Contacts of the strand formed by residues 409 - 417 (chain C) in PDB entry 2C11


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 THR 409 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323C  PHE*     4.0    15.8    +      -       -      -
    325C  VAL*     3.8    36.1    -      -       +      +
    408C  ALA*     1.3    72.4    -      -       -      +
    410C  TYR*     1.3    68.2    +      -       -      +
    411C  VAL*     4.0     5.3    +      -       +      +
    430C  CYS*     3.3     3.5    -      -       -      -
    431C  VAL*     2.7    40.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 410 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398C  LEU*     4.1    14.6    -      -       +      -
    400C  ARG*     3.0    70.9    -      -       +      +
    404C  CYS*     3.3    16.4    +      -       +      +
    405C  PRO      2.7    20.2    +      -       -      -
    406C  TYR      3.7    10.1    -      -       -      -
    408C  ALA*     3.4    28.0    +      -       +      -
    409C  THR*     1.3    77.5    -      -       -      +
    411C  VAL*     1.3    63.6    +      -       -      +
    412C  ASP*     4.7     1.7    -      -       -      +
    427C  ASP*     3.6    30.1    -      -       +      +
    429C  PHE      3.6     2.5    -      -       -      -
    430C  CYS*     3.9    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 411 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325C  VAL*     4.3    16.8    -      -       +      -
    327C  GLY      4.8     6.7    -      -       -      +
    339C  PHE*     4.0    26.0    -      -       +      -
    409C  THR*     4.5     9.0    -      -       +      +
    410C  TYR*     1.3    77.9    -      -       -      +
    412C  ASP*     1.3    82.6    +      -       -      +
    427C  ASP*     2.8     3.5    -      -       -      -
    428C  ALA      2.6    32.9    +      -       -      -
    429C  PHE*     2.8    30.5    +      -       +      +
    431C  VAL*     5.1     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 412 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  ARG*     5.3     2.7    +      -       -      +
    410C  TYR      4.7     1.4    -      -       -      +
    411C  VAL*     1.3    93.3    -      -       -      +
    413C  TRP*     1.3    65.2    +      -       -      +
    414C  HIS*     4.6     2.8    +      -       +      -
    424C  THR*     3.7    18.8    -      -       +      +
    425C  ILE      3.3     5.4    -      -       -      +
    426C  ARG*     3.3    31.3    -      -       -      +
    427C  ASP*     3.2    19.4    +      -       -      +
    428C  ALA*     4.4     1.1    -      -       -      -
    429C  PHE*     3.8     7.3    -      -       -      -
   1744C   CU      4.5    11.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 413 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62C  ASP*     2.9    39.2    +      -       +      +
    100C  GLU*     5.6     5.4    -      -       +      -
    341C  LEU*     3.3    30.2    +      -       +      +
    343C  ALA*     4.3    12.1    -      -       +      -
    392C  GLY*     3.7    30.5    -      -       -      -
    393C  LYS*     4.2     6.7    -      -       -      -
    395C  THR*     4.0    14.1    -      -       +      -
    412C  ASP*     1.3    78.7    -      -       -      +
    414C  HIS*     1.3    75.6    +      -       -      +
    415C  PHE*     3.7    43.5    -      +       +      -
    417C  LEU*     4.6     4.3    -      -       +      -
    423C  LYS      3.9     0.3    -      -       -      +
    424C  THR*     3.2     2.4    -      -       -      -
    425C  ILE*     2.8    36.6    +      -       +      +
    428C  ALA*     3.8    17.9    -      -       +      -
    429C  PHE*     3.8    16.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with HIS 414 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62C  ASP*     5.4     1.1    -      -       -      +
     63C  LEU      3.9    18.4    +      -       -      +
     64C  SER*     3.4    29.9    -      -       -      -
     65C  ARG*     3.4    42.7    +      -       +      +
     68C  LEU*     4.1     5.6    -      -       +      +
    412C  ASP*     4.6     3.5    -      -       +      -
    413C  TRP*     1.3    92.2    +      -       -      +
    415C  PHE*     1.3    64.4    +      -       -      +
    422C  PRO*     5.5     1.1    -      -       +      -
    423C  LYS      3.4     7.0    -      -       -      +
    424C  THR*     3.1    36.9    +      -       +      +
   1744C   CU      2.3    30.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 415 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68C  LEU*     3.8    10.8    -      -       -      +
     99C  VAL      5.5     0.2    -      -       -      -
    393C  LYS      6.1     1.3    -      -       -      -
    413C  TRP*     3.7    37.5    -      +       +      -
    414C  HIS*     1.3    77.8    -      -       -      +
    416C  LEU*     1.3    60.8    +      -       -      +
    417C  LEU*     3.9    28.3    -      -       +      -
    421C  ALA      4.4     0.9    -      -       -      +
    422C  PRO*     3.1     2.3    -      -       -      +
    423C  LYS*     3.0    83.1    +      -       +      +
    424C  THR      4.0     2.0    -      -       -      -
    425C  ILE*     3.5    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 416 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68C  LEU*     3.5    41.7    -      -       +      +
     72C  MET*     3.7    44.6    -      -       +      -
     96C  VAL*     6.0     0.2    -      -       +      -
     98C  SER*     3.4     3.5    -      -       -      -
     99C  VAL*     3.0    38.9    +      -       +      +
    415C  PHE*     1.3    72.7    -      -       -      +
    417C  LEU*     1.3    62.7    +      -       -      +
    419C  SER      3.9     9.6    -      -       -      +
    420C  GLN      3.6     3.6    -      -       -      +
    421C  ALA      3.1    46.7    -      -       -      +
    422C  PRO*     3.1     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 417 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97C  PHE*     3.7     4.0    -      -       +      +
     98C  SER*     3.2    28.5    -      -       -      -
     99C  VAL      5.7     1.1    -      -       -      +
    343C  ALA*     4.2    15.7    -      -       +      -
    344C  PHE*     4.2    16.4    -      -       +      -
    393C  LYS*     3.7    52.9    -      -       +      +
    413C  TRP*     4.6     2.2    -      -       +      -
    415C  PHE*     3.7    34.6    +      -       +      -
    416C  LEU*     1.3    79.3    -      -       -      +
    418C  GLU*     1.3    59.2    +      -       -      +
    419C  SER*     2.5    26.3    +      -       -      -
    423C  LYS*     3.7    10.2    +      -       -      -
----------------------------------------------------------
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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