Contacts of the strand formed by residues 4 - 10 (chain C) in PDB entry 3CB4


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 ILE 4 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  MET*     3.0    34.8    +      -       -      +
      3C  ASN*     1.3    81.2    -      -       +      +
      5C  ARG*     1.3    80.4    +      -       -      +
      6C  ASN*     3.5    28.7    -      -       -      +
     72C  GLN*     3.2    37.2    -      -       +      +
     74C  ASN*     3.6     3.8    -      -       -      +
    182C  PRO*     3.3     1.9    -      -       -      +
    183C  PRO*     3.2    18.0    -      -       +      +
    251C  LYS*     6.1     0.9    -      -       +      -
    252C  CYS      4.1    11.9    -      -       -      +
    253C  GLY      3.6    19.5    -      -       -      +
    254C  GLU*     4.3     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 5 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  LYS      3.0    26.8    +      -       -      -
      3C  ASN      4.1     4.0    -      -       -      +
      4C  ILE*     1.3   100.3    +      -       -      +
      6C  ASN*     1.3    65.8    +      -       -      +
      7C  PHE*     3.5     9.9    -      -       -      -
     71C  TYR*     3.8    19.9    +      -       +      -
     72C  GLN      3.0     8.3    +      -       -      -
     73C  LEU*     3.6    23.9    -      -       +      -
     74C  ASN      3.1    19.7    +      -       -      -
    176C  LEU*     3.8    12.1    -      -       +      -
    177C  VAL*     2.8    44.9    +      -       +      +
    180C  ILE*     3.0    28.9    +      -       +      -
    181C  PRO      4.4     3.8    -      -       -      -
    182C  PRO*     3.4    17.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 6 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  ILE*     3.5     2.3    -      -       -      +
      5C  ARG*     1.3    69.3    -      -       -      +
      7C  PHE*     1.3    60.9    +      -       -      +
     74C  ASN*     3.1    37.8    +      -       +      +
     76C  ILE*     5.2     0.7    -      -       +      -
     94C  ALA      3.6    20.0    -      -       -      +
     95C  CYS*     3.9     3.1    -      -       -      -
     96C  GLU*     2.9    53.8    +      -       -      +
     97C  GLY      3.4     5.7    +      -       -      -
    180C  ILE*     4.2     3.5    -      -       -      +
    181C  PRO      5.2     0.4    +      -       -      -
    183C  PRO*     3.6    13.9    -      -       -      +
    211C  ARG*     3.6     7.7    -      -       -      +
    253C  GLY      3.1    22.7    +      -       -      +
    255C  VAL*     3.7     8.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 7 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  ARG      3.5    16.2    -      -       -      -
      6C  ASN*     1.3    74.1    -      -       -      +
      8C  SER*     1.3    70.5    +      -       -      +
      9C  ILE*     4.2    17.9    -      -       +      -
     24C  ILE*     4.6    19.3    -      -       +      -
     61C  LEU*     6.3     0.7    -      -       +      -
     73C  LEU*     4.2    20.6    -      -       +      -
     74C  ASN      3.0     9.3    +      -       -      +
     75C  PHE*     3.1    37.8    -      +       +      -
     76C  ILE      3.1    20.6    +      -       -      -
     95C  CYS*     3.4     8.5    -      -       -      -
     97C  GLY      3.1    17.9    -      -       -      +
     98C  ALA*     4.5     0.4    -      -       -      -
     99C  LEU*     4.2    10.1    -      -       +      -
    176C  LEU*     3.6    38.1    -      -       +      -
    180C  ILE*     4.1    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 8 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  PHE*     1.3    77.4    -      -       -      +
      9C  ILE*     1.3    68.3    +      -       -      +
     10C  ILE*     5.3     0.5    -      -       -      +
     75C  PHE*     4.5     0.7    -      -       -      -
     76C  ILE*     3.2    23.1    -      -       -      -
     78C  THR*     3.3    14.5    +      -       -      -
     91C  SER      5.5     1.1    -      -       -      -
     92C  LEU*     3.4    29.7    -      -       -      +
     95C  CYS*     3.5    13.1    -      -       -      -
     97C  GLY      3.4     4.6    +      -       -      -
     98C  ALA*     3.2     6.7    -      -       -      +
     99C  LEU      3.0    24.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 9 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  PHE*     4.2    11.4    -      -       +      -
      8C  SER*     1.3    80.6    -      -       -      +
     10C  ILE*     1.3    63.7    +      -       -      +
     11C  ALA*     4.0    15.3    +      -       +      -
     20C  LEU*     4.9     6.3    -      -       +      -
     21C  SER*     4.1    28.7    -      -       -      +
     24C  ILE*     4.4    14.8    -      -       +      -
     75C  PHE*     3.8    27.8    -      -       +      -
     76C  ILE      3.9     4.6    +      -       -      -
     77C  ASP*     5.6     1.6    -      -       -      +
     78C  THR*     3.7    25.4    +      -       -      +
     99C  LEU*     3.8    10.5    -      -       +      +
    101C  VAL*     3.9    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 10 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8C  SER*     5.2     0.7    -      -       -      +
      9C  ILE*     1.3    74.4    -      -       -      +
     11C  ALA*     1.3    63.7    +      -       -      +
     78C  THR*     5.5     5.2    -      -       +      -
     92C  LEU*     4.7     8.1    -      -       +      -
     98C  ALA*     4.2    17.9    -      -       +      -
     99C  LEU      2.8    15.9    +      -       -      +
    100C  LEU*     3.6    11.6    -      -       +      +
    101C  VAL*     2.9    27.5    +      -       -      +
    112C  THR*     3.7    31.0    -      -       -      +
    115C  ASN*     3.8    34.3    -      -       +      +
    116C  CYS*     4.3    10.1    -      -       +      +
    119C  ALA*     4.2    25.1    -      -       +      -
    126C  VAL*     5.3     2.9    -      -       +      -
----------------------------------------------------------
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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