Contacts of the strand formed by residues 185 - 197 (chain A) in PDB entry 6YB9


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 185 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  GLU      5.0     0.7    -      -       -      +
    180A  TRP*     3.4    42.1    +      -       +      +
    181A  LEU*     3.9    11.3    +      -       -      +
    183A  GLN*     3.2    14.5    -      -       -      -
    184A  ASN*     1.3    78.6    -      -       -      +
    186A  THR*     1.3    61.7    +      -       -      +
    187A  LEU      3.7     2.6    +      -       -      -
    216A  LEU*     3.8    22.9    -      -       +      -
    217A  TRP      3.7     5.8    -      -       -      +
    218A  PRO*     4.4     8.1    -      -       +      -
    251A  TRP*     3.6    36.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  ARG*     6.0     1.6    -      -       +      -
    103A  ILE*     3.7    30.3    -      -       +      -
    120A  LYS*     5.5     2.7    -      -       -      +
    177A  GLU*     6.1     0.4    -      -       -      +
    181A  LEU*     5.7     4.6    -      -       -      +
    184A  ASN      4.3     0.2    -      -       -      -
    185A  CYS*     1.3    70.9    -      -       -      +
    187A  LEU*     1.3    70.4    +      -       -      +
    188A  VAL*     3.4     7.3    +      -       +      +
    215A  ARG      3.8     0.3    -      -       -      +
    216A  LEU*     3.6     4.5    -      -       -      -
    217A  TRP*     2.9    38.0    +      -       +      -
    219A  SER      4.4     0.3    -      -       -      -
    220A  GLY*     3.3    26.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  ARG*     4.0     6.9    -      -       -      +
    173A  PHE*     3.6    39.3    -      -       +      +
    176A  LEU*     3.6    17.7    -      -       +      +
    177A  GLU*     3.5    47.3    +      -       -      +
    180A  TRP*     4.3    10.5    -      -       +      +
    185A  CYS      3.7     4.6    +      -       -      -
    186A  THR*     1.3    73.4    -      -       -      +
    188A  VAL*     1.3    61.1    +      -       -      +
    189A  ASP      4.1     2.2    -      -       -      +
    190A  MET*     4.9     5.2    -      -       -      -
    214A  TRP*     3.6    43.7    -      -       +      -
    215A  ARG      3.6     7.9    -      -       -      +
    216A  LEU*     4.2    10.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  ARG*     2.9    26.7    +      -       -      -
    103A  ILE*     3.3    31.3    +      -       +      +
    105A  THR*     3.7    29.4    -      -       +      -
    173A  PHE*     4.1     1.1    -      -       -      -
    186A  THR*     3.8    14.4    -      -       +      +
    187A  LEU*     1.3    72.3    -      -       -      +
    189A  ASP*     1.3    67.3    +      -       -      +
    215A  ARG*     3.0    16.5    +      -       +      +
    217A  TRP*     3.4    49.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  VAL*     4.9     0.2    -      -       +      -
    100A  CYS      3.1    17.3    -      -       -      +
    101A  ARG*     3.7    21.8    +      -       +      -
    103A  ILE      4.6     1.6    -      -       -      +
    105A  THR*     3.6    13.3    -      -       -      +
    173A  PHE*     3.8     6.5    -      -       -      -
    187A  LEU*     3.7     3.5    -      -       -      +
    188A  VAL*     1.3    82.3    -      -       +      +
    190A  MET*     1.3    64.7    +      -       -      +
    214A  TRP*     3.3     4.3    -      -       -      +
    215A  ARG*     2.8    52.6    +      -       -      +
    502A  OK8      2.7    31.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  TRP      3.9     0.4    -      -       -      +
     99A  VAL*     3.2     7.8    -      -       -      +
    100A  CYS*     3.0    32.7    +      -       +      +
    169A  THR*     3.7    10.8    -      -       +      +
    172A  ILE*     3.7    13.5    -      -       +      -
    173A  PHE*     3.4    55.2    -      -       +      +
    176A  LEU*     4.0    23.3    -      -       -      -
    187A  LEU*     4.9     3.6    -      -       +      -
    189A  ASP*     1.3    78.3    +      -       -      +
    191A  LYS*     1.3    61.9    -      -       -      +
    192A  ILE*     3.8    24.9    -      -       +      -
    209A  ILE*     5.2     2.5    -      -       +      -
    213A  SER*     3.1    14.1    -      -       -      +
    214A  TRP*     4.0    10.1    -      -       +      -
    502A  OK8      3.8     7.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  GLU*     3.7    35.2    +      -       +      -
     98A  TRP      3.2     8.7    -      -       -      +
     99A  VAL*     4.2     4.3    -      -       +      -
    131A  LYS*     5.1     0.2    -      -       -      +
    190A  MET*     1.3    71.7    -      -       -      +
    192A  ILE*     1.3    81.5    +      -       -      +
    193A  GLU*     3.0    26.1    +      -       -      +
    207A  ASP*     4.4     9.7    +      -       -      -
    208A  VAL      5.0     2.7    +      -       -      +
    209A  ILE*     5.0     0.7    -      -       -      +
    213A  SER*     2.7    36.0    +      -       -      +
    502A  OK8      3.4    60.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  TRP*     3.0    45.9    +      -       +      +
    169A  THR*     3.8    17.9    -      -       +      +
    172A  ILE*     3.8    20.4    -      -       +      -
    190A  MET*     3.8    24.0    -      -       +      -
    191A  LYS*     1.3    81.4    -      -       -      +
    193A  GLU*     1.3    68.6    +      -       -      +
    194A  PHE*     3.6    30.3    -      -       +      -
    205A  LEU*     3.8    11.7    -      -       +      -
    208A  VAL      5.2     5.4    -      -       -      -
    209A  ILE*     3.9    26.7    -      -       +      -
    213A  SER*     6.0     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  MET*     3.9    24.9    -      -       +      +
     94A  ILE      4.8     2.7    -      -       -      +
     96A  ILE      3.9    15.7    -      -       -      +
     97A  GLU*     3.8     3.9    -      -       +      +
    131A  LYS*     2.9    42.9    +      -       -      +
    191A  LYS*     3.0    28.4    +      -       +      +
    192A  ILE*     1.3    79.9    -      -       -      +
    194A  PHE*     1.3    65.6    +      -       -      +
    205A  LEU*     3.7     6.4    -      -       -      +
    206A  ALA      3.1    28.3    +      -       -      +
    207A  ASP*     4.3    20.0    -      -       +      +
    208A  VAL      5.5     0.8    +      -       -      -
    501A  ANP      4.2     8.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  MET*     3.7    10.3    -      -       -      +
     94A  ILE*     3.0    27.3    +      -       -      +
     96A  ILE      4.9     1.2    +      -       -      -
     98A  TRP*     3.5    17.0    -      +       -      -
    165A  MET*     3.2    54.4    -      -       +      +
    168A  ALA*     3.9    12.3    -      -       +      -
    169A  THR*     3.4    17.3    -      -       -      -
    172A  ILE*     4.3     5.4    -      -       +      -
    192A  ILE*     3.6    24.9    -      -       +      -
    193A  GLU*     1.3    72.8    -      -       -      +
    195A  GLY*     1.3    58.7    +      -       -      +
    203A  ILE*     3.9    15.3    -      -       +      -
    204A  VAL      3.3     9.4    -      -       -      +
    205A  LEU*     3.5    23.8    -      -       -      -
    504A  EDO      3.9    21.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  CYS*     4.0     7.9    -      -       -      -
     92A  GLU      3.3    12.8    -      -       -      -
     93A  MET*     4.0    12.6    -      -       -      -
     94A  ILE*     4.1     5.2    -      -       -      -
    194A  PHE*     1.3    73.5    -      -       -      +
    196A  VAL*     1.3    63.1    +      -       -      -
    197A  ASP      4.0     0.2    -      -       -      -
    202A  GLU      3.8     0.3    -      -       -      +
    203A  ILE*     3.4     3.1    -      -       -      +
    204A  VAL*     2.9    35.3    +      -       -      +
    206A  ALA*     4.1     4.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  CYS*     3.1     2.9    -      -       -      -
     92A  GLU*     2.9    36.3    +      -       -      +
     94A  ILE*     4.1    14.6    -      -       +      -
    152A  PHE*     3.7    39.7    -      -       +      +
    153A  ALA*     3.9     8.4    -      -       +      +
    155A  LEU*     4.1    23.6    -      -       +      -
    157A  ILE*     4.6     2.5    -      -       +      -
    195A  GLY*     1.3    73.8    -      -       -      +
    197A  ASP*     1.3    67.8    +      -       -      +
    198A  VAL*     3.3     2.1    +      -       -      +
    201A  LYS*     3.8    33.0    -      -       +      +
    202A  GLU      3.5     3.6    -      -       -      +
    203A  ILE*     4.4     2.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  GLY      5.2     1.0    -      -       -      +
     89A  PRO*     3.3    31.2    -      -       -      +
     90A  GLN      3.6     8.1    -      -       -      +
     91A  CYS*     4.0     9.0    -      -       -      -
    195A  GLY      4.0     2.2    +      -       -      -
    196A  VAL*     1.3    68.8    -      -       -      +
    198A  VAL*     1.3    58.2    +      -       -      +
    199A  THR*     2.7    36.4    +      -       -      -
    200A  THR*     3.1    34.2    +      -       -      +
    201A  LYS*     2.8    33.1    +      -       -      +
    202A  GLU      3.1    14.3    +      -       -      +
    204A  VAL*     4.6    10.8    -      -       +      +
----------------------------------------------------------
 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