Contacts of the strand formed by residues 66 - 71 (chain C) in PDB entry 1AXC


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 LEU 66 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  PHE*     3.4    39.5    -      -       +      +
     28C  TRP      4.0     0.2    -      -       -      -
     29C  ASP*     3.3     4.7    -      -       -      +
     30C  ILE*     2.8    47.9    +      -       +      +
     62C  CYS*     5.0     0.2    -      -       -      -
     64C  ARG      3.5    14.1    +      -       -      +
     65C  ASN*     1.3    74.4    -      -       -      +
     67C  ALA*     1.3    61.9    +      -       -      +
     68C  MET*     4.0    12.3    -      -       +      -
     92C  ALA*     4.3    15.3    -      -       +      +
     93C  GLU      3.9    19.7    -      -       -      +
     94C  ASP*     4.1    22.7    -      -       +      +
     96C  ALA      6.0     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 67 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  CYS*     4.0     9.4    -      -       -      -
     28C  TRP      3.3     5.8    -      -       -      -
     29C  ASP*     4.1     1.8    -      -       -      +
     66C  LEU*     1.3    75.9    -      -       -      +
     68C  MET*     1.3    60.4    +      -       -      +
     69C  GLY      4.0     0.2    -      -       -      -
    156D  ARG*     3.9    24.2    -      -       -      +
    158D  ILE*     3.5    24.2    -      -       +      +
    159D  PHE      4.6     2.1    -      -       -      +
    160D  SER*     3.8     8.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 68 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  PHE*     4.6     6.3    -      -       +      -
     27C  CYS*     3.6     0.6    -      -       -      -
     28C  TRP*     2.9    44.9    +      -       +      +
     30C  ILE*     3.3    32.8    -      -       +      -
     66C  LEU*     4.4    14.6    -      -       +      -
     67C  ALA*     1.3    73.9    -      -       -      +
     69C  GLY*     1.3    61.0    +      -       -      +
     70C  VAL*     3.1    17.0    +      -       +      +
     90C  LEU*     6.4     0.9    -      -       +      -
     92C  ALA*     4.0    17.3    -      -       -      -
     99C  LEU*     3.9    37.9    -      -       +      -
    118C  LEU*     3.6    26.0    -      -       +      -
    158D  ILE*     4.4     1.1    -      -       -      -
    160D  SER*     3.9     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 69 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  ALA      4.0     0.2    -      -       -      -
     27C  CYS*     4.6     0.4    -      -       -      -
     68C  MET*     1.3    69.6    -      -       -      +
     70C  VAL*     1.3    58.9    +      -       -      -
    118C  LEU*     3.3     7.1    -      -       -      +
    119C  MET*     2.6    49.7    +      -       -      +
    121C  LEU*     3.5    18.6    -      -       -      -
    158D  ILE*     3.8     8.4    -      -       -      +
    160D  SER*     2.9    14.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 70 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25C  GLU*     3.4     5.2    -      -       -      +
     26C  ALA      2.9    33.3    +      -       -      -
     28C  TRP*     3.6    27.8    -      -       +      +
     68C  MET*     3.5    18.8    -      -       +      +
     69C  GLY*     1.3    75.7    -      -       -      +
     71C  ASN*     1.3    75.2    +      -       -      +
     72C  LEU*     3.5     2.8    +      -       +      +
     75C  MET*     3.9    19.1    -      -       +      -
     99C  LEU*     5.0     4.7    -      -       +      -
    116C  MET*     3.5    34.5    -      -       +      -
    118C  LEU*     4.1     9.4    -      -       +      +
    119C  MET*     4.4     4.3    -      -       -      -
    121C  LEU*     3.8     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 71 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24C  ASN*     3.5     9.8    -      -       -      +
     25C  GLU*     4.5     6.6    +      -       -      +
     70C  VAL*     1.3    77.4    -      -       -      +
     72C  LEU*     1.3    57.3    +      -       -      +
     73C  THR*     2.9    28.8    +      -       -      -
     74C  SER*     3.1    23.7    +      -       -      +
     75C  MET      2.9    23.0    +      -       -      -
    116C  MET*     4.7     1.3    -      -       -      +
    117C  LYS      5.4     5.1    +      -       -      +
    118C  LEU*     5.9     0.2    -      -       -      +
    119C  MET*     3.3    31.0    -      -       +      +
----------------------------------------------------------
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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