125A  TYR*     3.7    18.8    -      -       +      +
    172A  VAL*     4.1     6.1    -      -       +      -
    173A  THR      3.2    10.1    -      -       -      +
    174A  ILE*     3.5    23.6    -      -       +      -
    198A  SER*     3.2     7.3    -      -       -      -
    199A  ARG*     2.7    41.9    +      -       +      +
    201A  ALA*     3.5    30.3    -      -       +      -
    204A  GLU*     4.0     9.2    -      -       +      +
    205A  THR*     1.3    74.2    -      -       -      +
    207A  SER*     1.3    61.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LEU*     4.5     1.1    -      -       -      -
    171A  LEU      3.6     1.0    -      -       -      +
    172A  VAL*     3.6     1.4    -      -       -      -
    173A  THR*     2.8    54.9    +      -       -      -
    174A  ILE      6.1     0.2    -      -       -      -
    179A  PRO*     4.8    11.1    -      -       -      +
    195A  THR*     4.2     6.1    +      -       -      +
    197A  LEU      3.6     4.9    -      -       -      -
    198A  SER*     2.9    19.4    +      -       -      -
    205A  THR*     4.0     5.4    +      -       -      +
    206A  LEU*     1.3    72.5    +      -       -      +
    208A  VAL*     1.3    62.2    +      -       -      +
    209A  LEU*     3.7    15.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LEU*     3.6    31.4    -      -       +      -
     32A  LEU*     4.2    25.8    -      -       +      +
     35A  ALA*     3.9    17.9    -      -       +      -
    170A  TYR*     3.9    28.7    -      -       +      -
    171A  LEU      3.3     7.4    -      -       -      +
    172A  VAL*     4.4    11.7    -      -       +      -
    195A  THR*     3.6     3.1    -      -       -      +
    196A  ALA*     2.7    33.7    +      -       +      -
    197A  LEU      2.8    15.6    +      -       -      +
    207A  SER*     1.3    71.3    -      -       -      +
    209A  LEU*     1.3    58.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  PHE      3.6     1.1    -      -       -      +
    170A  TYR*     3.3     4.9    -      -       -      -
    171A  LEU*     2.8    36.8    +      -       +      +
    173A  THR*     4.0    26.9    -      -       +      +
    179A  PRO*     4.0    25.8    -      -       +      +
    182A  ILE*     4.0    23.8    -      -       +      -
    183A  LEU*     4.3     8.3    -      -       +      -
    194A  THR      3.4     5.2    -      -       -      +
    195A  THR*     3.6    26.0    -      -       -      +
    207A  SER*     4.1    13.7    -      -       -      -
    208A  VAL*     1.3    81.1    -      -       -      +
    210A  LYS*     1.3    60.7    +      -       -      +
    211A  PHE*     3.7    22.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ALA*     5.4     0.6    -      -       -      +
     42A  GLU*     2.4    43.2    +      -       -      -
    168A  LEU*     4.2    12.6    -      -       +      -
    169A  PHE      3.3     5.4    -      -       -      +
    170A  TYR*     3.6    37.5    +      -       +      +
    192A  GLN      3.7     0.5    -      -       -      +
    193A  GLY*     3.4     4.0    -      -       -      -
    194A  THR*     2.8    50.7    +      -       +      +
    196A  ALA*     4.2    13.0    -      -       +      -
    208A  VAL      4.1     0.2    +      -       -      -
    209A  LEU*     1.3    73.4    -      -       -      +
    211A  PHE*     1.3    65.5    +      -       -      +
    212A  THR*     4.4     9.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  LEU*     4.1     2.0    -      -       -      +
    167A  GLY      3.9     0.3    -      -       -      +
    168A  LEU*     3.4     5.9    -      -       -      +
    169A  PHE*     2.7    79.9    +      +       +      +
    171A  LEU*     4.4     9.0    -      -       +      -
    182A  ILE*     4.0    12.6    -      -       +      -
    183A  LEU*     3.7    26.2    -      -       +      -
    186A  MET*     3.4    42.0    -      -       +      -
    191A  LEU*     4.4    14.4    -      -       +      -
    192A  GLN      3.0     8.3    -      -       -      +
    193A  GLY*     3.6    15.3    -      -       -      -
    209A  LEU*     3.7    31.0    -      -       +      -
    210A  LYS*     1.3    74.0    -      -       -      +
    212A  THR*     1.3    61.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  GLU*     5.3     0.4    +      -       -      +
    163A  LEU*     4.8     0.2    -      -       -      -
    165A  PRO      5.0     1.8    -      -       -      +
    166A  ARG      4.6     6.5    -      -       -      +
    167A  GLY      3.4    17.0    -      -       -      +
    168A  LEU*     3.6    21.1    -      -       +      +
    191A  LEU*     3.3     9.9    -      -       -      +
    192A  GLN*     2.8    37.4    +      -       -      +
    210A  LYS*     4.4    11.6    +      -       -      +
    211A  PHE*     1.3    75.6    +      -       -      +
    213A  LYS*     1.3    61.9    +      -       -      +
    214A  SER*     3.2    31.3    +      -       -      +
----------------------------------------------------------
 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