Contacts of the strand formed by residues 183 - 187 (chain A) in PDB entry 1KKU


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 183 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  LEU*     3.4    33.7    -      -       +      +
    155A  CYS*     4.3    14.1    -      -       -      -
    159A  LEU*     4.3     7.4    -      -       +      -
    160A  LEU*     4.0    20.0    -      -       +      -
    163A  PHE*     4.0    24.5    -      -       +      -
    177A  ILE*     3.9    15.7    -      -       +      -
    178A  VAL*     4.9    11.1    +      -       +      -
    182A  GLY*     1.3    81.9    -      -       -      +
    184A  ILE*     1.3    62.8    +      -       -      +
    185A  CYS*     3.9     2.2    -      -       +      +
    203A  LEU*     5.1     0.2    -      -       +      -
    209A  ASN      3.1     8.7    +      -       -      +
    210A  ILE*     3.3    23.8    -      -       +      +
    211A  HIS*     2.8    32.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     5.0     0.4    -      -       +      -
     11A  LEU*     3.5    31.2    -      -       +      -
     31A  ALA*     4.0    14.4    -      -       +      -
     35A  MET*     3.8    34.1    -      -       +      -
    152A  LYS*     4.1    16.8    -      -       +      -
    153A  LEU      2.8    12.8    +      -       -      +
    154A  LEU*     3.3    23.4    -      -       +      +
    155A  CYS*     3.0    27.9    +      -       -      +
    183A  LEU*     1.3    77.0    -      -       -      +
    185A  CYS*     1.3    59.3    +      -       -      +
    186A  VAL*     4.8     0.9    -      -       +      -
    211A  HIS*     3.6    12.1    -      -       +      +
    213A  VAL*     4.1    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  CYS*     3.4    11.7    -      -       -      -
    156A  GLY      3.4    32.5    -      -       -      -
    157A  ALA*     3.6    10.1    -      -       -      -
    160A  LEU*     3.9    21.5    -      -       +      -
    183A  LEU*     3.9     2.0    -      -       +      -
    184A  ILE*     1.3    70.2    -      -       -      +
    186A  VAL*     1.3    57.9    +      -       -      +
    187A  THR*     3.8    13.6    +      -       -      +
    193A  ALA*     4.4     4.0    -      -       -      -
    210A  ILE*     5.2     5.4    -      -       +      -
    211A  HIS      2.9    13.4    +      -       -      +
    212A  VAL*     3.5     9.2    -      -       +      -
    213A  VAL*     2.6    33.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  LEU*     3.3    42.1    -      -       +      +
     30A  LEU*     3.8    26.7    -      -       +      -
     31A  ALA*     3.9    29.2    -      -       +      +
    154A  LEU*     4.1     9.9    -      -       +      -
    155A  CYS      3.1     8.1    +      -       -      +
    156A  GLY*     3.6    14.6    -      -       -      -
    184A  ILE*     3.7     0.6    +      -       +      -
    185A  CYS*     1.3    71.6    -      -       -      +
    187A  THR*     1.3    69.5    +      -       -      +
    213A  VAL*     3.4    22.9    -      -       +      +
    215A  GLU*     4.6     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  LEU*     5.8     0.4    -      -       -      -
    156A  GLY*     5.0     0.2    -      -       -      -
    157A  ALA*     4.3    19.5    -      -       +      +
    185A  CYS*     4.2    11.7    -      -       -      +
    186A  VAL*     1.3    80.8    -      -       -      +
    188A  ARG*     1.3    67.5    +      -       -      +
    189A  ALA*     2.8    19.6    +      -       -      +
    190A  GLY*     3.8    23.6    -      -       -      -
    193A  ALA*     4.1    15.0    -      -       +      -
    212A  VAL*     4.6     1.6    -      -       +      -
    213A  VAL      2.8    16.1    +      -       -      +
    214A  ASN*     3.5     5.7    -      -       -      +
    215A  GLU*     2.9    25.3    +      -       -      -
----------------------------------------------------------
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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