Contacts of the helix formed by residues 4 - 17 (chain W) in PDB entry 1I84


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 SER 4 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3W  PHE*     1.3    69.9    -      -       -      +
      5W  GLU*     1.3    65.9    +      -       -      +
      6W  GLU*     3.3    28.4    +      -       -      +
      7W  GLN*     2.6    41.4    +      -       -      +
      8W  THR      2.8     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 5 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3W  PHE      3.3     1.8    +      -       -      -
      4W  SER*     1.3    72.0    -      -       -      +
      6W  GLU*     1.3    55.9    +      -       -      +
      8W  THR*     3.1    27.6    -      -       -      +
      9W  ALA*     2.5    44.3    +      -       +      +
     12W  LYS*     4.3    13.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 6 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4W  SER*     2.9    16.5    +      -       -      +
      5W  GLU*     1.3    81.2    -      -       -      +
      7W  GLN*     1.3    67.0    +      -       -      +
      9W  ALA*     3.6     6.4    -      -       -      +
     10W  GLU*     3.6    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 7 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3W  PHE*     3.0    34.8    -      -       +      +
      4W  SER*     2.6    55.6    +      -       -      +
      6W  GLU*     1.3    80.8    -      -       +      +
      8W  THR*     1.3    57.8    +      -       -      +
      9W  ALA      3.0     1.8    -      -       -      -
     10W  GLU*     2.6    13.9    +      -       -      -
     11W  PHE*     2.6    53.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 8 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3W  PHE*     2.6    36.7    +      -       -      +
      4W  SER      2.8     4.7    +      -       -      -
      5W  GLU*     3.1    22.3    -      -       -      +
      7W  GLN*     1.3    78.0    -      -       -      +
      9W  ALA*     1.3    57.9    +      -       -      +
     11W  PHE*     3.3    18.3    +      -       -      +
     12W  LYS*     2.9    27.4    -      -       -      +
     66W  PHE*     3.7     6.5    -      -       +      -
     70W  LEU*     3.5    29.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 9 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5W  GLU*     2.5    28.1    +      -       +      +
      6W  GLU*     3.6     7.9    -      -       -      +
      8W  THR*     1.3    74.4    -      -       -      +
     10W  GLU*     1.3    57.6    +      -       -      +
     12W  LYS*     3.0    41.2    -      -       -      +
     13W  GLU*     3.4    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 10 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6W  GLU*     3.6    20.6    +      -       -      +
      7W  GLN*     2.6    17.5    +      -       -      +
      9W  ALA*     1.3    72.8    -      -       -      +
     11W  PHE*     1.3    58.3    +      -       +      +
     12W  LYS      3.0     2.5    -      -       -      -
     13W  GLU*     2.5    60.5    +      -       -      +
     14W  ALA*     3.0     6.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 11 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3W  PHE*     3.3    57.0    -      +       +      -
      7W  GLN*     2.6    41.0    +      -       +      -
      8W  THR*     3.4    17.0    -      -       -      +
     10W  GLU*     1.3    70.9    -      -       +      +
     12W  LYS*     1.3    51.4    +      -       -      +
     14W  ALA*     2.8     8.8    +      -       -      +
     15W  PHE*     2.7    33.6    +      -       -      +
     38W  LEU*     3.6    33.0    -      -       +      +
     66W  PHE*     3.4    13.9    -      +       +      -
     69W  PHE*     5.6     0.6    -      +       +      -
     70W  LEU*     4.1    14.6    -      -       +      -
     73W  MET*     3.4    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 12 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5W  GLU*     4.3    16.2    +      -       -      +
      8W  THR*     2.9    26.2    -      -       -      +
      9W  ALA*     3.0    30.2    -      -       -      +
     11W  PHE*     1.3    73.4    -      -       -      +
     13W  GLU*     1.3    54.8    +      -       +      +
     16W  GLN*     2.7    47.3    +      -       +      +
     66W  PHE*     3.0    29.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 13 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9W  ALA*     3.4     9.8    -      -       -      +
     10W  GLU*     2.5    55.5    +      -       +      +
     12W  LYS*     1.3    72.4    -      -       +      +
     14W  ALA*     1.3    54.7    +      -       -      +
     16W  GLN*     4.1     5.2    -      -       -      +
     17W  LEU*     3.1    28.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 14 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    812V  PHE*     5.5     8.3    -      -       +      -
     10W  GLU      3.0     5.4    +      -       -      +
     11W  PHE*     2.8     9.1    +      -       -      +
     13W  GLU*     1.3    76.5    -      -       -      +
     15W  PHE*     1.3    66.6    +      -       -      +
     17W  LEU*     3.0    19.0    +      -       -      +
     18W  PHE*     3.1    24.6    -      -       +      -
     34W  VAL*     5.0     0.7    -      -       +      -
     37W  ALA*     5.8     0.2    -      -       +      -
     38W  LEU*     3.2    35.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 15 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11W  PHE      2.7    11.8    +      -       -      +
     12W  LYS      3.7     0.9    -      -       -      +
     14W  ALA*     1.3    72.1    -      -       -      +
     16W  GLN*     1.3    71.0    +      -       +      +
     18W  PHE*     3.0    21.1    +      -       -      +
     24W  GLY      4.1    10.3    -      -       -      -
     26W  ILE*     3.4    44.3    -      -       +      +
     34W  VAL*     4.2    16.5    -      -       +      +
     64W  LEU*     3.6    21.8    -      -       +      -
     65W  LYS      3.9     0.7    -      -       -      -
     66W  PHE*     3.6    48.2    -      +       +      -
     69W  PHE*     3.2    51.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLN 16 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12W  LYS*     2.7    30.6    +      -       +      +
     13W  GLU*     4.1     5.4    -      -       -      +
     15W  PHE*     1.3    75.4    -      -       +      +
     17W  LEU*     1.3    52.9    +      -       -      +
     18W  PHE      2.6    18.3    +      -       -      -
     19W  ASP*     3.6    13.7    +      -       -      +
     24W  GLY*     5.0    14.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 17 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    812V  PHE*     3.9    27.2    -      -       +      -
    816V  GLN*     4.0    26.9    -      -       +      +
    819V  LEU*     4.7    23.8    -      -       +      -
     13W  GLU      3.1    18.0    +      -       -      +
     14W  ALA*     3.0    11.0    +      -       -      +
     16W  GLN*     1.3    74.6    -      -       -      +
     18W  PHE*     1.3    69.0    +      -       -      +
     19W  ASP      4.0     0.4    -      -       -      -
----------------------------------------------------------
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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