Contacts of the strand formed by residues 72 - 77 (chain A) in PDB entry 6K0X


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 72 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  GLU      2.9    11.5    +      -       -      +
     48A  ILE*     3.5    17.6    -      -       +      -
     49A  CYS*     2.9    29.8    +      -       -      +
     71A  ALA*     1.3    72.3    -      -       -      +
     73A  TYR*     1.3    65.8    +      -       -      +
     74A  MET*     3.8    33.9    -      -       +      -
     98A  GLN*     4.1    17.7    -      -       +      +
    112A  LEU*     5.9     0.2    -      -       +      -
      4B  LEU*     3.9    30.5    -      -       +      -
      5B  THR*     5.8     0.2    -      -       -      +
      8B  LEU*     4.2    13.0    -      -       +      -
     41B  PHE*     3.7    19.3    -      -       +      -
     45B  MET*     4.4    10.1    -      -       -      -
     89B  LEU*     5.8     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  CYS*     3.6    34.8    -      -       +      -
     60A  SER*     4.5     8.1    -      -       -      +
     63A  LEU*     4.0     5.2    -      -       +      -
     64A  ALA*     3.4    38.0    -      -       +      -
     67A  ILE*     3.2    28.5    -      -       +      +
     68A  GLY      2.7    28.5    +      -       -      -
     69A  PRO*     5.0     2.2    -      -       +      -
     71A  ALA*     3.3    29.7    -      -       +      +
     72A  LEU*     1.3    73.9    -      -       -      +
     74A  MET*     1.3    57.1    +      -       -      +
     96A  HIS      3.7    22.5    +      -       -      +
     97A  ILE*     3.5    14.6    -      -       +      -
     98A  GLN*     2.8    35.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  ILE*     5.0     6.7    -      -       +      -
     49A  CYS*     2.9    11.8    +      -       -      +
     50A  LEU*     3.3    20.0    -      -       +      -
     51A  GLU*     3.0    21.1    +      -       -      +
     60A  SER*     4.3     2.9    +      -       -      -
     72A  LEU*     3.8    33.7    -      -       +      +
     73A  TYR*     1.3    75.1    -      -       -      +
     75A  CYS*     1.3    66.0    +      -       -      +
     97A  ILE*     4.8     0.9    -      -       -      -
     98A  GLN*     3.4    25.4    -      -       -      +
    100A  VAL*     5.0     3.1    -      -       +      -
    108A  LEU*     3.5    33.7    -      -       +      -
    112A  LEU*     4.6     6.3    -      -       +      -
      4B  LEU*     6.3     0.2    -      -       -      -
      5B  THR*     4.5    15.5    -      -       +      -
      8B  LEU*     3.5    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  LEU*     4.1     1.8    -      -       -      -
     51A  GLU*     3.0    19.7    -      -       +      +
     54A  SER*     3.5    29.2    -      -       -      -
     60A  SER*     4.1     4.7    -      -       -      +
     74A  MET*     1.3    78.7    -      -       -      +
     76A  THR*     1.3    67.9    +      -       -      +
     86A  THR*     3.6    12.6    -      -       -      -
     97A  ILE*     3.6    23.1    -      -       +      -
     98A  GLN      3.0     7.6    +      -       -      +
     99A  PRO*     3.2    17.4    -      -       -      +
    100A  VAL*     2.8    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  LEU*     4.5     6.5    -      -       +      -
     51A  GLU      2.9     7.1    +      -       -      -
     52A  VAL*     3.5    16.8    -      -       -      +
     53A  GLY      2.8    22.0    +      -       -      -
     54A  SER*     2.8    14.6    +      -       -      -
     75A  CYS*     1.3    80.2    -      -       -      +
     77A  ASP*     1.3    61.2    -      -       -      +
     83A  ALA*     6.3     0.2    -      -       -      -
     99A  PRO*     6.1     0.9    -      -       -      -
    100A  VAL*     3.1    11.2    -      -       +      +
    102A  THR*     3.7    19.1    -      -       +      -
    104A  LEU      2.8    29.3    +      -       -      +
    105A  VAL*     4.4     1.8    -      -       +      -
    108A  LEU*     3.9    24.0    -      -       +      -
    301A  SAM      4.1     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  GLY      3.3     7.6    -      -       -      -
     54A  SER*     4.2     6.1    -      -       -      +
     55A  GLY      2.9    13.5    +      -       -      -
     76A  THR*     1.3    76.2    -      -       -      +
     78A  ILE*     1.3    65.1    +      -       -      +
     79A  ASN*     2.9    27.7    +      -       -      +
     82A  ALA*     3.4    20.0    -      -       +      -
     83A  ALA*     4.6     7.4    -      -       +      +
    100A  VAL      3.2     4.2    +      -       -      -
    101A  ILE*     3.2    10.6    -      -       -      +
    102A  THR      3.1    20.8    +      -       -      -
    301A  SAM      2.6    53.5    +      -       -      -
----------------------------------------------------------
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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