Contacts of the strand formed by residues 195 - 201 (chain C) in PDB entry 2IK8


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 HIS 195 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33C  GLU*     3.7    26.1    -      -       +      +
     34C  VAL*     3.1    24.5    +      -       -      +
    189C  PHE      3.5     3.4    -      -       -      -
    190C  THR*     2.8    34.6    +      -       +      +
    193C  ASP      6.1     0.7    -      -       -      -
    194C  LEU*     1.3    70.1    -      -       -      +
    196C  PHE*     1.3    63.3    +      -       -      +
    197C  LYS*     3.6     1.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 196 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34C  VAL*     3.5    29.6    -      -       +      -
     36C  LEU*     4.4    14.4    -      -       +      -
    188C  HIS*     3.4     8.3    -      -       -      +
    189C  PHE*     2.6    81.3    +      +       +      +
    191C  PHE*     3.8    16.6    -      +       +      -
    194C  LEU*     3.5    42.4    -      -       +      -
    195C  HIS*     1.3    70.3    -      -       -      +
    197C  LYS*     1.3    60.9    +      -       -      +
    198C  MET      3.6     2.9    +      -       -      +
    336C  PHE*     3.7    23.6    -      +       -      -
    340C  THR*     4.0    13.0    -      -       +      -
    343C  ILE*     4.7     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 197 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33C  GLU*     3.2    27.1    -      -       -      +
     34C  VAL      2.8    13.1    +      -       -      +
     35C  LYS*     3.4     6.8    -      -       +      -
     36C  LEU      3.0    22.3    +      -       -      -
    187C  THR      3.8     5.4    -      -       -      -
    188C  HIS*     4.0    23.3    -      -       +      +
    195C  HIS*     4.7     2.5    -      -       +      +
    196C  PHE*     1.3    72.5    -      -       -      +
    198C  MET*     1.3    59.0    +      -       -      +
    199C  PHE*     3.4    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 198 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  LEU*     3.4    39.5    -      -       +      +
     38C  LEU*     3.9    16.8    -      -       +      -
     49C  ILE*     5.1     3.4    -      -       +      -
     50C  VAL*     3.5    37.2    -      -       +      -
     53C  MET*     3.6    36.1    -      -       +      -
    185C  VAL      3.9     0.5    -      -       -      +
    186C  GLU*     3.5     2.8    -      -       -      -
    187C  THR*     2.9    42.8    +      -       -      +
    189C  PHE*     3.8    21.3    -      -       +      -
    196C  PHE*     3.6     1.9    -      -       +      -
    197C  LYS*     1.3    72.6    -      -       -      +
    199C  PHE*     1.3    65.0    +      -       -      +
    200C  ASP      4.8     0.2    -      -       -      +
    222C  ILE*     5.5     0.4    -      -       +      -
    336C  PHE*     4.6     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 199 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  LYS*     4.0    33.2    -      -       +      -
     36C  LEU      2.6    16.9    +      -       -      +
     37C  LEU*     3.8    11.4    -      -       +      -
     38C  LEU*     2.9    30.7    +      -       -      +
    184C  ILE*     3.8    26.7    -      -       +      -
    185C  VAL      3.6     2.0    -      -       -      -
    186C  GLU*     3.8    24.2    -      -       +      -
    188C  HIS*     6.4     1.1    -      +       -      -
    197C  LYS*     3.4    31.6    -      -       +      -
    198C  MET*     1.3    75.2    -      -       -      +
    200C  ASP*     1.3    60.5    +      -       -      +
    201C  VAL*     4.6     2.9    -      -       +      +
    214C  CYS*     4.2    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 200 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  LEU*     4.1     3.6    -      -       -      +
     46C  LYS*     3.2    24.8    -      -       -      +
     47C  SER*     2.8    31.1    +      -       -      -
     50C  VAL*     3.7    28.8    -      -       +      +
    181C  THR*     4.0     8.4    +      -       -      +
    183C  GLY      3.9     0.2    -      -       -      +
    184C  ILE*     3.4     5.4    -      -       -      +
    185C  VAL*     2.8    50.5    +      -       +      +
    187C  THR*     5.9     0.4    -      -       -      +
    198C  MET*     4.1     0.8    +      -       -      +
    199C  PHE*     1.3    71.2    -      -       -      +
    201C  VAL*     1.3    76.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 201 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  LEU      3.2    20.6    +      -       -      +
     39C  LEU*     3.7    18.4    -      -       +      -
     46C  LYS*     3.0    27.7    -      -       +      -
    181C  THR*     4.4     5.6    -      -       -      -
    183C  GLY      3.4     8.1    -      -       -      +
    184C  ILE*     4.1    22.2    -      -       +      -
    199C  PHE*     4.6     3.6    -      -       +      +
    200C  ASP*     1.3    92.6    +      -       -      +
    202C  GLY*     1.3    61.7    +      -       -      +
    211C  TRP*     3.6    32.5    -      -       +      +
    214C  CYS*     4.5    11.7    -      -       -      -
    355C  ALF      3.8     6.1    -      -       -      -
----------------------------------------------------------
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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