Contacts of the strand formed by residues 176 - 187 (chain C) in PDB entry 4A12


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 LEU 176 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141C  ILE*     3.3    44.7    -      -       +      +
    142C  GLU*     3.6     9.0    -      -       -      +
    169C  LYS*     3.8    25.4    -      -       +      -
    170C  SER      3.6     8.7    -      -       -      +
    171C  TYR*     3.5    28.0    -      -       +      +
    175C  THR*     1.3    70.2    -      -       -      +
    177C  VAL*     1.3    58.9    +      -       -      +
    178C  PHE      3.4    22.2    -      -       -      +
    179C  LYS*     4.4    15.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 177 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114C  LEU*     5.8     0.2    -      -       -      +
    140C  PHE*     3.6     5.0    -      -       -      +
    141C  ILE*     2.9    25.9    +      -       -      -
    142C  GLU*     3.2    34.0    +      -       +      +
    143C  LYS      5.1     2.7    -      -       -      +
    144C  VAL*     3.7    29.4    -      -       +      +
    150C  VAL*     4.5     3.4    -      -       +      -
    170C  SER*     3.0    25.4    +      -       -      +
    171C  TYR*     4.1     0.9    -      -       -      -
    172C  VAL*     3.9    27.6    -      -       +      -
    175C  THR*     3.4    16.8    -      -       +      +
    176C  LEU*     1.3    72.8    -      -       -      +
    178C  PHE*     1.3    63.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 178 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114C  LEU*     4.1    21.1    -      -       +      -
    115C  PHE*     4.3    10.5    -      -       -      -
    118C  ALA*     3.7    29.4    -      -       +      -
    138C  ILE*     3.5    38.8    -      -       +      -
    139C  GLN      3.3    14.8    -      -       -      -
    140C  PHE*     3.8    33.0    -      +       +      -
    141C  ILE*     3.7     3.8    -      -       -      -
    168C  VAL*     4.5     4.3    -      -       +      -
    169C  LYS*     3.6     0.2    -      -       -      -
    170C  SER*     2.9    54.4    +      -       -      -
    176C  LEU*     3.4     9.4    -      -       -      +
    177C  VAL*     1.3    80.5    -      -       -      +
    179C  LYS*     1.3    60.4    +      -       -      +
    180C  GLY*     3.9    17.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 179 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138C  ILE*     3.4     2.6    -      -       -      +
    139C  GLN*     2.7    65.3    +      -       +      +
    141C  ILE*     3.5    14.6    -      -       +      +
    167C  GLU*     6.5     1.1    -      -       +      -
    168C  VAL      3.4    10.8    -      -       -      +
    169C  LYS*     4.3    23.3    -      -       +      +
    176C  LEU*     4.4    15.0    -      -       +      -
    178C  PHE*     1.3    77.5    -      -       -      +
    180C  GLY*     1.3    59.5    +      -       -      +
    181C  ASN*     4.8    15.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 180 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137C  SER      3.3     8.5    -      -       -      -
    138C  ILE*     3.9    13.0    -      -       -      -
    167C  GLU*     3.5     2.6    -      -       -      -
    168C  VAL*     2.7    43.4    +      -       -      +
    178C  PHE*     3.9     7.4    -      -       -      -
    179C  LYS*     1.3    76.1    -      -       -      +
    181C  ASN*     1.3    65.0    +      -       -      -
    182C  PHE*     3.7     7.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 181 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135C  GLU      4.6     0.2    -      -       -      -
    136C  SER*     3.2     8.5    +      -       -      -
    137C  SER*     2.8    51.3    +      -       -      +
    139C  GLN*     5.7     1.0    +      -       -      -
    157C  VAL*     5.8     0.2    -      -       -      +
    166C  VAL      3.4     4.0    -      -       -      +
    167C  GLU*     3.3    29.2    -      -       -      +
    179C  LYS*     4.8    16.4    -      -       -      +
    180C  GLY*     1.3    79.3    -      -       -      +
    182C  PHE*     1.3    60.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 182 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115C  PHE*     3.5    24.9    -      +       -      -
    118C  ALA*     3.7    22.2    -      -       +      -
    119C  ASN*     3.7    22.2    -      -       -      -
    122C  CYS*     3.7    18.4    -      -       -      -
    133C  THR*     4.0    18.4    -      -       +      -
    135C  GLU      3.7     1.6    -      -       -      -
    136C  SER*     3.4    21.5    -      -       -      -
    138C  ILE*     4.3     1.8    -      -       +      -
    164C  TYR      3.5     1.2    -      -       -      +
    165C  TYR*     3.4     7.7    -      -       -      +
    166C  VAL*     2.7    42.3    +      -       +      +
    168C  VAL*     3.8    25.6    -      -       +      -
    180C  GLY*     3.7    21.3    -      -       -      -
    181C  ASN*     1.3    78.1    -      -       -      +
    183C  LYS*     1.3    59.1    +      -       -      +
    184C  MSE      3.8     9.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 183 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133C  THR*     3.8     1.0    -      -       -      -
    134C  HIS*     2.8    37.9    +      -       +      +
    135C  GLU*     2.9    57.6    +      -       +      +
    163C  HIS*     3.6    32.4    -      -       +      +
    164C  TYR      3.8     2.5    -      -       -      -
    165C  TYR*     3.3    40.6    +      -       +      -
    182C  PHE*     1.3    70.0    -      -       -      +
    184C  MSE      1.3    55.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MSE 184 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119C  ASN      4.7     0.7    -      -       -      +
    122C  CYS*     3.8    25.1    -      -       +      -
    123C  VAL*     3.8    16.2    -      -       +      +
    126C  ILE*     3.7    28.0    -      -       +      -
    131C  VAL*     3.7    26.2    -      -       +      -
    132C  LEU      3.6     2.5    -      -       -      +
    133C  THR*     3.4    44.9    -      -       -      +
    163C  HIS*     3.3     3.6    -      -       -      -
    164C  TYR*     2.7    47.2    +      -       +      +
    166C  VAL*     4.0    10.8    -      -       +      -
    182C  PHE*     4.0    12.3    -      -       +      -
    183C  LYS*     1.3    71.8    -      -       -      +
    185C  PHE*     1.3    63.4    +      -       -      +
    186C  TYR*     3.7     0.4    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 185 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130C  THR*     5.1     5.6    -      -       -      -
    131C  VAL*     3.4     7.1    -      -       -      +
    132C  LEU*     2.7    59.0    +      -       +      +
    134C  HIS*     3.4    42.2    -      +       +      +
    162C  LYS*     3.2    47.3    -      -       +      -
    163C  HIS*     3.7     8.9    -      +       +      -
    183C  LYS      3.8     0.8    +      -       -      -
    184C  MSE      1.3    72.9    -      -       -      +
    186C  TYR*     1.3    68.5    +      -       -      +
    187C  ASP*     3.9    29.2    -      -       +      -
    143D  LYS*     6.0     2.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 186 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126C  ILE*     4.5     4.5    -      -       +      -
    128C  GLN*     3.7    33.9    -      -       +      -
    130C  THR      3.4     7.0    -      -       -      +
    131C  VAL*     5.0     0.4    -      -       +      -
    159C  GLN*     3.2    18.2    +      -       -      -
    160C  THR      2.7    30.0    +      -       -      -
    161C  ALA*     3.1    22.4    +      -       -      +
    162C  LYS*     3.1    26.9    +      -       -      +
    163C  HIS      3.4    18.8    -      -       -      -
    164C  TYR*     3.4    31.9    -      +       +      -
    184C  MSE      6.2     0.2    -      -       +      -
    185C  PHE*     1.3    85.7    -      -       -      +
    187C  ASP*     1.3    63.1    +      -       -      +
    188C  LYS*     3.8    31.3    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 187 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128C  GLN*     4.5     1.3    -      -       -      +
    129C  PRO*     3.4    15.5    -      -       -      +
    130C  THR*     3.0    33.3    +      -       -      +
    185C  PHE*     3.9    20.0    -      -       +      -
    186C  TYR*     1.3    75.1    -      -       -      +
    188C  LYS*     1.3    65.3    +      -       -      +
    189C  ARG*     3.0    31.0    +      -       -      +
    190C  GLY      4.2     0.9    +      -       -      -
----------------------------------------------------------
 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