Contacts of the helix formed by residues 316 - 323 (chain A) in PDB entry 9ICA


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 GLU 316 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  ARG*     2.4    34.0    +      -       -      +
    266A  TYR*     3.9    14.9    -      -       +      +
    269A  VAL*     3.6    12.4    -      -       +      +
    270A  LEU*     2.9    39.7    +      -       +      +
    315A  SER*     1.3    78.6    +      -       -      +
    317A  LYS*     1.3    54.8    +      -       -      +
    319A  ILE*     3.7    13.4    -      -       -      +
    320A  PHE*     2.8    38.6    +      -       +      -
    327A  TYR*     3.6    22.0    +      -       +      +
    330A  PRO*     4.9     0.2    -      -       -      +
    333A  ARG*     3.2    23.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  SER*     2.8    16.0    +      -       -      +
    316A  GLU*     1.3    73.6    -      -       -      +
    318A  ASP*     1.3    60.4    +      -       -      +
    319A  ILE      2.7     4.4    +      -       -      -
    320A  PHE*     2.6    32.2    +      -       +      +
    321A  ASP*     2.7    44.1    +      -       -      +
    325A  TRP      5.6     3.2    +      -       -      -
    327A  TYR*     4.3    36.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    312A  PRO      4.4     9.5    -      -       -      +
    313A  VAL*     4.1    16.4    -      -       -      -
    314A  ASP*     3.3    26.0    +      -       -      +
    315A  SER*     3.2    16.2    +      -       -      +
    317A  LYS*     1.3    80.8    -      -       -      +
    319A  ILE*     1.3    56.3    +      -       -      +
    321A  ASP*     3.5    15.4    -      -       -      +
    322A  TYR*     2.8    45.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  TYR*     4.0    16.8    -      -       +      +
    267A  CYS*     4.3     7.2    -      -       -      +
    270A  LEU*     3.8    34.1    -      -       +      -
    282A  MET*     4.4    13.7    -      -       -      -
    293A  ILE*     5.2    11.0    -      -       +      -
    298A  ILE*     5.0    12.8    -      -       +      -
    313A  VAL*     3.8    34.8    -      -       +      -
    315A  SER      3.9     0.2    +      -       -      -
    316A  GLU*     3.7    20.9    -      -       -      +
    317A  LYS      2.7     5.1    +      -       -      -
    318A  ASP*     1.3    72.8    -      -       -      +
    320A  PHE*     1.3    72.5    +      -       +      +
    322A  TYR*     3.0    21.1    -      -       -      +
    323A  ILE*     3.1    11.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270A  LEU*     4.4     9.0    -      -       +      -
    278A  PHE*     3.3    25.6    -      +       -      -
    282A  MET*     3.5    18.2    -      -       +      -
    316A  GLU      2.8    26.5    -      -       -      -
    317A  LYS*     2.6    13.4    +      -       +      +
    319A  ILE*     1.3    79.9    -      -       +      +
    321A  ASP*     1.4    52.2    -      -       -      +
    323A  ILE*     3.0     4.7    +      -       -      +
    324A  GLN      2.6    29.8    +      -       -      -
    325A  TRP*     2.9    53.0    +      +       +      +
    326A  LYS      3.3    15.3    -      -       -      -
    327A  TYR*     3.9    36.3    -      +       +      -
    328A  ARG*     3.4    16.6    -      -       +      -
    333A  ARG*     4.3     7.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  LYS*     2.7    61.1    +      -       -      +
    318A  ASP*     3.5    21.1    -      -       -      +
    320A  PHE*     1.4    72.5    -      -       -      +
    322A  TYR*     1.3    61.8    +      -       +      +
    324A  GLN*     2.5    32.4    +      -       -      +
    325A  TRP      4.8     2.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291A  PHE*     3.4    21.8    -      +       +      -
    298A  ILE*     3.9    33.0    -      -       +      -
    311A  LEU*     3.2    37.5    -      -       +      +
    312A  PRO*     2.6    38.5    +      -       -      +
    313A  VAL*     4.7     3.1    -      -       +      -
    318A  ASP*     2.8    31.6    +      -       +      -
    319A  ILE*     3.0    13.2    -      -       -      +
    321A  ASP*     1.3    83.5    -      -       +      +
    323A  ILE*     1.3    59.3    +      -       -      +
    324A  GLN*     3.0    10.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  MET*     3.6    41.7    -      -       +      +
    285A  HIS*     2.8    50.8    +      -       +      -
    286A  ALA*     3.3    25.6    -      -       +      +
    289A  LYS*     3.5     7.2    -      -       +      +
    291A  PHE*     3.3    27.6    -      -       +      -
    293A  ILE*     4.2     7.9    -      -       +      -
    298A  ILE*     4.3     4.0    -      -       +      -
    319A  ILE*     3.4     7.9    -      -       +      +
    320A  PHE*     3.3    11.0    -      -       -      +
    322A  TYR*     1.3    76.2    -      -       -      +
    324A  GLN*     1.3    69.5    +      -       -      +
    325A  TRP*     3.2    10.0    +      -       +      -
----------------------------------------------------------
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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