Contacts of the strand formed by residues 236 - 241 (chain B) 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 HIS 236 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  ASP*     3.2    20.4    -      -       -      -
    195A  PHE*     3.7    16.0    -      +       -      -
    197B  ARG*     5.8     2.3    -      -       +      +
    217B  LYS*     3.2     5.1    -      -       -      +
    218B  ILE*     2.9    29.2    +      -       +      +
    233B  LEU*     3.6    38.5    -      -       +      +
    234B  THR      2.9    18.6    +      -       -      -
    235B  GLU*     1.3    80.0    +      -       -      +
    237B  ASN*     1.3    62.4    +      -       -      +
    238B  ILE      3.7     0.5    +      -       -      -
    269B  ILE*     3.5    33.9    -      -       +      -
    270B  MET      3.4     6.3    -      -       -      +
    271B  PRO*     3.3    39.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 237 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154B  PHE*     4.0    33.3    -      -       +      -
    215B  ASN      5.0     2.1    -      -       -      +
    216B  GLY      3.6     6.6    -      -       -      +
    217B  LYS*     4.0    13.3    -      -       -      +
    235B  GLU      4.3     0.2    -      -       -      -
    236B  HIS*     1.3    72.0    -      -       -      +
    238B  ILE*     1.3    64.8    +      -       -      +
    239B  CYS*     3.5     3.1    +      -       -      -
    247B  ILE*     5.0     4.0    -      -       +      -
    269B  ILE*     3.2     8.7    -      -       -      -
    270B  MET*     2.8    34.6    +      -       +      +
    271B  PRO      4.5     1.2    +      -       -      -
    272B  ALA*     3.5    34.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 238 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211B  PHE*     4.2    11.4    -      -       +      -
    213B  PHE*     4.0    36.3    -      -       +      -
    216B  GLY*     3.0    20.1    +      -       -      +
    218B  ILE*     3.9    27.1    -      -       +      -
    236B  HIS      4.6     0.2    -      -       -      +
    237B  ASN*     1.3    69.4    -      -       -      +
    239B  CYS*     1.3    60.5    +      -       -      +
    240B  GLU      4.5     0.7    -      -       -      +
    241B  ILE*     3.8    24.7    -      -       +      -
    246B  VAL*     3.4    30.8    -      -       +      +
    247B  ILE*     3.5    13.5    -      -       -      +
    254B  ILE*     4.3    11.0    -      -       +      +
    267B  ILE*     3.9    12.8    -      -       +      -
    268B  THR      4.0     2.9    -      -       -      -
    269B  ILE*     4.5     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 239 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154B  PHE*     3.9    24.7    -      -       -      -
    193B  ARG*     3.6    39.9    -      -       -      +
    237B  ASN      3.9    12.1    -      -       -      -
    238B  ILE*     1.3    73.9    -      -       -      +
    240B  GLU*     1.3    61.7    +      -       -      +
    245B  ASN*     3.6    10.7    -      -       -      +
    246B  VAL*     3.0    25.8    +      -       -      +
    247B  ILE*     3.8     7.3    +      -       +      +
    268B  THR      2.8    17.2    +      -       -      +
    269B  ILE      4.4     0.9    -      -       -      -
    270B  MET*     4.0    19.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 240 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153B  ARG*     4.3    16.9    +      -       -      +
    193B  ARG*     2.9    43.0    +      -       -      -
    196B  GLU*     4.6     0.2    -      -       -      +
    239B  CYS*     1.3    82.6    -      -       -      +
    241B  ILE*     1.3    65.2    +      -       -      +
    242B  ASN      4.2     0.4    -      -       -      -
    243B  GLY*     4.1    19.1    -      -       -      +
    244B  GLN      3.0    20.9    -      -       -      +
    245B  ASN*     4.0    10.8    -      -       +      +
    246B  VAL*     4.5     0.7    -      -       -      +
    247B  ILE*     5.8     0.3    -      -       -      +
    266B  THR      3.9     0.2    -      -       -      +
    267B  ILE*     3.4     6.1    -      -       -      +
    268B  THR*     2.9    46.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 241 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  ILE*     3.8    20.2    -      -       +      -
    240B  GLU*     1.3    77.3    -      -       -      +
    242B  ASN*     1.3    85.5    +      -       -      +
    243B  GLY      3.1     0.2    -      -       -      -
    244B  GLN*     3.0    24.2    +      -       -      +
    246B  VAL*     4.2    11.4    -      -       +      +
    254B  ILE*     3.9    28.7    -      -       +      +
    257B  ILE*     3.8    28.2    -      -       +      +
    258B  LEU*     4.0    22.2    -      -       +      -
    261B  SER*     5.6     0.4    -      -       -      +
    265B  VAL*     4.2    16.6    -      -       +      -
    266B  THR      3.4     6.5    -      -       -      +
    267B  ILE*     4.3     9.2    -      -       +      -
----------------------------------------------------------
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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