Contacts of the helix formed by residues 230 - 241 (chain A) in PDB entry 3N4E


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 HIS 230 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  VAL*     4.1     5.3    -      -       +      +
    227A  GLN*     2.9    38.8    +      -       +      +
    228A  HIS      4.2     1.1    -      -       -      -
    229A  TYR*     1.3    96.1    -      +       -      +
    231A  VAL*     1.3    57.8    +      -       -      +
    232A  GLY      3.3     2.7    -      -       -      -
    233A  ALA*     3.2    19.3    +      -       +      +
    234A  MSE      2.9    27.6    +      -       -      +
    255B  GLN*     3.5    25.2    -      -       +      +
    258B  LYS*     6.0     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  HIS      3.7    16.2    -      -       -      +
    229A  TYR*     3.3     7.9    +      -       -      +
    230A  HIS*     1.3    72.0    -      -       -      +
    232A  GLY*     1.3    63.5    +      -       -      +
    234A  MSE      3.3     7.3    +      -       -      +
    235A  GLY      3.1    19.1    +      -       -      -
    256A  ALA      5.9     0.2    -      -       -      +
    259A  ASP*     4.3     9.0    -      -       +      +
    260A  LEU*     4.3    24.7    -      -       +      +
    263A  SER*     3.5    24.2    +      -       -      +
    258B  LYS*     5.6     0.8    -      -       -      +
    259B  ASP*     4.4    15.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  HIS      3.3     1.0    -      -       -      -
    231A  VAL*     1.3    79.4    -      -       -      +
    233A  ALA*     1.3    55.6    +      -       -      +
    235A  GLY*     3.9     0.9    -      -       -      -
    236A  GLU*     3.0    29.9    +      -       -      +
    263A  SER*     4.7     7.9    -      -       -      +
    258B  LYS*     4.5    18.8    -      -       -      +
    259B  ASP*     5.0     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  VAL*     3.6    26.7    -      -       +      -
    226A  VAL*     4.2     8.1    -      -       +      -
    230A  HIS*     3.2    25.5    +      -       +      +
    232A  GLY*     1.3    73.0    -      -       -      +
    234A  MSE      1.3    60.6    +      -       -      +
    236A  GLU*     3.6     8.2    -      -       -      +
    237A  VAL*     2.8    36.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with MSE 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224A  GLU*     4.0    14.8    -      -       +      +
    225A  PRO*     3.5    31.4    -      -       -      -
    226A  VAL*     3.4    37.2    -      -       +      +
    228A  HIS*     3.9    22.2    -      -       +      +
    230A  HIS      2.9    17.0    +      -       -      +
    231A  VAL*     3.3     9.8    +      -       -      +
    233A  ALA*     1.3    77.7    -      -       -      +
    235A  GLY*     1.3    56.2    +      -       -      +
    237A  VAL*     3.5     4.6    +      -       -      +
    238A  ALA*     3.0    27.5    +      -       -      +
    245A  VAL*     4.1     5.7    -      -       +      +
    247A  ALA*     3.9    31.0    -      -       +      -
    260A  LEU*     4.3     5.4    -      -       +      -
    265A  VAL*     4.0    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  VAL      3.1     7.7    +      -       -      -
    232A  GLY      3.9     1.3    -      -       -      -
    234A  MSE      1.3    76.9    -      -       -      +
    236A  GLU*     1.3    64.7    +      -       -      +
    238A  ALA*     3.1     3.0    +      -       -      +
    239A  GLN*     2.9    27.9    +      -       -      +
    263A  SER*     3.3    35.3    +      -       -      -
    264A  GLY*     3.9     4.7    -      -       -      -
    265A  VAL*     4.0     6.3    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    204A  VAL*     3.8    15.7    -      -       +      +
    232A  GLY      3.0    19.1    +      -       -      +
    233A  ALA*     3.6     9.5    -      -       -      +
    235A  GLY*     1.3    73.7    -      -       -      +
    237A  VAL*     1.3    64.0    +      -       -      +
    239A  GLN*     3.2     5.7    +      -       -      +
    240A  ARG*     2.9    66.0    +      -       +      +
    263A  SER      4.0     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  VAL*     3.9    31.0    -      -       +      +
    207A  ALA*     3.9    28.0    -      -       +      -
    208A  ILE*     4.9     4.3    -      -       +      -
    225A  PRO*     4.0    18.4    -      -       +      -
    226A  VAL*     4.3     5.8    -      -       +      -
    233A  ALA      2.8    25.3    +      -       -      +
    234A  MSE      3.7     4.5    -      -       -      +
    236A  GLU*     1.3    71.2    -      -       -      +
    238A  ALA*     1.3    62.5    +      -       -      +
    240A  ARG*     3.4     5.9    +      -       -      +
    241A  LEU*     3.2    45.9    +      -       +      +
    245A  VAL*     4.2     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  MSE      3.0    15.4    +      -       -      +
    235A  GLY      3.1     9.2    +      -       -      +
    237A  VAL*     1.3    76.9    -      -       -      +
    239A  GLN*     1.3    61.7    +      -       -      +
    241A  LEU*     3.5    15.9    -      -       -      +
    243A  ILE      4.8     2.4    -      -       -      +
    245A  VAL*     3.6    32.7    +      -       +      +
    264A  GLY      3.6    20.2    -      -       -      +
    265A  VAL*     4.0     8.7    -      -       +      -
    266A  ARG*     5.0     1.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  GLY      2.9    19.0    +      -       -      +
    236A  GLU*     4.0     5.4    -      -       -      +
    238A  ALA*     1.3    76.8    +      -       -      +
    240A  ARG*     1.3    64.8    +      -       +      +
    241A  LEU      3.4     4.1    +      -       -      +
    263A  SER      4.7     1.6    -      -       -      +
    264A  GLY*     2.8    31.5    +      -       -      -
    266A  ARG*     3.5    30.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  VAL*     3.9     6.1    -      -       -      +
    208A  ILE*     3.3    38.7    -      -       +      +
    212A  ARG*     3.2    21.7    +      -       -      -
    236A  GLU*     2.9    53.7    +      -       +      +
    237A  VAL*     3.4     5.8    +      -       -      +
    239A  GLN*     1.3    80.4    -      -       +      +
    241A  LEU*     1.3    61.2    +      -       -      +
    242A  ASP*     5.2     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  ALA      4.2     3.8    -      -       -      +
    208A  ILE*     4.1    19.1    -      -       +      +
    211A  GLY*     4.0    23.3    -      -       -      -
    212A  ARG*     3.8    20.0    -      -       -      +
    215A  GLU*     3.4    15.3    -      -       -      +
    222A  PHE*     3.9    24.5    -      -       +      -
    237A  VAL*     3.2    36.3    +      -       +      +
    238A  ALA      3.5    12.6    -      -       -      +
    239A  GLN      4.2     3.6    -      -       -      +
    240A  ARG*     1.3    81.2    -      -       -      +
    242A  ASP*     1.3    66.2    +      -       -      +
    243A  ILE*     4.0    13.1    -      -       +      +
    245A  VAL*     3.9     5.4    -      -       +      -
----------------------------------------------------------
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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