Contacts of the strand formed by residues 65 - 73 (chain C) in PDB entry 5D4D


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 VAL 65 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53C  PRO*     4.4    14.4    -      -       +      -
     54C  ILE      3.6     3.6    -      -       -      +
     55C  GLU*     4.0    30.5    -      -       +      +
     56C  GLU      4.9     0.4    -      -       -      +
     64C  LEU*     1.3    78.5    -      -       +      +
     66C  LEU*     1.3    68.7    +      -       -      +
     67C  ASP*     4.6     5.6    -      -       +      +
     99C  GLN      3.8     0.7    -      -       -      +
    100C  LEU*     3.3     4.3    -      -       -      +
    101C  ILE*     2.6    58.6    +      -       +      +
    103C  LYS*     3.9    30.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 66 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  PHE*     3.7    18.1    -      -       +      -
     53C  PRO*     3.4     2.8    -      -       -      +
     54C  ILE*     2.8    45.3    +      -       +      +
     64C  LEU      4.3     0.2    -      -       -      -
     65C  VAL*     1.3    74.2    -      -       -      +
     67C  ASP*     1.3    64.2    +      -       -      +
     98C  LEU*     3.9    19.1    -      -       +      -
     99C  GLN      3.8    11.0    -      -       -      +
    100C  LEU*     3.8    23.1    -      -       +      +
    355C  VAL*     3.8    25.4    -      -       +      -
    359C  MET*     4.9     2.2    -      -       -      -
    369C  PRO*     4.5     6.7    -      -       +      -
    372C  LEU*     4.0    15.9    -      -       +      -
    373C  VAL*     4.0    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 67 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  ARG*     5.8     1.2    +      -       -      -
     52C  PHE*     4.2     4.3    -      -       -      +
     53C  PRO*     3.3    30.3    -      -       +      +
     65C  VAL*     4.8     4.0    -      -       +      -
     66C  LEU*     1.3    75.2    -      -       -      +
     68C  PHE*     1.3    77.9    +      -       -      +
     69C  LEU*     4.6     4.7    -      -       -      +
     98C  LEU*     3.1    10.7    -      -       -      +
     99C  GLN*     3.0    55.0    +      -       +      +
    101C  ILE*     4.8     9.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 68 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45C  GLN*     3.2    32.8    -      -       -      -
     48C  PHE*     3.6    54.5    -      +       +      -
     49C  ARG*     4.4    17.1    +      -       -      -
     52C  PHE*     3.5    27.5    -      -       +      +
     67C  ASP*     1.3    87.0    +      -       -      +
     69C  LEU*     1.3    74.9    +      -       -      +
     70C  GLU*     3.3    36.8    -      -       -      -
     71C  TYR*     3.7     5.6    -      +       +      -
     96C  ALA*     4.7     1.3    -      -       +      -
     97C  ARG      3.9     2.0    -      -       -      -
     98C  LEU*     3.9    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 69 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45C  GLN*     5.0     2.3    +      -       -      -
     67C  ASP*     4.6     5.6    -      -       -      +
     68C  PHE*     1.3    90.9    -      -       -      +
     70C  GLU*     1.3    66.2    +      -       +      +
     97C  ARG*     2.8    54.0    +      -       +      +
     99C  GLN*     3.9    35.4    -      -       +      +
    110C  GLU*     3.8    22.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 70 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  PRO*     3.2    40.8    -      -       +      +
     37C  GLU*     4.9     4.9    +      -       -      +
     39C  ARG*     5.4     0.4    -      -       -      +
     45C  GLN*     5.2     2.5    -      -       -      +
     68C  PHE*     3.3    18.2    -      -       -      -
     69C  LEU*     1.3    83.3    -      -       +      +
     71C  TYR*     1.3    61.2    +      -       -      +
     96C  ALA*     3.6     0.2    -      -       -      -
     97C  ARG*     2.9    66.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 71 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  ALA      4.6     0.2    +      -       -      -
     30C  LEU      2.5    30.2    +      -       -      -
     31C  GLN*     3.7     5.2    +      -       -      +
     36C  PRO*     3.8     8.7    -      -       -      +
     39C  ARG*     2.9    49.5    +      -       -      +
     44C  ILE*     3.6    26.4    -      -       +      +
     45C  GLN*     3.0    34.1    +      -       -      -
     48C  PHE*     3.7    34.5    -      +       +      -
     68C  PHE*     4.2     3.1    -      +       +      -
     70C  GLU*     1.3    79.1    -      -       -      +
     72C  ARG*     1.3    72.7    +      -       -      +
     73C  LEU*     4.5     9.0    -      -       +      -
     94C  LEU*     3.7    13.2    -      -       +      -
     95C  TYR      3.2    15.3    -      -       -      +
     96C  ALA*     4.2     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 72 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  PRO*     5.4     4.7    -      -       +      -
     39C  ARG*     4.5     5.6    -      -       -      +
     71C  TYR*     1.3    82.8    -      -       -      +
     73C  LEU*     1.3    66.0    +      -       -      +
     74C  GLY*     4.2    14.8    -      -       -      -
     93C  PRO      3.7     0.5    -      -       -      +
     94C  LEU*     3.5     4.5    -      -       -      +
     95C  TYR*     2.9    76.2    +      -       +      +
    112C  GLU*     2.7    40.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 73 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30C  LEU*     4.0    38.8    -      -       +      +
     32C  ALA*     3.8    31.9    -      -       +      +
     39C  ARG*     5.0     2.6    -      -       -      +
     44C  ILE*     5.0     0.9    -      -       +      -
     71C  TYR*     4.5     7.8    -      -       +      -
     72C  ARG*     1.3    80.5    +      -       -      +
     74C  GLY*     1.3    67.5    +      -       -      +
     92C  ALA*     4.3    16.2    -      -       +      +
     93C  PRO      3.3     9.4    -      -       -      +
     94C  LEU*     3.7    28.3    -      -       +      -
    118C  ILE*     4.4    17.7    -      -       +      -
    120C  LEU*     5.4     3.1    -      -       +      -
----------------------------------------------------------
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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