Contacts of the helix formed by residues 129 - 140 (chain C) in PDB entry 4LQL


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 GLY 129 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80C  MET*     3.7    14.6    -      -       -      +
     82C  THR      3.3    23.6    -      -       -      -
     83C  PHE*     4.3     8.3    -      -       -      -
     84C  SER      4.4     5.4    -      -       -      +
    125C  GLN      3.8     0.2    +      -       -      -
    126C  SER      2.6    10.0    +      -       -      -
    128C  HIS*     1.3    75.8    -      -       -      +
    130C  ASP*     1.3    68.7    +      -       -      +
    132C  GLU*     3.6     5.4    +      -       -      +
    133C  TYR*     3.1    19.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 130 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440B  MET*     5.1     6.5    -      -       +      -
     79C  TRP*     5.9     2.7    -      -       +      +
     80C  MET*     4.7     6.6    +      -       -      +
    102C  HIS*     5.3     4.3    -      -       +      -
    104C  ALA*     3.8    29.4    -      -       +      -
    105C  THR      5.8     0.2    -      -       -      +
    126C  SER*     2.8    15.5    +      -       -      +
    127C  ALA*     4.7     6.5    -      -       -      +
    129C  GLY*     1.3    77.4    -      -       -      +
    131C  ARG*     1.3    57.9    +      -       +      +
    133C  TYR*     2.7    30.0    +      -       -      +
    134C  ALA*     2.9    13.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 131 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332B  ASP*     2.9    30.1    +      -       -      +
    344B  ILE*     4.7     8.7    -      -       -      +
    432B  LEU*     5.6     1.4    -      -       -      +
    436B  ALA*     3.5    34.7    +      -       -      +
    439B  TRP*     3.8    28.4    -      -       +      +
    440B  MET*     4.9     7.4    -      -       +      +
    443B  GLY      5.4     0.5    -      -       -      -
    444B  GLY      4.5     5.1    +      -       -      +
    445B  GLY*     3.7    43.5    +      -       -      -
    446B  HIS*     4.2     8.7    -      -       -      +
    127C  ALA*     3.0    27.1    +      -       -      +
    128C  HIS*     4.1     7.5    -      -       -      +
    130C  ASP*     1.3    81.8    -      -       +      +
    132C  GLU*     1.3    59.3    +      -       -      +
    134C  ALA*     3.9     8.5    +      -       -      +
    135C  TYR*     3.4    16.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 132 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188B  VAL*     3.0    28.2    -      -       -      +
    189B  ALA      3.1    13.5    +      -       -      -
    190B  VAL*     2.9    36.5    -      -       -      +
    446B  HIS*     3.8     8.4    +      -       +      +
     83C  PHE*     4.6     7.4    -      -       +      -
     84C  SER      3.8    14.1    -      -       -      +
     85C  PRO*     4.0     0.3    -      -       -      +
     86C  ALA*     2.9    47.4    +      -       +      +
    128C  HIS      3.8    15.3    +      -       -      +
    129C  GLY*     3.6     5.0    +      -       -      +
    130C  ASP      2.9     1.0    +      -       -      -
    131C  ARG*     1.3    79.2    -      -       -      +
    133C  TYR*     1.3    64.4    +      -       -      +
    135C  TYR*     3.7     9.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 133 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78C  THR*     5.7     8.1    -      -       -      -
     80C  MET*     4.0    22.0    -      -       +      -
     84C  SER      5.3     0.8    +      -       -      -
     86C  ALA*     4.5     5.4    -      -       -      -
     89C  TRP*     4.7    18.4    -      +       -      -
    100C  LEU*     6.6     0.2    -      -       +      -
    102C  HIS*     4.6    17.3    -      +       +      -
    129C  GLY      3.1    13.4    +      -       -      +
    130C  ASP*     2.7    17.4    +      -       -      +
    132C  GLU*     1.3    71.0    -      -       -      +
    134C  ALA*     1.3    62.7    +      -       -      +
    136C  ILE*     3.0    23.9    +      -       +      +
    137C  ASN*     3.2    14.8    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 134 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440B  MET*     3.4    44.4    -      -       +      +
    443B  GLY*     4.6     3.1    -      -       -      -
    102C  HIS*     5.4     7.4    -      -       +      -
    130C  ASP      2.9    12.3    +      -       -      +
    131C  ARG*     4.0     6.3    -      -       -      +
    133C  TYR*     1.3    75.2    -      -       -      +
    135C  TYR*     1.3    68.2    +      -       -      +
    137C  ASN*     3.8     8.1    -      -       -      +
    138C  SER*     2.9    22.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 135 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  ALA*     4.9     3.6    -      -       +      -
    190B  VAL*     3.4    44.0    -      -       +      -
    394B  SER*     6.2     2.9    -      -       -      -
    395B  TYR      5.8     2.5    -      -       -      -
    396B  PHE*     6.4     2.0    -      +       -      -
    443B  GLY*     4.6    12.7    -      -       -      -
    444B  GLY      4.9     5.2    -      -       -      +
     86C  ALA*     5.6     1.1    -      -       +      -
    131C  ARG      3.4     8.4    +      -       -      +
    132C  GLU      3.8     6.7    -      -       -      +
    133C  TYR      3.1     0.8    +      -       -      -
    134C  ALA*     1.3    79.2    -      -       -      +
    136C  ILE*     1.3    65.2    +      -       +      +
    138C  SER*     2.9     1.2    +      -       -      -
    139C  ARG*     2.6    47.4    +      -       +      +
    196D  VAL*     5.7     1.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 136 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  ALA*     4.4     8.7    -      -       +      -
     86C  ALA*     3.8    17.0    -      -       +      +
     89C  TRP*     4.0    26.7    -      -       +      +
     90C  ILE*     3.6    39.9    -      -       +      -
     93C  THR*     4.4    10.2    -      -       -      +
    132C  GLU      4.0     0.2    +      -       -      -
    133C  TYR*     3.0    15.6    +      -       +      +
    135C  TYR*     1.3    81.2    -      -       +      +
    137C  ASN*     1.3    61.6    +      -       +      +
    139C  ARG*     3.7    13.7    -      -       +      -
    140C  LEU*     3.0    42.7    +      -       +      +
    196D  VAL*     4.0    20.9    -      -       +      -
    200D  ILE*     4.7     2.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 137 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93C  THR*     5.1     5.2    -      -       -      +
    100C  LEU*     4.8    14.8    -      -       +      -
    102C  HIS*     6.5     0.9    -      -       +      -
    133C  TYR*     3.2    18.6    +      -       +      +
    134C  ALA*     3.8     6.3    -      -       -      +
    135C  TYR      3.2     1.2    -      -       -      -
    136C  ILE*     1.3    77.7    -      -       +      +
    138C  SER*     1.3    59.4    +      -       -      +
    140C  LEU      4.2     0.9    -      -       -      -
    142C  VAL*     3.2    46.9    +      -       +      +
    144C  ALA*     5.8     3.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 138 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    396B  PHE*     6.6     0.4    -      -       -      -
    440B  MET      4.4     1.3    +      -       -      -
    441B  LYS      3.0    28.3    -      -       -      -
    442B  TYR      4.4     1.3    -      -       -      -
    443B  GLY*     4.1    13.5    -      -       -      -
    134C  ALA      2.9    16.5    +      -       -      -
    135C  TYR      2.9     3.1    +      -       -      -
    137C  ASN*     1.3    74.2    -      -       -      +
    139C  ARG*     1.3    65.4    -      -       -      +
    140C  LEU      3.1     1.8    -      -       -      -
    141C  ASN*     2.9    19.3    +      -       -      +
    142C  VAL      5.8     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 139 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  GLU      5.4     1.2    +      -       -      -
    395B  TYR*     3.4    21.6    +      -       -      -
    396B  PHE*     4.2    23.2    -      -       +      +
    397B  ASP*     3.6    37.5    -      -       -      +
    135C  TYR*     2.6    31.1    +      -       +      +
    136C  ILE*     3.7    17.3    -      -       +      +
    138C  SER*     1.3    72.9    -      -       -      +
    140C  LEU*     1.3    56.8    +      -       -      +
    141C  ASN*     3.4     9.9    +      -       -      -
    194D  ASP*     2.9    27.1    +      -       -      -
    196D  VAL*     4.0    18.7    -      -       -      +
    197D  ALA*     3.6    16.8    -      -       -      +
    200D  ILE*     3.6    28.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 140 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  ILE*     5.5     2.2    -      -       +      +
     93C  THR*     4.7    12.6    -      -       -      -
     94C  GLU*     5.3    11.7    -      -       +      +
    136C  ILE*     3.0    39.1    +      -       +      +
    138C  SER      3.1     0.2    -      -       -      -
    139C  ARG*     1.3    77.0    -      -       +      +
    141C  ASN*     1.3    59.3    +      -       -      +
    142C  VAL*     2.8    29.1    +      -       +      +
    200D  ILE*     4.3    27.1    -      -       +      -
----------------------------------------------------------
 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