Contacts of the strand formed by residues 409 - 417 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321B  PRO*     5.5     2.4    -      -       -      +
    323B  PHE*     3.4    23.6    -      -       -      -
    325B  VAL*     3.8    26.4    -      -       +      +
    408B  ALA*     1.3    74.2    -      -       -      +
    410B  TYR*     1.3    68.8    +      -       -      +
    411B  VAL*     4.6     4.9    -      -       +      -
    430B  CYS*     3.0     8.7    -      -       -      +
    431B  VAL      2.9    37.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 410 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398B  LEU*     4.1    12.1    -      -       +      -
    399B  THR      4.7     0.2    -      -       -      -
    400B  ARG*     3.2    55.3    -      -       +      +
    401B  GLY      3.7     0.2    +      -       -      -
    404B  CYS*     3.0    48.1    +      -       +      +
    405B  PRO      3.2     5.6    +      -       -      -
    406B  TYR*     4.5     3.3    -      -       -      -
    408B  ALA*     3.0    37.9    -      -       +      -
    409B  THR*     1.3    78.0    -      -       -      +
    411B  VAL*     1.3    64.3    +      -       -      +
    412B  ASP*     5.3     2.1    -      -       -      +
    427B  ASP*     3.1    41.5    -      -       +      +
    429B  PHE      3.4     4.9    -      -       -      +
    430B  CYS*     3.8     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 411 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325B  VAL*     3.9    28.0    -      -       +      -
    327B  GLY      4.7     5.6    -      -       -      +
    339B  PHE*     3.9    17.7    -      -       +      -
    409B  THR*     4.6     8.3    -      -       +      -
    410B  TYR*     1.3    79.5    -      -       -      +
    412B  ASP*     1.3    74.2    +      -       -      +
    427B  ASP*     3.2     2.0    -      -       -      -
    428B  ALA      2.8    31.7    +      -       -      -
    429B  PHE*     2.8    34.5    +      -       +      +
    431B  VAL*     5.4     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 412 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    410B  TYR      5.3     2.4    -      -       -      +
    411B  VAL*     1.3    91.8    -      -       -      +
    413B  TRP*     1.3    63.0    +      -       -      +
    414B  HIS*     4.3     6.9    +      -       +      -
    424B  THR*     3.7    16.8    -      -       +      -
    425B  ILE      3.4     4.0    -      -       -      +
    426B  ARG*     3.0    34.9    -      -       -      +
    427B  ASP*     3.1     6.8    +      -       -      +
    428B  ALA*     4.4     0.4    -      -       -      -
    429B  PHE*     4.0     5.4    -      -       -      -
   1747B   CU      4.3    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 413 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  ASP*     3.5    29.6    +      -       +      +
    100B  GLU*     5.2     3.6    -      -       +      -
    341B  LEU*     3.5    36.0    -      -       +      +
    343B  ALA*     3.8    15.9    -      -       +      -
    392B  GLY*     3.0    36.8    -      -       -      -
    393B  LYS*     3.7     7.9    -      -       -      -
    412B  ASP*     1.3    76.4    -      -       -      +
    414B  HIS*     1.3    72.6    +      -       -      +
    415B  PHE*     3.8    27.9    +      +       +      -
    417B  LEU*     4.4     2.5    -      -       +      -
    424B  THR*     3.4     2.1    -      -       -      +
    425B  ILE*     2.8    60.7    +      -       +      +
    428B  ALA*     3.5    19.5    -      -       +      -
    429B  PHE*     4.1    15.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with HIS 414 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  ASP*     5.5     1.6    -      -       -      +
     63B  LEU      4.2    11.0    +      -       -      +
     64B  SER*     4.8     5.2    -      -       -      -
     65B  ARG*     4.1    42.5    -      -       +      +
     68B  LEU*     4.0    20.5    -      -       +      +
    412B  ASP*     4.5     6.4    -      -       +      +
    413B  TRP*     1.3    87.7    +      -       -      +
    415B  PHE*     1.3    60.7    +      -       -      +
    422B  PRO*     5.5     0.7    -      -       +      -
    423B  LYS      3.3     7.2    -      -       -      +
    424B  THR*     3.1    35.1    +      -       +      +
   1747B   CU      2.2    31.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 415 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  LEU*     3.9     6.5    -      -       -      +
     99B  VAL      5.6     0.2    -      -       -      -
    393B  LYS*     5.8     5.4    -      -       +      -
    413B  TRP*     3.8    33.4    -      +       +      -
    414B  HIS*     1.3    75.4    -      -       -      +
    416B  LEU*     1.3    62.7    +      -       -      +
    417B  LEU*     3.7    39.7    -      -       +      -
    419B  SER*     5.9     1.6    -      -       -      -
    421B  ALA      4.7     0.2    -      -       -      +
    422B  PRO*     3.5     3.1    -      -       -      +
    423B  LYS*     2.8    78.6    +      -       +      -
    424B  THR      4.1     2.9    -      -       -      -
    425B  ILE*     3.6    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 416 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  LEU*     3.5    41.5    -      -       +      +
     72B  MET*     4.0    20.2    -      -       +      -
     98B  SER*     3.4     2.1    -      -       -      -
     99B  VAL*     3.0    57.4    +      -       +      +
    415B  PHE*     1.3    75.4    -      -       -      +
    417B  LEU*     1.3    62.5    +      -       -      +
    419B  SER*     4.2     7.0    -      -       -      +
    420B  GLN*     3.7    11.4    -      -       -      +
    421B  ALA      3.5    41.7    -      -       -      +
    422B  PRO*     3.6     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 417 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  PHE      3.3     6.1    -      -       -      +
     98B  SER*     3.6    20.4    -      -       -      -
     99B  VAL      4.4     7.0    -      -       -      +
    100B  GLU*     5.2     1.6    -      -       +      -
    343B  ALA*     3.9    25.6    -      -       +      -
    344B  PHE*     5.1     1.8    -      -       +      -
    393B  LYS*     3.5    53.8    -      -       +      -
    413B  TRP*     4.4     1.6    -      -       +      -
    415B  PHE*     3.7    39.6    -      -       +      -
    416B  LEU*     1.3    88.7    -      -       -      +
    418B  GLU*     1.3    76.1    +      -       -      +
    419B  SER*     3.4     6.4    +      -       -      -
----------------------------------------------------------
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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