Contacts of the helix formed by residues 203 - 221 (chain A) in PDB entry 5WIU


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 LEU 203 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  VAL*     2.9    37.5    +      -       +      +
    199A  CYS*     4.7     6.5    -      -       -      +
    202A  PHE*     1.3    78.3    -      -       -      +
    204A  PRO*     1.3    67.0    -      -       +      +
    205A  CYS      3.3     0.2    -      -       -      -
    206A  PRO*     3.3    11.7    -      -       +      +
    207A  LEU*     3.3    36.5    -      -       +      +
   1208A  OLA      4.8    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  ILE*     4.1     7.9    -      -       +      -
    124A  PHE*     4.2     4.7    -      -       +      -
    127A  CYS*     3.3    25.4    -      -       -      -
    198A  VAL      3.6     2.0    -      -       -      +
    199A  CYS      3.3    20.9    -      -       -      +
    200A  SER      3.3    26.0    -      -       -      +
    201A  PHE*     3.4     7.9    -      -       -      +
    203A  LEU*     1.3    92.4    -      -       +      +
    205A  CYS*     1.3    56.3    +      -       -      +
    207A  LEU*     3.2     6.8    +      -       +      +
    208A  MET*     2.8    34.5    +      -       -      +
   1208A  OLA      4.2    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  ILE*     4.6     4.7    -      -       -      -
    201A  PHE*     3.0    49.1    +      -       -      +
    204A  PRO*     1.3    77.4    -      -       -      +
    206A  PRO*     1.3    69.0    -      -       +      +
    208A  MET*     3.4    17.0    +      -       -      +
    209A  LEU*     3.0    33.4    +      -       +      +
    403A  PHE*     5.6     1.3    -      -       -      -
    404A  LEU*     3.6    29.8    -      -       +      -
   1213A  OLA      3.9    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  PHE      3.0    29.8    -      -       -      +
    203A  LEU*     3.3    16.6    -      -       +      +
    205A  CYS*     1.3    88.8    -      -       +      +
    207A  LEU*     1.3    66.2    +      -       +      +
    209A  LEU*     3.3     9.8    +      -       +      +
    210A  LEU*     3.0    23.9    +      -       -      +
   1213A  OLA      4.8     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  CYS*     5.8     1.6    -      -       -      -
    203A  LEU*     3.3    32.3    -      -       +      +
    204A  PRO*     3.2     7.7    +      -       +      +
    206A  PRO*     1.3    79.9    -      -       +      +
    208A  MET*     1.3    63.9    +      -       -      +
    210A  LEU*     3.3    15.4    +      -       +      +
    211A  LEU*     3.1    32.6    +      -       +      +
   1208A  OLA      4.7    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  ILE*     4.0    19.7    -      -       +      +
    126A  LEU*     3.7    30.1    -      -       +      -
    127A  CYS*     3.5    30.0    -      -       -      -
    130A  SER*     3.9    16.4    -      -       -      +
    204A  PRO      2.8    19.3    +      -       -      +
    205A  CYS*     3.7    21.1    -      -       -      +
    207A  LEU*     1.3    74.2    -      -       -      +
    209A  LEU*     1.3    59.9    +      -       +      +
    211A  LEU*     3.3     1.8    +      -       -      +
    212A  TYR*     2.9    52.8    +      -       +      -
    400A  VAL*     4.3    17.7    -      -       +      -
    403A  PHE*     6.3     0.9    -      -       +      -
    404A  LEU*     5.8     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  CYS*     3.0    27.7    +      -       +      +
    206A  PRO*     3.8     8.5    -      -       +      +
    208A  MET*     1.3    76.4    -      -       +      +
    210A  LEU*     1.3    62.6    +      -       -      +
    212A  TYR*     3.6     3.9    +      -       +      +
    213A  TRP*     3.1    23.6    +      -       -      +
    400A  VAL*     4.0    14.6    -      -       +      -
    404A  LEU*     4.2    18.2    -      -       +      -
   1210A  OLA      3.6    46.5    -      -       +      +
   1213A  OLA      5.8     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206A  PRO      3.0    17.3    +      -       -      +
    207A  LEU*     3.3    15.7    +      -       +      +
    209A  LEU*     1.3    75.5    -      -       -      +
    211A  LEU*     1.3    66.2    +      -       +      +
    213A  TRP*     3.4    25.3    +      -       +      +
    214A  ALA*     3.0    27.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  SER*     3.7    24.9    -      -       -      +
    131A  VAL*     3.6    34.3    -      -       +      -
    134A  PHE*     4.1    33.4    -      -       +      -
    207A  LEU*     3.1    22.2    +      -       +      +
    208A  MET      3.8     0.2    -      -       -      +
    210A  LEU*     1.3    83.6    -      -       +      +
    212A  TYR*     1.3    65.2    +      -       -      +
    214A  ALA*     3.4     4.6    +      -       +      +
    215A  THR*     2.9    29.2    +      -       -      -
   1211A  OLA      4.0    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  LEU*     2.8    23.3    +      -       -      +
    129A  ILE*     3.3    26.0    -      -       +      +
    130A  SER*     3.5    28.5    -      -       -      -
    133A  ARG*     5.7     1.8    -      -       +      -
    208A  MET*     2.9    41.3    +      -       +      +
    209A  LEU*     4.0     2.9    -      -       -      +
    211A  LEU*     1.3    75.4    -      -       -      +
    213A  TRP*     1.3    62.5    +      -       -      +
    215A  THR*     3.3     6.2    +      -       -      -
    216A  PHE*     3.0    44.9    +      +       +      -
    393A  MET*     5.2     4.0    -      -       +      -
    396A  LEU*     4.3    22.3    -      -       +      +
    397A  PRO      6.2     0.2    -      -       -      -
    400A  VAL*     3.6    30.4    -      -       +      +
   1210A  OLA      3.9    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  LEU      3.1    18.6    +      -       -      +
    210A  LEU*     3.6    28.5    -      -       +      +
    211A  LEU      3.2     0.2    -      -       -      -
    212A  TYR*     1.3    77.6    -      -       -      +
    214A  ALA*     1.3    81.4    +      -       +      +
    216A  PHE*     3.5     3.3    +      -       +      +
    217A  ARG*     3.0    41.3    +      -       +      +
   1210A  OLA      4.0    19.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 214 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  PHE*     3.9    24.6    -      -       +      -
    210A  LEU*     3.0    20.0    +      -       +      +
    211A  LEU*     3.8     8.7    -      -       +      +
    213A  TRP*     1.3    92.1    -      -       +      +
    215A  THR*     1.3    52.5    +      -       -      +
    217A  ARG*     3.3     4.5    +      -       -      +
    218A  GLY*     2.7    32.9    +      -       -      -
    221A  ARG*     5.3     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  SER*     4.1     2.6    +      -       -      -
    133A  ARG*     3.9    11.9    -      -       +      +
    134A  PHE*     3.2    30.1    +      -       -      +
    137A  VAL*     3.7    26.8    -      -       +      +
    211A  LEU      2.9    21.2    +      -       -      -
    212A  TYR*     3.5     8.0    -      -       -      -
    214A  ALA*     1.3    73.4    -      -       -      +
    216A  PHE*     1.3    66.4    +      -       -      +
    218A  GLY*     3.2     2.9    +      -       -      -
    219A  LEU*     3.0    24.0    +      -       +      +
    393A  MET*     3.6    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  TYR*     3.0    40.2    +      +       -      +
    213A  TRP*     4.0     4.7    -      -       +      +
    215A  THR*     1.3    75.4    -      -       -      +
    217A  ARG*     1.3    63.4    +      -       -      +
    219A  LEU*     3.4     3.3    +      -       -      +
    220A  GLN*     3.1    26.5    +      -       -      +
    390A  ARG*     3.7    26.2    -      -       +      -
    393A  MET*     3.4    56.1    -      -       +      -
    394A  ARG*     4.8     2.7    -      -       -      -
    396A  LEU*     5.3     0.4    -      -       +      -
    397A  PRO*     3.8    24.0    -      -       +      -
   1210A  OLA      3.6    58.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  TRP*     3.0    40.1    +      -       +      +
    214A  ALA*     3.7     6.1    -      -       -      +
    216A  PHE*     1.3    78.0    -      -       -      +
    218A  GLY*     1.3    62.7    +      -       -      +
    220A  GLN*     3.3    11.4    +      -       +      +
    221A  ARG*     3.3    43.3    +      -       -      +
   1210A  OLA      5.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  PHE*     6.5     0.2    -      -       -      -
    137A  VAL*     3.8    14.4    -      -       -      -
    214A  ALA      2.7    21.4    +      -       -      -
    215A  THR      3.2     2.6    +      -       -      -
    217A  ARG*     1.3    74.0    -      -       -      +
    219A  LEU*     1.3    59.8    +      -       -      +
    221A  ARG*     3.4    28.7    +      -       -      +
    222A  TRP*     3.1    20.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  VAL*     3.6    29.2    -      -       +      -
    215A  THR      3.0    19.3    +      -       -      +
    216A  PHE      3.9     0.2    -      -       -      +
    218A  GLY*     1.3    73.1    -      -       -      +
    220A  GLN*     1.3    57.6    +      -       -      +
    222A  TRP*     2.8    31.6    +      -       -      +
    223A  GLU*     3.5    10.9    +      -       +      +
    384A  LYS*     3.5    32.4    -      -       +      +
    389A  GLU*     3.7    14.8    -      -       +      +
    390A  ARG*     3.9    38.1    -      -       +      +
    393A  MET*     3.7    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  PHE      3.1    14.8    +      -       -      +
    217A  ARG*     3.3    14.1    +      -       +      +
    219A  LEU*     1.3    75.9    -      -       -      +
    221A  ARG*     1.3    61.7    +      -       -      +
    223A  GLU*     3.1    29.9    +      -       -      +
    390A  ARG*     3.0    46.1    -      -       -      +
   1046A  PRO*     5.1     1.2    -      -       -      +
   1203A  PO4      3.9     7.5    +      -       -      -
   1210A  OLA      3.6    11.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  ALA      5.3     0.8    +      -       -      -
    217A  ARG*     3.3    36.4    +      -       -      +
    218A  GLY*     3.5    23.6    -      -       -      +
    219A  LEU      3.1     0.8    -      -       -      -
    220A  GLN*     1.3    78.5    -      -       -      +
    222A  TRP*     1.3    60.1    +      -       +      +
   1046A  PRO*     3.4    18.8    -      -       +      +
   1047A  LYS*     3.1    39.9    +      -       +      +
----------------------------------------------------------
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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