Contacts of the helix formed by residues 50 - 64 (chain C) in PDB entry 3ER8


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 ASP 50 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  ASN*     2.9    16.8    +      -       -      +
     49C  LYS*     1.3    80.8    -      -       -      +
     51C  ILE*     1.3    55.2    -      -       -      +
     52C  PHE      2.7     4.7    -      -       -      -
     53C  VAL*     2.5    36.1    +      -       -      +
     54C  SER*     2.9    11.1    +      -       -      -
     75C  LYS*     5.9     5.3    +      -       -      -
     79C  LEU*     5.3     4.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 51 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  ASN*     3.0    18.9    +      -       +      +
     50C  ASP*     1.3    74.5    -      -       -      +
     52C  PHE*     1.3    61.5    +      -       -      +
     54C  SER*     3.0    15.9    -      -       -      -
     55C  LEU*     3.0    39.4    +      -       +      -
    702F    U      3.4    22.4    -      -       +      +
    703F    U      2.8    67.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 52 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47C  PHE*     4.1    15.3    -      +       +      -
     48C  ASN      4.0    10.3    -      -       -      +
     49C  LYS*     4.2    11.4    -      -       -      +
     50C  ASP*     2.7     0.8    -      -       -      +
     51C  ILE*     1.3    80.4    -      -       -      +
     53C  VAL*     1.3    57.0    +      -       -      +
     55C  LEU*     2.8    20.0    +      -       -      +
     56C  VAL*     3.1    26.3    +      -       +      +
     78C  ILE*     3.9    11.9    -      -       +      -
     82C  PHE*     3.6    19.7    -      +       -      -
    104C  LEU*     4.1    29.2    -      -       +      -
    108C  TYR*     3.4    46.2    -      +       +      -
    223C  PHE*     3.6    28.0    -      +       -      -
    703F    U      3.3    20.6    +      +       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 53 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  LYS      3.6    20.6    -      -       -      +
     50C  ASP*     2.5    26.6    +      -       -      +
     52C  PHE*     1.3    72.5    -      -       -      +
     54C  SER*     1.3    54.4    +      -       -      -
     56C  VAL      3.8     0.5    +      -       -      -
     57C  LYS*     3.0    49.4    +      -       -      +
     74C  ILE      3.6     3.0    -      -       -      +
     75C  LYS*     3.3    41.3    -      -       +      +
     78C  ILE*     3.7    28.7    -      -       +      -
     79C  LEU*     4.2    11.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 54 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50C  ASP*     2.9     7.3    +      -       -      -
     51C  ILE*     3.0    26.7    -      -       -      -
     53C  VAL*     1.3    78.9    -      -       -      +
     55C  LEU*     1.3    62.2    +      -       -      +
     57C  LYS*     4.0     5.7    -      -       -      +
     58C  LYS*     3.1    27.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 55 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51C  ILE*     3.0    32.8    +      -       +      +
     52C  PHE*     2.8     7.6    +      -       -      +
     54C  SER*     1.3    82.0    -      -       -      +
     56C  VAL*     1.3    62.8    +      -       -      +
     57C  LYS      3.1     1.8    -      -       -      -
     58C  LYS*     3.2    25.3    +      -       +      +
     59C  ASN*     3.4     6.9    -      -       -      +
    108C  TYR*     3.6    32.4    +      -       +      -
    109C  THR*     4.9     2.2    -      -       -      +
    113C  GLY*     4.9     1.1    -      -       -      -
    702F    U      3.0    70.7    -      -       +      +
    703F    U      4.2     6.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 56 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  PHE*     3.1    24.4    +      -       +      +
     53C  VAL      4.4     0.4    -      -       -      +
     55C  LEU*     1.3    76.0    -      -       -      +
     57C  LYS*     1.3    57.1    +      -       -      +
     59C  ASN*     3.3     4.7    -      -       -      +
     60C  LYS*     3.1    21.7    +      -       -      +
     74C  ILE*     3.5    20.2    -      -       +      -
     78C  ILE*     3.4    27.8    -      -       +      -
    108C  TYR*     3.9    13.2    -      -       +      +
    220C  LEU*     4.0    10.8    -      -       +      -
    223C  PHE*     3.7    27.8    -      -       +      -
    224C  ILE*     3.5    20.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 57 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53C  VAL*     3.0    42.0    +      -       +      +
     54C  SER*     4.0     5.8    -      -       -      +
     55C  LEU      3.1     0.2    -      -       -      -
     56C  VAL*     1.3    74.8    -      -       -      +
     58C  LYS*     1.3    52.9    +      -       -      +
     59C  ASN      2.6    16.9    +      -       -      -
     60C  LYS*     3.0    16.4    +      -       -      +
     61C  LYS*     3.3    17.0    +      -       -      +
     71C  ALA*     2.6    48.5    +      -       +      +
     74C  ILE*     3.7    15.5    -      -       +      +
     75C  LYS*     3.7    14.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 58 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54C  SER      3.1    19.3    +      -       -      +
     55C  LEU*     3.2    10.4    +      -       +      +
     57C  LYS*     1.3    75.6    -      -       -      +
     59C  ASN*     1.3    57.8    +      -       -      +
     61C  LYS*     2.7    31.5    +      -       -      +
     62C  ARG*     5.9     0.8    -      -       -      +
    116C  THR*     2.9    54.1    +      -       -      +
    702F    U      3.1    31.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 59 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55C  LEU      3.4     8.5    -      -       -      +
     56C  VAL*     3.3    12.3    -      -       -      +
     57C  LYS      2.6     7.3    +      -       -      -
     58C  LYS*     1.3    76.0    -      -       -      +
     60C  LYS*     1.3    56.4    +      -       -      +
     61C  LYS*     3.0     5.5    -      -       -      +
     62C  ARG*     2.7    22.9    +      -       -      -
     63C  PHE*     2.7    39.9    +      -       -      -
     64C  PHE*     3.4    11.6    +      -       -      -
    108C  TYR*     4.4     6.3    -      -       -      +
    112C  LEU*     5.0     3.0    -      -       -      +
    115C  LEU*     4.7     5.7    -      -       -      +
    116C  THR*     4.7     2.9    -      -       -      +
    171C  LEU*     4.6     4.2    -      -       -      +
    220C  LEU*     3.0    43.9    -      -       -      +
    224C  ILE*     3.6     9.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 60 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56C  VAL      3.1    11.5    +      -       -      +
     57C  LYS*     3.0    11.8    +      -       -      +
     59C  ASN*     1.3    76.9    -      -       -      +
     61C  LYS*     1.3    63.5    +      -       +      +
     64C  PHE*     2.5    60.2    +      -       -      +
     65C  SER*     2.8    25.1    +      -       -      +
     67C  VAL*     3.3    30.2    +      -       +      -
     69C  THR      4.7     7.1    +      -       -      -
     74C  ILE*     4.7    10.8    -      -       +      -
    224C  ILE*     3.7    24.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 61 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  LYS      3.4    11.2    -      -       -      +
     58C  LYS*     2.7    56.1    +      -       -      +
     59C  ASN      3.0     0.6    -      -       -      -
     60C  LYS*     1.3    87.0    -      -       +      +
     62C  ARG*     1.3    87.1    +      -       +      +
     65C  SER*     3.7    17.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 62 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58C  LYS*     5.9     1.1    -      -       -      +
     59C  ASN*     2.7    16.0    +      -       -      +
     61C  LYS*     1.3   104.5    -      -       +      +
     63C  PHE*     1.3    96.5    +      -       +      +
     65C  SER*     5.3     2.0    -      -       -      -
    115C  LEU      3.9     6.7    +      -       -      -
    116C  THR*     3.9    20.5    -      -       +      +
    174C  GLU*     4.3    13.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 63 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59C  ASN*     2.7    29.8    +      -       -      -
     62C  ARG*     1.3   109.2    -      -       +      +
     64C  PHE*     1.3    83.0    +      -       +      +
     65C  SER      3.8     2.0    -      -       -      -
     66C  ASP*     4.9     0.3    -      -       -      +
    115C  LEU*     3.4    33.2    -      -       +      -
    116C  THR*     4.3     1.1    -      -       +      -
    167C  ASN*     3.2    23.9    -      -       -      +
    170C  LYS*     3.8    20.5    -      -       +      +
    171C  LEU*     3.4    33.4    -      -       +      +
    174C  GLU*     3.6    27.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 64 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59C  ASN*     3.7    21.3    -      -       -      -
     60C  LYS*     2.5    34.8    +      -       -      +
     63C  PHE*     1.3    94.7    -      -       +      +
     65C  SER*     1.3    66.4    +      -       -      +
     66C  ASP*     3.4     2.7    -      -       -      -
     67C  VAL*     3.1    22.7    -      -       +      +
    164C  LEU*     4.3     9.2    -      -       +      -
    167C  ASN*     3.0    39.3    -      -       -      -
    168C  VAL*     4.6     9.2    -      -       +      -
    171C  LEU*     3.3    35.9    -      -       +      -
    220C  LEU*     4.2     8.3    -      -       +      -
    221C  ILE*     4.9    12.3    -      -       +      -
    224C  ILE*     3.7    24.9    -      -       +      -
    225C  THR*     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