Contacts of the strand formed by residues 416 - 423 (chain C) in PDB entry 2CKJ


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 416 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322C  GLN*     2.5    29.2    +      -       -      +
    325C  GLU*     3.7     7.5    -      -       -      +
    326C  VAL*     5.9     2.1    -      -       -      +
    411C  TYR      4.6     1.9    -      -       -      +
    412C  SER*     3.5    13.4    +      -       -      +
    413C  ARG*     3.0    67.6    +      -       -      +
    415C  GLY*     1.4    73.9    -      -       -      +
    417C  TYR*     1.3    69.4    +      -       -      +
    439C  ARG*     2.8    37.5    +      -       +      +
    440C  VAL      3.7    10.1    -      -       -      +
    441C  LEU*     4.2    13.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 417 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322C  GLN*     3.3    20.9    -      -       -      -
    325C  GLU*     3.4    13.2    -      -       -      +
    415C  GLY*     3.9    27.8    +      -       -      -
    416C  GLU*     1.3    88.3    -      -       -      +
    418C  PHE*     1.4    59.8    +      -       -      +
    439C  ARG*     3.5     7.4    -      -       -      +
    440C  VAL*     2.9    39.8    +      -       +      +
    442C  PHE*     4.3    19.7    -      +       -      -
    519C  PHE*     4.5     3.9    -      -       +      -
    523C  VAL*     4.2    27.4    -      -       +      -
    526C  LYS*     3.0    47.6    +      -       +      -
    527C  LEU*     3.9    24.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 418 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325C  GLU*     2.8    40.7    +      -       +      +
    326C  VAL*     3.6    41.5    -      -       +      -
    329C  GLY*     5.5     6.4    +      -       -      -
    364C  VAL*     3.6    31.9    -      -       +      -
    367C  ALA*     4.2    11.9    -      -       +      -
    368C  SER*     3.9    16.8    -      -       -      -
    417C  TYR*     1.4    72.9    -      -       -      +
    419C  SER*     1.3    94.5    +      -       -      +
    420C  ALA*     5.0     1.1    -      -       +      -
    437C  GLY*     4.0     4.5    -      -       -      -
    438C  MET      2.7    32.8    -      -       -      -
    439C  ARG*     4.5    13.9    -      -       +      -
    519C  PHE*     4.4     3.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 419 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329C  GLY*     5.4     3.4    -      -       -      -
    418C  PHE*     1.3    98.1    +      -       -      +
    420C  ALA*     1.4    60.4    +      -       -      +
    421C  PHE*     3.8    28.0    -      -       -      -
    438C  MET*     3.0    20.7    +      -       -      +
    519C  PHE*     3.8    18.5    -      -       -      -
    522C  THR*     4.2    12.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 420 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329C  GLY*     4.0    30.1    -      -       -      +
    332C  GLU*     4.6    18.6    -      -       +      +
    333C  GLN*     4.2    17.7    -      -       +      +
    364C  VAL*     4.5     9.6    -      -       +      -
    418C  PHE*     5.1     0.7    -      -       +      -
    419C  SER*     1.4    74.1    -      -       -      +
    421C  PHE*     1.4    74.6    +      -       -      +
    436C  SER      3.4    11.2    -      -       -      +
    437C  GLY*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 421 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333C  GLN*     3.9     4.5    -      -       -      +
    419C  SER*     3.8    25.4    -      -       -      -
    420C  ALA*     1.4    80.3    -      -       -      +
    422C  LYS*     1.3    60.1    +      -       -      +
    435C  THR*     3.4     4.5    +      -       -      -
    436C  SER*     2.8    37.1    +      -       -      +
    438C  MET*     4.1    15.9    -      -       +      -
    515C  PHE*     3.4    68.4    -      +       +      -
    518C  LYS*     4.1    26.5    -      -       +      -
    519C  PHE*     4.0    16.8    -      -       +      -
    522C  THR*     5.4     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 422 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333C  GLN*     3.7    16.5    +      -       -      +
    336C  TRP*     3.3    42.9    +      -       +      -
    337C  PHE*     4.0     3.0    -      -       -      +
    360C  ASP*     3.1    45.2    +      -       +      +
    421C  PHE*     1.3    75.5    -      -       -      +
    423C  GLN*     1.3    71.0    +      -       -      +
    424C  ALA*     5.0     4.9    -      -       -      +
    432C  ALA*     4.6    12.6    -      -       +      +
    434C  VAL      3.9     5.4    -      -       -      +
    435C  THR*     4.3     4.0    -      -       -      +
    515C  PHE*     4.0     4.9    -      -       -      -
   1169C  THR*     6.0     0.2    -      -       -      +
   3006C  FAD      3.5    13.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 423 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422C  LYS*     1.3    80.1    -      -       -      +
    424C  ALA*     1.3    94.3    +      -       -      +
    425C  SER*     3.6     1.4    -      -       -      +
    426C  ARG      5.4     1.2    +      -       -      +
    427C  ARG*     6.0     2.8    -      -       -      +
    432C  ALA      2.6    21.7    -      -       -      +
    433C  LYS*     3.8     8.5    -      -       -      +
    434C  VAL      3.1    14.7    +      -       -      +
    507C  PHE*     4.3     6.3    -      -       +      -
    511C  LEU*     4.1    19.5    -      -       +      +
    515C  PHE*     3.9    16.7    -      -       +      -
   1169C  THR*     3.2    27.2    +      -       +      +
   1170C  GLY      4.0     1.7    -      -       -      -
   1171C  ASP*     3.6    30.6    +      -       -      +
   1303C  PRO*     4.6     6.1    -      -       -      +
----------------------------------------------------------
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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