Contacts of the helix formed by residues 908 - 919 (chain A) in PDB entry 4BIC


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 908 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    777A  GLU*     2.9    32.5    +      -       -      -
    906A  SER      3.8     0.4    +      -       -      -
    907A  MET*     1.3    76.5    -      -       -      +
    909A  ALA*     1.3    58.2    +      -       -      +
    910A  GLU*     3.3    19.4    +      -       -      +
    911A  ALA      3.1    14.7    +      -       -      -
    912A  LYS*     2.9    27.3    +      -       -      +
    937A  PHE*     4.7     0.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 909 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    907A  MET      3.8     0.8    +      -       -      -
    908A  SER*     1.3    72.9    -      -       -      +
    910A  GLU*     1.4    64.3    +      -       -      +
    912A  LYS*     3.5    11.6    +      -       -      +
    913A  ALA*     3.0    30.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 910 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    908A  SER*     3.2    16.8    +      -       -      +
    909A  ALA*     1.4    81.6    +      -       -      +
    911A  ALA*     1.4    58.5    +      -       -      +
    913A  ALA*     3.7     5.3    -      -       -      +
    914A  PHE*     3.1    29.3    +      -       -      +
    935A  ASP*     4.6     1.9    -      -       -      +
    936A  GLU*     4.5    22.9    -      -       +      +
    937A  PHE*     3.7    24.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 911 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    777A  GLU*     3.5    22.4    -      -       -      +
    907A  MET*     3.8    24.2    -      -       +      -
    908A  SER*     3.1    14.1    +      -       -      +
    910A  GLU*     1.4    73.2    -      -       -      +
    912A  LYS*     1.4    55.3    +      -       -      +
    914A  PHE*     3.2     3.7    +      -       -      +
    915A  ILE*     2.9    41.8    +      -       +      +
    937A  PHE*     3.7    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 912 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    903A  ILE*     3.6    32.4    -      -       +      +
    904A  PRO      3.8     7.4    -      -       -      -
    905A  GLU*     2.4    43.6    +      -       -      +
    907A  MET*     3.6    18.2    +      -       +      +
    908A  SER      2.9    16.0    +      -       -      +
    909A  ALA*     3.8     9.4    -      -       -      +
    910A  GLU      3.5     0.2    -      -       -      -
    911A  ALA*     1.4    72.9    -      -       -      +
    913A  ALA*     1.3    57.1    +      -       -      +
    915A  ILE*     3.5     0.5    +      -       -      +
    916A  LEU*     3.0    41.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 913 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    909A  ALA      3.0    19.6    +      -       -      +
    910A  GLU*     3.7     6.7    -      -       -      +
    912A  LYS*     1.3    75.0    -      -       -      +
    914A  PHE*     1.4    62.0    +      -       -      +
    916A  LEU*     3.2    18.0    +      -       -      +
    917A  LYS*     3.2    25.0    +      -       -      +
    935A  ASP*     6.0     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 914 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    784A  THR*     3.9     7.2    -      -       +      -
    788A  LEU*     3.8    25.8    -      -       +      -
    867A  LEU*     5.2     0.4    -      -       +      -
    871A  ILE*     3.6    29.6    -      -       +      -
    910A  GLU      3.1    18.6    +      -       -      +
    911A  ALA      3.4     4.0    -      -       -      +
    913A  ALA*     1.4    74.4    -      -       -      +
    915A  ILE*     1.3    66.7    +      -       +      +
    917A  LYS*     3.3    22.9    +      -       -      +
    918A  CYS*     3.7     9.4    +      -       -      -
    932A  LEU*     3.3    42.0    -      -       +      +
    935A  ASP*     3.4    28.2    +      -       +      +
    937A  PHE*     3.8    24.9    -      +       +      -
    938A  LEU*     3.8    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 915 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    868A  GLY*     4.4     7.2    -      -       -      +
    871A  ILE*     3.7    37.2    -      -       +      -
    872A  ILE*     4.3    11.7    -      -       +      -
    903A  ILE*     3.8    36.3    -      -       +      -
    907A  MET*     4.3    18.4    -      -       +      -
    911A  ALA*     2.9    27.6    +      -       +      +
    914A  PHE*     1.3    75.4    -      -       +      +
    916A  LEU*     1.4    57.1    +      -       -      +
    918A  CYS*     2.9    31.1    +      -       -      +
    919A  PHE*     3.4    31.1    +      -       +      -
    937A  PHE*     6.2     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 916 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    900A  HIS*     3.6    29.2    -      -       +      +
    903A  ILE*     3.7    14.6    -      -       +      -
    912A  LYS*     3.0    29.4    +      -       +      +
    913A  ALA*     3.2     9.3    +      -       -      +
    915A  ILE*     1.4    74.8    -      -       -      +
    917A  LYS*     1.3    56.1    +      -       -      +
    919A  PHE*     2.9    22.7    +      -       +      +
    920A  GLU*     3.5     8.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 917 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    913A  ALA*     3.2    21.6    +      -       -      +
    914A  PHE*     3.3     8.2    +      -       -      +
    916A  LEU*     1.3    75.4    -      -       -      +
    918A  CYS*     1.3    59.7    +      -       -      +
    920A  GLU*     3.7    10.5    +      -       -      +
    926A  ARG*     3.6    17.0    -      -       -      +
    927A  ALA*     3.9    27.8    +      -       +      +
    931A  ASP*     5.5     7.7    +      -       +      +
    932A  LEU*     4.1    14.6    -      -       +      -
    935A  ASP*     3.3    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 918 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    864A  ILE*     3.5    33.7    -      -       -      +
    865A  TRP*     3.5    15.9    -      -       -      -
    867A  LEU*     4.2    11.0    -      -       -      -
    868A  GLY*     3.7    21.1    -      -       -      -
    871A  ILE*     4.6     1.6    -      -       -      -
    914A  PHE*     3.9    20.0    -      -       -      -
    915A  ILE*     2.9    15.5    +      -       -      +
    917A  LYS*     1.3    75.9    -      -       -      +
    919A  PHE*     1.3    56.9    +      -       +      +
    920A  GLU      3.4     1.3    -      -       -      -
    926A  ARG*     3.4    19.3    +      -       -      -
    932A  LEU*     4.2    16.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 919 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    865A  TRP*     3.4    46.9    -      +       -      -
    868A  GLY*     3.3    25.6    -      -       -      -
    869A  CYS*     3.5    12.3    -      -       -      -
    872A  ILE*     4.0     9.2    -      -       +      -
    898A  LYS      5.0     1.6    -      -       -      +
    900A  HIS*     3.3    52.7    -      +       +      -
    901A  PRO*     3.7    16.8    -      -       +      -
    903A  ILE*     5.0     0.4    -      -       +      -
    915A  ILE*     3.4    36.1    +      -       +      +
    916A  LEU*     2.9    14.0    +      -       +      +
    918A  CYS*     1.3    82.2    -      -       -      +
    920A  GLU*     1.4    63.0    +      -       -      +
    921A  PRO*     3.1     9.9    -      -       -      +
----------------------------------------------------------
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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