Contacts of the helix formed by residues 218 - 228 (chain N) in PDB entry 5X6E


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 ALA 218 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133N  ASP*     3.1    22.2    -      -       +      +
    141N  GLY      4.9     0.7    -      -       -      +
    144N  CYS      4.5     0.7    -      -       -      +
    145N  GLY*     3.6    33.0    -      -       -      +
    148N  LEU*     4.4     6.7    -      -       +      +
    214N  LEU      3.0    13.2    +      -       -      +
    215N  LYS      3.4     5.7    -      -       -      +
    217N  TYR*     1.3    78.2    -      -       -      +
    219N  PRO*     1.3    64.8    -      -       -      +
    221N  LEU*     3.7     6.2    -      -       +      +
    222N  ASP*     3.3    17.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 219 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52M  SER*     5.8     8.7    -      -       -      -
    132N  ASN*     4.8     3.8    -      -       -      +
    133N  ASP*     3.2    12.3    -      -       +      +
    136N  ILE*     4.7    13.5    -      -       +      -
    215N  LYS      3.3    13.0    -      -       -      +
    216N  ARG*     4.1     8.1    -      -       -      +
    217N  TYR      3.4     9.2    -      -       -      +
    218N  ALA*     1.3    89.3    -      -       -      +
    220N  LYS*     1.3    64.1    +      -       +      +
    222N  ASP*     3.2     7.2    +      -       +      +
    223N  GLU*     3.0    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 220 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31M  GLN*     5.8     2.2    -      -       -      +
     50M  SER*     3.1    23.3    -      -       -      +
     51M  ILE      5.6     3.6    -      -       -      +
     82M  TYR*     3.3    19.6    +      -       -      +
     83M  TYR*     3.5    27.0    +      -       +      +
    129N  ALA*     3.5    15.3    -      -       +      +
    132N  ASN*     3.2    23.8    -      -       +      +
    133N  ASP*     3.1    16.7    +      -       -      +
    219N  PRO*     1.3    82.9    -      -       +      +
    221N  LEU*     1.3    58.0    +      -       -      +
    223N  GLU*     2.6    43.9    +      -       -      +
    224N  TRP*     2.9    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 221 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126N  TYR*     4.2    16.6    -      -       +      -
    129N  ALA*     3.9    12.3    -      -       +      +
    130N  LYS*     4.0    19.5    -      -       -      +
    133N  ASP*     2.6    23.0    +      -       +      +
    134N  PHE*     4.2    12.8    -      -       +      -
    145N  GLY*     3.7    35.7    -      -       -      +
    148N  LEU*     4.3     8.7    -      -       +      -
    149N  ILE*     3.9    28.0    -      -       +      -
    218N  ALA*     3.7     7.4    -      -       +      +
    220N  LYS*     1.3    70.3    -      -       -      +
    222N  ASP*     1.3    66.2    +      -       -      +
    224N  TRP*     3.2    12.2    +      -       +      +
    225N  PHE*     3.1    25.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 222 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148N  LEU*     4.0    18.9    -      -       +      +
    152N  TYR*     2.9    28.6    +      -       -      -
    215N  LYS*     3.4    27.6    +      -       +      +
    218N  ALA      3.3    10.1    +      -       -      +
    219N  PRO*     3.2    11.3    +      -       +      +
    221N  LEU*     1.3    77.5    -      -       -      +
    223N  GLU*     1.3    65.7    +      -       -      +
    225N  PHE*     3.1    14.9    +      -       -      +
    226N  TYR*     3.2     9.4    +      -       -      +
    233N  TRP*     3.0    19.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 223 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81M  GLY*     3.9     4.5    -      -       -      -
     82M  TYR*     2.9    44.7    +      -       +      +
     83M  TYR*     5.2     0.3    +      -       -      -
    219N  PRO      3.0    16.7    +      -       -      +
    220N  LYS*     2.6    43.6    +      -       -      +
    222N  ASP*     1.3    81.0    +      -       -      +
    224N  TRP*     1.3    65.1    +      -       -      +
    226N  TYR*     3.0    18.7    +      -       +      +
    227N  LEU*     3.1    26.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 224 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80M  VAL      4.1     7.9    -      -       -      -
    122N  LYS*     3.2    31.2    -      -       +      -
    125N  SER*     2.5    47.6    +      -       -      -
    126N  TYR*     3.3    37.3    -      +       +      +
    129N  ALA*     4.2     7.6    -      -       +      -
    220N  LYS      2.9    15.5    +      -       -      +
    221N  LEU*     3.2    11.2    +      -       +      +
    223N  GLU*     1.3    77.2    -      -       -      +
    225N  PHE*     1.3    92.3    +      +       -      +
    227N  LEU*     3.2     4.2    +      -       -      +
    228N  ALA*     2.7    47.6    +      -       +      +
    229N  CYS*     4.3    18.2    -      -       -      -
    301N  GSH      3.9    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 225 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126N  TYR*     5.1     1.1    -      +       -      -
    148N  LEU*     4.4     4.9    -      -       +      -
    149N  ILE*     4.3    38.4    -      -       +      -
    152N  TYR*     3.4    35.7    -      +       +      -
    153N  VAL*     4.0    23.3    -      -       +      -
    221N  LEU*     3.1    26.6    +      -       +      -
    222N  ASP      3.1     8.8    +      -       -      +
    224N  TRP*     1.3   107.3    -      +       -      +
    226N  TYR*     1.3    55.5    +      -       -      +
    228N  ALA      2.9    10.7    -      -       -      +
    229N  CYS*     2.9    26.9    -      -       +      +
    230N  PRO*     3.2     4.0    -      -       -      +
    232N  THR*     4.0    16.6    -      -       -      -
    233N  TRP*     3.1    24.4    -      -       +      +
    301N  GSH      5.0     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 226 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82M  TYR*     4.7     9.2    -      +       -      -
    222N  ASP*     3.2    10.4    +      -       -      +
    223N  GLU*     3.0    14.4    +      -       +      +
    225N  PHE*     1.3    79.5    -      -       -      +
    227N  LEU*     1.3    79.9    +      -       +      +
    230N  PRO*     3.7    16.9    -      -       +      +
    233N  TRP*     3.9    45.5    -      +       +      +
----------------------------------------------------------
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Residues in contact with LEU 227 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73M  PHE*     4.1     5.2    -      -       -      -
     78M  THR*     4.6    12.9    +      -       -      +
     79M  SER*     3.6    27.3    -      -       -      +
     80M  VAL      4.2     5.8    -      -       -      +
     81M  GLY*     3.6    32.5    -      -       -      +
     82M  TYR*     3.4    36.1    -      -       +      +
    223N  GLU*     3.1    29.7    +      -       +      +
    224N  TRP*     4.1     2.7    -      -       -      +
    226N  TYR*     1.3   101.8    -      -       +      +
    228N  ALA*     1.3    58.8    +      -       -      +
    230N  PRO*     4.7     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 228 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73M  PHE*     3.7    26.2    -      -       +      -
     80M  VAL      5.8     0.2    -      -       -      +
    122N  LYS*     4.3    14.6    -      -       +      -
    224N  TRP*     2.7    45.1    +      -       +      +
    225N  PHE*     2.9    15.4    -      -       -      +
    227N  LEU*     1.3    73.9    -      -       +      +
    229N  CYS*     1.3    68.6    +      -       -      +
    230N  PRO*     3.4     1.8    -      -       -      -
----------------------------------------------------------
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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