Contacts of the helix formed by residues 222 - 233 (chain s) in PDB entry 6QXT


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 PHE 222 (chain s).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184s  LEU*     5.9     6.5    -      -       +      -
    218s  ILE      5.5     0.6    +      -       -      +
    219s  MET*     3.4    14.4    +      -       +      +
    220s  GLU      3.2     1.4    -      -       -      -
    221s  PRO*     1.3    76.9    -      -       -      +
    223s  ARG*     1.3    64.0    +      -       -      +
    224s  PRO      3.3     2.9    -      -       -      -
    225s  ILE*     3.3    24.1    +      -       +      +
    226s  ILE*     3.9     2.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 223 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219s  MET      3.9     6.4    +      -       -      +
    220s  GLU*     3.5    14.3    +      -       -      +
    221s  PRO      3.4     1.6    -      -       -      -
    222s  PHE*     1.3    77.0    -      -       -      +
    224s  PRO*     1.3    59.1    -      -       -      +
    226s  ILE*     2.9    25.5    +      -       -      +
    227s  ASP*     2.9    11.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 224 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113s  LYS      5.7     0.7    -      -       -      +
    116s  ASN*     4.4    30.1    -      -       +      +
    117s  GLN*     4.8     6.1    -      -       +      +
    120s  TYR*     4.7    14.4    -      -       +      +
    221s  PRO      4.5     3.3    -      -       -      +
    222s  PHE      3.3     0.6    -      -       -      -
    223s  ARG*     1.3    78.0    -      -       -      +
    225s  ILE*     1.3    58.3    +      -       -      +
    227s  ASP*     3.5    11.6    -      -       +      +
    228s  ARG*     2.9    29.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 225 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222s  PHE*     3.3    17.3    +      -       +      +
    223s  ARG      3.1     0.6    -      -       -      -
    224s  PRO*     1.3    79.0    -      -       -      +
    226s  ILE*     1.3    61.0    +      -       -      +
    228s  ARG*     3.5    11.6    +      -       -      +
    229s  ILE*     3.7    12.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 226 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176s  ALA      6.1     0.4    -      -       -      +
    177s  LEU*     5.9     5.2    -      -       -      +
    180s  GLY*     5.1    18.6    -      -       -      -
    181s  TYR      5.7     0.4    -      -       -      +
    222s  PHE      3.9     2.1    +      -       -      +
    223s  ARG*     2.9    14.3    +      -       -      +
    225s  ILE*     1.3    76.3    -      -       -      +
    227s  ASP*     1.3    59.8    +      -       -      +
    228s  ARG      3.2     0.2    +      -       -      -
    229s  ILE*     3.4     4.3    +      -       -      +
    230s  VAL*     2.9    32.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 227 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223s  ARG      2.9    12.0    +      -       -      +
    224s  PRO*     3.2    16.1    +      -       +      +
    226s  ILE*     1.3    77.3    -      -       -      +
    228s  ARG*     1.3    55.8    +      -       -      +
    230s  VAL*     3.8     6.5    -      -       -      +
    231s  TYR*     2.9    30.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 228 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120s  TYR*     6.4     1.6    -      -       +      -
    224s  PRO      2.9    16.0    +      -       -      +
    225s  ILE*     3.8     8.1    -      -       -      +
    226s  ILE      3.2     0.6    -      -       -      -
    227s  ASP*     1.3    72.0    -      -       -      +
    229s  ILE*     1.3    60.2    +      -       -      +
    231s  TYR*     3.0     8.2    +      -       -      +
    232s  GLN*     2.9    28.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 229 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225s  ILE      3.7     8.2    +      -       -      +
    226s  ILE*     3.4     7.0    +      -       -      +
    228s  ARG*     1.3    79.1    -      -       -      +
    230s  VAL*     1.3    58.5    +      -       -      +
    232s  GLN*     3.8     6.1    -      -       -      +
    233s  ASN*     2.9    34.5    +      -       -      +
    244s  GLU*     4.9    22.2    -      -       +      +
    245s  LEU*     5.5     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 230 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173s  ILE*     5.5     6.5    -      -       +      +
    176s  ALA*     5.3    13.7    -      -       +      -
    177s  LEU*     5.7     7.4    -      -       +      +
    226s  ILE      2.9    19.5    +      -       -      +
    227s  ASP*     3.9     7.9    -      -       -      +
    229s  ILE*     1.3    77.5    -      -       -      +
    231s  TYR*     1.3    57.2    +      -       -      +
    233s  ASN*     3.9     1.5    -      -       -      -
    234s  ARG*     3.1    30.9    +      -       -      +
    241s  ILE*     6.3     2.5    -      -       -      -
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Residues in contact with TYR 231 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160s  LEU*     5.5    11.0    -      -       +      -
    227s  ASP      2.9    19.9    +      -       -      +
    228s  ARG*     3.0     6.7    +      -       -      +
    230s  VAL*     1.3    77.4    -      -       -      +
    232s  GLN*     1.3    63.4    +      -       -      +
    234s  ARG*     3.9    12.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 232 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228s  ARG      2.9    15.4    +      -       -      +
    229s  ILE*     3.9     7.0    -      -       -      +
    231s  TYR*     1.3    79.2    -      -       -      +
    233s  ASN*     1.3    59.1    +      -       +      +
    234s  ARG      3.3     1.3    +      -       -      -
    235s  HIS*     4.6     4.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 233 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229s  ILE      2.9    16.1    +      -       -      +
    230s  VAL*     3.9     1.3    -      -       -      -
    232s  GLN*     1.3    75.7    -      -       +      +
    234s  ARG*     1.3    55.7    +      -       -      +
    235s  HIS      3.1     3.8    -      -       -      -
    236s  ASN*     2.8    42.2    +      -       +      +
    240s  LYS      5.3     0.7    -      -       -      +
    241s  ILE*     4.4    26.0    -      -       +      +
    244s  GLU*     4.8    11.9    -      -       +      -
----------------------------------------------------------
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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