Contacts of the helix formed by residues 231 - 243 (chain A) in PDB entry 4Z3A


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 231 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  ILE*     4.7     3.4    -      -       -      -
    229A  PHE*     3.1     8.7    +      -       -      +
    230A  ASN*     1.3    75.5    -      -       -      +
    232A  LYS*     1.3    65.7    +      -       -      +
    233A  CYS      3.4     2.0    -      -       -      -
    234A  ILE*     3.3    20.5    -      -       -      +
    235A  TYR      3.6     3.5    +      -       -      -
    268A  VAL*     4.0     2.0    -      -       -      +
    269A  MET      3.0    15.9    +      -       -      -
    271A  SER*     3.8     6.3    -      -       -      -
     19D    T      3.3    17.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  GLY*     1.3    71.9    -      -       -      -
    233A  CYS*     1.4    63.7    +      -       -      +
    235A  TYR*     3.0     5.4    +      -       -      +
    236A  GLU*     3.0    33.0    +      -       -      +
    250A  LEU*     3.0    50.3    +      -       +      +
    251A  GLU*     4.1     4.8    -      -       -      +
    252A  PHE*     3.7    45.2    -      -       +      -
    268A  VAL*     3.9     9.2    -      -       +      -
    269A  MET      3.8     3.2    +      -       -      -
     19D    T      3.0    18.0    +      -       -      +
     20D    A      2.9    37.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  ILE*     3.8    33.0    -      -       -      -
    200A  SER*     5.1     5.8    -      -       -      -
    208A  PHE*     5.3     5.6    -      -       +      -
    231A  GLY      4.8     0.7    -      -       -      -
    232A  LYS*     1.4    74.1    -      -       -      +
    234A  ILE*     1.3    75.5    +      -       -      +
    236A  GLU*     3.4    19.2    +      -       -      +
    237A  ILE*     3.4    30.5    +      -       +      +
     18D    G      4.5     7.2    -      -       +      -
     19D    T      2.9    25.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  ILE*     3.4    30.1    -      -       +      +
    138A  GLY      3.7    15.7    -      -       -      +
    139A  ILE*     3.9    18.8    -      -       +      -
    192A  MET*     3.6    28.7    -      -       +      +
    208A  PHE*     3.7    30.1    -      -       +      -
    229A  PHE*     4.0    17.9    -      -       +      -
    230A  ASN      4.2     7.9    -      -       -      +
    231A  GLY      3.3    19.5    -      -       -      +
    233A  CYS*     1.3    75.3    -      -       -      +
    235A  TYR*     1.3    61.0    +      -       -      +
    237A  ILE*     3.6     2.4    +      -       -      -
    238A  PHE*     3.0    28.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  PHE*     3.7    32.3    -      +       +      -
    231A  GLY      3.6     0.2    +      -       -      -
    232A  LYS      3.0     8.2    +      -       -      +
    234A  ILE*     1.3    82.1    -      -       -      +
    236A  GLU*     1.4    56.2    +      -       -      +
    238A  PHE*     4.0    18.6    -      +       -      -
    239A  SER*     2.8    51.3    +      -       -      -
    243A  PHE*     3.5    20.1    -      +       -      -
    250A  LEU*     3.6    22.9    -      -       +      -
    255A  GLN*     3.4    36.4    +      -       +      +
    256A  PRO*     5.2     0.2    -      -       -      +
    257A  HIS*     4.3     7.6    +      -       -      +
    266A  CYS*     3.9    20.4    -      -       +      +
    268A  VAL*     3.5    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  LYS*     3.0    29.5    +      -       -      +
    233A  CYS*     3.4    22.1    +      -       -      +
    235A  TYR*     1.4    76.8    -      -       -      +
    237A  ILE*     1.3    64.5    +      -       +      +
    239A  SER*     3.7     4.0    +      -       -      -
    240A  LYS*     3.4    26.8    +      -       -      +
    245A  VAL      4.9     0.7    -      -       -      +
    246A  LYS*     5.8     6.1    -      -       -      +
    250A  LEU*     3.5    26.6    -      -       +      +
     20D    A      4.9     4.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192A  MET*     3.9     9.4    -      -       +      -
    205A  SER*     5.2     1.8    -      -       -      +
    208A  PHE*     3.5    58.3    -      -       +      +
    209A  ARG*     4.0    21.8    -      -       +      -
    233A  CYS*     3.4    22.4    +      -       +      +
    234A  ILE*     3.9     6.1    -      -       -      +
    235A  TYR      3.2     0.2    -      -       -      -
    236A  GLU*     1.3    75.7    -      -       +      +
    238A  PHE*     1.3    65.0    +      -       -      +
    240A  LYS*     3.4     8.5    +      -       -      +
    241A  GLU*     3.1    23.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192A  MET*     4.1     6.3    -      -       +      +
    212A  GLY*     4.0    21.5    -      -       -      -
    215A  LEU*     3.9    29.4    -      -       +      -
    216A  VAL*     3.9    13.2    -      -       +      -
    219A  LEU*     4.5     2.5    -      -       +      -
    229A  PHE*     3.7    24.5    -      +       +      -
    234A  ILE      3.0    18.8    +      -       -      +
    235A  TYR*     3.7     7.9    -      +       -      +
    237A  ILE*     1.3    75.4    -      -       -      +
    239A  SER*     1.3    55.1    +      -       -      +
    241A  GLU*     3.3     4.9    +      -       -      -
    242A  VAL*     2.8    71.1    +      -       +      +
    243A  PHE*     4.0    14.4    -      +       -      -
    259A  ILE*     3.6    33.0    -      -       +      -
    266A  CYS*     4.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  TYR*     2.8    43.1    +      -       -      -
    236A  GLU*     4.0     4.7    -      -       -      -
    238A  PHE*     1.3    75.0    -      -       -      +
    240A  LYS*     1.3    55.9    +      -       -      +
    243A  PHE*     2.9    40.2    +      -       -      -
    244A  GLY      3.1     6.9    +      -       -      -
    245A  VAL*     3.0    31.2    +      -       -      +
    250A  LEU*     5.6     2.2    -      -       -      +
    257A  HIS*     5.1     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  ARG*     6.5     0.7    -      -       -      -
    236A  GLU*     3.4    18.5    +      -       -      +
    237A  ILE*     3.7     7.0    -      -       -      +
    238A  PHE      3.4     0.2    -      -       -      -
    239A  SER*     1.3    77.4    -      -       -      +
    241A  GLU*     1.3    58.1    +      -       -      +
    244A  GLY*     3.2    22.4    -      -       -      -
    245A  VAL      3.3    15.3    +      -       -      +
    246A  LYS*     3.6    36.8    -      -       +      +
      5C    T      5.5     3.6    +      -       -      -
      6C    C      4.6    12.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208A  PHE      4.3     0.9    -      -       -      +
    209A  ARG*     2.6    56.6    -      -       +      +
    212A  GLY*     3.5    17.6    -      -       -      -
    213A  ARG*     3.6    17.7    +      -       -      +
    237A  ILE*     3.1    19.1    +      -       -      +
    238A  PHE*     3.8     4.4    -      -       -      +
    240A  LYS*     1.3    80.1    -      -       -      +
    242A  VAL*     1.3    62.7    +      -       +      +
    244A  GLY*     4.5     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  GLY      4.7     4.0    -      -       -      +
    216A  VAL*     4.0    18.8    -      -       +      -
    238A  PHE*     2.8    58.5    +      -       +      +
    241A  GLU*     1.3    82.6    -      -       +      +
    243A  PHE*     1.3    72.0    +      -       +      +
    244A  GLY      3.5     0.7    -      -       -      -
    260A  PRO*     3.7    36.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  TYR*     3.5    27.8    -      +       -      -
    238A  PHE*     4.0    20.9    -      +       -      -
    239A  SER*     2.9    23.1    +      -       -      +
    242A  VAL*     1.3    88.5    -      -       +      +
    244A  GLY*     1.3    61.9    +      -       -      +
    245A  VAL*     3.3    23.2    -      -       +      +
    257A  HIS*     3.6    33.9    -      +       +      -
    258A  LYS      3.2    26.9    -      -       -      -
    259A  ILE*     4.4     1.8    -      -       +      -
    260A  PRO*     3.8    16.4    -      -       +      -
    266A  CYS*     4.1    15.0    -      -       -      -
----------------------------------------------------------
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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