Contacts of the strand formed by residues 185 - 191 (chain A) in PDB entry 1OBZ


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 LYS 185 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  ILE*     3.9    22.2    -      -       +      -
    117A  LEU      3.0     9.2    -      -       -      +
    118A  CYS*     4.2    22.9    -      -       +      -
    162A  ASN*     4.5     5.0    +      -       -      +
    181A  ALA*     5.1     0.3    -      -       -      +
    182A  PHE      3.9    14.6    -      -       -      +
    183A  GLY      3.6     0.4    -      -       -      -
    184A  GLU*     1.3    88.1    -      -       +      +
    186A  ILE*     1.3    67.3    +      -       -      +
    187A  THR*     5.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  ILE*     3.4     2.5    -      -       -      -
    117A  LEU*     2.8    45.2    +      -       +      +
    119A  LYS*     3.9    26.2    -      -       +      -
    125A  ILE*     4.0    25.4    -      -       +      -
    161A  ILE*     3.9    20.4    -      -       +      -
    162A  ASN*     3.8     9.0    -      -       -      +
    178A  LEU*     4.1    29.2    -      -       +      +
    181A  ALA*     3.9    13.5    -      -       +      -
    185A  LYS*     1.3    79.4    -      -       -      +
    187A  THR*     1.3    73.8    +      -       -      +
    188A  MET*     4.3     9.2    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
    114A  GLU*     3.5    40.8    -      -       +      +
    115A  VAL      3.3     5.4    -      -       -      +
    116A  ILE*     3.9    15.7    -      -       +      +
    161A  ILE*     3.5     1.0    -      -       -      -
    162A  ASN*     2.7    47.0    +      -       -      +
    163A  GLY      5.6     2.5    -      -       -      +
    185A  LYS      5.6     0.5    -      -       -      -
    186A  ILE*     1.3    77.0    -      -       -      +
    188A  MET*     1.3    68.2    +      -       -      +
    189A  THR*     5.4     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  ARG      3.8     0.3    -      -       -      +
    114A  GLU*     3.5     4.9    -      -       -      +
    115A  VAL*     2.9    43.9    +      -       +      +
    117A  LEU*     4.1    20.6    -      -       +      -
    127A  LEU*     4.1    27.8    -      -       +      -
    129A  LEU*     4.7     3.4    -      -       +      -
    152A  LEU*     4.2     7.6    -      -       +      -
    158A  VAL*     3.4    37.0    -      -       +      -
    160A  GLN      3.2     6.7    -      -       -      +
    161A  ILE*     4.1    18.6    -      -       +      -
    178A  LEU*     5.1     4.5    -      -       +      -
    186A  ILE*     4.3    11.7    -      -       +      -
    187A  THR*     1.3    82.7    -      -       -      +
    189A  THR*     1.3    62.7    +      -       -      +
    190A  ILE*     3.9     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  PRO*     3.7    27.6    -      -       +      -
    113A  ARG      3.4     8.3    -      -       -      +
    114A  GLU*     4.7    10.5    +      -       +      +
    158A  VAL*     3.6     4.0    -      -       -      -
    159A  LEU*     2.8    34.7    +      -       +      -
    160A  GLN*     2.9    41.5    +      -       -      +
    163A  GLY*     5.7     1.2    +      -       -      -
    187A  THR*     5.4     1.6    -      -       -      +
    188A  MET*     1.3    73.5    -      -       -      +
    190A  ILE*     1.3    59.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  ASP      4.8     0.2    -      -       -      +
    112A  PRO*     3.2     6.8    -      -       -      +
    113A  ARG*     2.8    50.4    +      -       +      +
    115A  VAL*     3.9    19.3    -      -       +      -
    152A  LEU*     3.8    26.2    -      -       +      -
    156A  ASP*     3.9    19.1    -      -       +      +
    157A  GLN      3.4     5.8    -      -       -      +
    158A  VAL*     3.9    23.3    -      -       +      -
    159A  LEU*     5.0     0.2    -      -       -      -
    188A  MET*     3.9    17.3    -      -       +      -
    189A  THR*     1.3    80.6    -      -       -      +
    191A  ARG*     1.3    70.0    +      -       -      +
    192A  ASP*     3.7    20.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  ASP      5.5     1.6    -      -       -      -
    112A  PRO*     4.6    10.1    -      -       +      +
    156A  ASP*     3.7     0.7    -      -       -      -
    157A  GLN*     2.9    70.4    +      -       +      +
    159A  LEU*     3.9    25.5    -      -       +      +
    189A  THR      4.4     0.4    +      -       -      -
    190A  ILE*     1.3    72.9    -      -       -      +
    192A  ASP*     1.3    66.5    +      -       -      +
    193A  ARG      3.3     0.2    +      -       -      -
    194A  PRO*     3.6    12.6    -      -       +      +
    197B  ARG*     3.5    48.3    -      -       -      +
    199B  ILE*     3.7    19.0    -      -       -      +
    230B  ASN*     2.7    28.9    +      -       -      +
    231B  GLY      3.2    20.2    +      -       -      -
    233B  LEU*     5.3     2.0    -      -       -      +
----------------------------------------------------------
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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