Contacts of the strand formed by residues 179 - 188 (chain C) in PDB entry 3Q3G


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 TYR 179 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  LYS*     6.4     1.3    -      -       -      -
    111C  GLU*     3.3    35.5    +      -       -      +
    144C  ASN      3.2     4.9    +      -       -      -
    145C  PHE*     2.8    60.0    +      -       +      +
    146C  TYR*     3.8    17.0    -      +       -      -
    148C  LYS*     3.7    45.3    -      -       +      +
    170C  THR*     4.0    13.7    -      -       -      +
    171C  ASP*     5.1     0.4    -      -       -      -
    172C  GLN*     3.4    50.6    +      -       +      +
    178C  THR*     1.3    75.5    -      -       -      +
    180C  SER*     1.3    63.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 180 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142C  LEU      3.3     5.4    -      -       -      -
    143C  ASN*     3.4     5.6    -      -       -      -
    144C  ASN*     3.0    24.1    +      -       -      -
    145C  PHE*     3.7     3.6    -      -       -      -
    169C  TRP*     3.6     3.8    -      -       -      +
    170C  THR*     3.0    38.1    +      -       -      +
    178C  THR*     4.9     0.7    +      -       -      -
    179C  TYR*     1.3    71.9    +      -       -      +
    181C  MET*     1.3    62.9    +      -       -      +
    628C  EDO      4.7     1.2    +      -       -      -
    175D  HIS*     3.2    36.6    +      -       -      -
    177D  PHE*     3.6     7.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 181 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140C  CYS      3.9     0.7    -      -       -      +
    141C  PHE*     3.5     2.8    -      -       -      -
    142C  LEU*     2.7    62.9    +      -       +      +
    145C  PHE*     4.0    10.8    -      -       +      -
    150C  ILE*     4.1    12.8    -      -       -      +
    152C  VAL*     3.5    33.4    -      -       +      -
    167C  ASN*     4.7     2.2    -      -       -      +
    168C  SER      3.4     8.7    -      -       -      +
    169C  TRP*     3.3    43.1    -      -       +      +
    180C  SER*     1.3    76.1    -      -       -      +
    182C  SER*     1.3    64.8    +      -       -      +
    183C  SER*     3.7    22.4    -      -       -      +
    177D  PHE*     3.4     7.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 182 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139C  VAL*     4.2     1.6    -      -       -      +
    140C  CYS      3.6     3.8    -      -       -      -
    141C  PHE*     3.6    10.5    -      -       -      -
    166C  LEU      3.9     0.7    -      -       -      +
    167C  ASN*     3.3     5.7    -      -       -      +
    168C  SER      2.7    35.0    +      -       -      -
    181C  MET*     1.3    75.5    -      -       -      +
    183C  SER*     1.3    61.0    +      -       -      +
    184C  THR*     4.1     4.3    +      -       -      -
    177D  PHE*     3.5    31.6    -      -       -      -
    189D  SER*     2.9    20.9    +      -       -      -
    605D  EDO      3.5    14.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 183 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139C  VAL*     3.5     1.9    -      -       -      +
    140C  CYS*     2.8    46.0    +      -       -      -
    152C  VAL*     4.3    13.1    -      -       -      +
    154C  TRP*     2.8    34.5    +      -       -      -
    165C  VAL*     3.7     0.2    -      -       -      +
    167C  ASN*     2.7    25.3    +      -       -      +
    181C  MET*     3.7    14.8    -      -       -      +
    182C  SER*     1.3    73.0    +      -       -      +
    184C  THR*     1.3    60.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 184 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137C  SER*     4.0    11.0    -      -       -      +
    138C  VAL      3.4     4.0    -      -       -      +
    139C  VAL*     3.8    29.0    -      -       +      +
    154C  TRP*     4.6     1.6    -      -       -      -
    164C  GLY      3.3     5.7    -      -       -      +
    165C  VAL*     3.3     2.4    -      -       -      -
    166C  LEU*     2.9    38.2    +      -       -      +
    182C  SER*     4.1     0.2    +      -       -      -
    183C  SER*     1.3    76.3    +      -       -      +
    185C  LEU*     1.3    59.6    +      -       -      +
    186C  THR*     3.7    18.0    +      -       -      +
    152D  LEU*     4.7     7.6    -      -       +      -
    154D  LYS*     6.3     0.7    -      -       -      -
    182D  GLN*     5.1     4.3    -      -       -      +
    187D  THR*     5.5     2.5    -      -       +      -
    605D  EDO      2.7    34.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 185 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136C  ALA      3.7     1.6    -      -       -      +
    137C  SER*     3.2     2.0    -      -       -      -
    138C  VAL*     2.7    40.8    +      -       +      +
    154C  TRP*     3.8    44.3    -      -       +      +
    156C  ILE*     3.8    28.0    -      -       +      -
    161C  ARG*     3.9    13.0    -      -       +      +
    163C  ASN      3.6    23.8    -      -       -      +
    164C  GLY*     3.8     2.7    -      -       -      -
    165C  VAL*     3.9    13.9    -      -       +      +
    184C  THR*     1.3    69.4    -      -       -      +
    186C  THR*     1.3    62.4    +      -       -      +
    187C  LEU*     3.9    20.6    +      -       +      +
    198C  TYR*     4.3     7.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 186 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130C  GLN*     5.0     1.6    -      -       -      +
    135C  GLY*     6.0     0.9    -      -       -      -
    136C  ALA      3.5     3.6    -      -       -      +
    137C  SER*     3.0    25.8    +      -       -      +
    161C  ARG*     5.2     1.7    +      -       -      -
    163C  ASN      4.7     0.9    -      -       -      +
    164C  GLY*     3.0    28.5    +      -       -      -
    166C  LEU*     5.4     0.2    -      -       -      -
    184C  THR*     3.7     7.6    -      -       -      +
    185C  LEU*     1.3    73.4    -      -       -      +
    187C  LEU*     1.3    71.1    +      -       -      +
    154D  LYS*     4.1    13.2    -      -       -      +
    182D  GLN*     3.0    30.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 187 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135C  GLY*     4.2     2.8    -      -       -      -
    136C  ALA      2.8    26.3    +      -       -      +
    138C  VAL*     4.4     6.7    -      -       +      -
    156C  ILE*     4.0    11.2    -      -       +      -
    161C  ARG*     3.9    31.0    -      -       -      +
    185C  LEU*     3.9    29.4    -      -       +      +
    186C  THR*     1.3    81.7    -      -       -      +
    188C  THR*     1.3    74.3    +      -       -      +
    191C  GLU*     4.0    25.1    -      -       +      +
    192C  TYR*     4.3     8.1    -      -       +      +
    195C  HIS*     5.1     2.0    -      -       -      +
    198C  TYR*     4.1    27.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 188 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134C  GLY      3.7     9.6    -      -       -      +
    135C  GLY*     4.5     0.4    -      -       -      -
    136C  ALA*     3.6     4.2    -      -       -      +
    187C  LEU*     1.3    79.8    -      -       -      +
    189C  LYS*     1.3    63.8    +      -       -      +
    190C  ASP*     3.9     5.5    +      -       -      +
    191C  GLU*     3.0    38.4    +      -       -      +
    192C  TYR*     3.1    23.9    +      -       -      +
    194C  ARG*     5.2     0.2    +      -       -      -
----------------------------------------------------------
 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