Contacts of the strand formed by residues 61 - 66 (chain C) in PDB entry 3E6C


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 61 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  VAL*     3.8    26.9    -      -       +      -
     54C  ILE*     5.4     0.2    -      -       +      -
     56C  LEU*     3.8    27.1    -      -       +      +
     60C  LYS*     1.3    78.7    -      -       -      +
     62C  LYS*     1.3    72.0    +      -       -      +
     63C  LEU*     4.0     4.6    +      -       +      +
     77C  TYR*     3.4     2.3    -      -       -      -
     78C  ALA*     2.8    38.9    +      -       +      +
     84C  ILE*     4.1    24.5    -      -       +      -
     96C  ALA*     3.8    20.0    -      -       +      -
     97C  THR      3.3    10.8    -      -       -      +
     98C  ALA*     4.4     1.1    -      -       -      -
     99C  MET*     3.2    10.2    -      -       -      +
    102C  THR*     4.1    12.8    -      -       +      -
    104C  THR*     4.2     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 62 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61C  ILE*     1.3    74.3    -      -       -      +
     63C  LEU*     1.3    60.9    +      -       -      +
     64C  ASP*     2.9    39.9    +      -       -      +
     74C  LEU*     3.9    14.3    -      -       +      +
     76C  TYR      4.0     2.0    -      -       -      -
     77C  TYR*     3.6    31.6    -      -       +      -
     95C  TYR      3.8     1.7    -      -       -      +
     96C  ALA*     3.2     2.6    -      -       -      -
     97C  THR*     2.9    41.2    +      -       -      +
     99C  MET*     3.5    23.4    -      -       +      +
    181C  LYS*     5.0     9.1    -      -       -      +
    185C  GLU*     4.8    10.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  ILE*     4.4     0.9    -      -       +      -
     61C  ILE*     4.0     3.3    -      -       +      -
     62C  LYS*     1.3    74.6    -      -       -      +
     64C  ASP*     1.3    57.7    +      -       -      +
     74C  LEU*     3.9     0.3    -      -       -      +
     75C  LEU*     2.8    60.0    +      -       +      -
     76C  TYR*     2.9    45.4    +      -       +      +
     84C  ILE*     4.0    34.8    -      -       +      -
     94C  ILE*     3.8    24.0    -      -       +      -
     95C  TYR      3.8     2.2    -      -       -      -
     96C  ALA*     3.9    18.8    -      -       +      +
    604C  3C4      3.9    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 64 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62C  LYS*     2.9    37.3    +      -       -      +
     63C  LEU*     1.3    80.5    -      -       -      +
     65C  ILE*     1.3    59.7    +      -       -      +
     72C  GLU*     2.4    41.2    -      -       +      +
     73C  LYS      3.1    17.5    -      -       -      +
     74C  LEU*     3.4    10.4    -      -       -      +
     75C  LEU*     4.0     5.2    -      -       -      +
     94C  ILE*     3.4    10.4    -      -       -      +
     95C  TYR*     2.9    37.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 65 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64C  ASP*     1.3    73.5    -      -       -      +
     66C  ILE*     1.3    71.3    +      -       -      +
     67C  PHE*     4.3    30.9    -      -       +      -
     71C  SER      4.0     0.5    -      -       -      +
     72C  GLU*     3.4     4.2    -      -       -      +
     73C  LYS*     2.9    51.7    +      -       +      +
     75C  LEU*     3.9    31.5    -      -       +      +
     92C  ASN*     3.7    39.0    -      -       +      +
     93C  ASN      3.4    11.4    -      -       -      +
     94C  ILE*     4.2     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 66 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  PRO*     3.9    24.7    -      -       +      -
     65C  ILE*     1.3    82.9    -      -       -      +
     67C  PHE*     1.3    76.3    +      -       -      +
     68C  GLU*     4.5     2.8    -      -       -      +
     70C  GLY*     4.2    13.7    -      -       -      +
     71C  SER      3.4     8.5    -      -       -      +
     72C  GLU*     4.0    21.3    -      -       +      +
     93C  ASN*     2.8    47.5    +      -       -      +
     95C  TYR*     3.8    28.7    -      -       +      -
----------------------------------------------------------
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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