Contacts of the strand formed by residues 264 - 271 (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 VAL 264 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200B  THR*     3.6    28.9    -      -       +      -
    201B  MET      3.6     4.5    -      -       -      +
    202B  HIS*     3.8    21.3    -      -       +      +
    242B  ASN*     3.6    12.3    +      -       -      +
    261B  SER*     3.6     9.4    +      -       -      -
    262B  GLY*     3.2     1.9    -      -       -      +
    263B  THR*     1.3    81.8    -      -       +      +
    265B  VAL*     1.3    62.3    +      -       -      +
    266B  THR*     4.1     9.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 265 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199B  ILE      3.6     1.9    -      -       -      +
    200B  THR*     3.6     0.7    -      -       -      -
    201B  MET*     2.9    40.0    +      -       +      +
    203B  LYS*     4.0    12.8    -      -       -      -
    209B  VAL*     3.7    30.1    -      -       +      -
    241B  ILE*     4.2     9.0    -      -       +      -
    242B  ASN*     3.7     2.2    -      -       -      -
    258B  LEU*     3.8    28.5    -      -       +      +
    261B  SER*     3.7    17.3    -      -       -      +
    262B  GLY      3.8     7.0    -      -       -      +
    263B  THR      3.9     3.8    -      -       -      +
    264B  VAL*     1.3    73.6    -      -       -      +
    266B  THR*     1.3    63.4    +      -       -      +
    267B  ILE*     3.8    18.1    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 266 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198B  THR*     3.5    28.0    -      -       +      -
    199B  ILE      3.5     3.1    -      -       -      +
    200B  THR*     3.7    22.2    +      -       -      +
    240B  GLU      3.9     0.9    -      -       -      +
    241B  ILE*     3.4     3.5    -      -       -      +
    242B  ASN*     2.8    48.2    +      -       -      +
    243B  GLY      4.7     1.5    +      -       -      +
    264B  VAL*     4.1     7.4    -      -       -      +
    265B  VAL*     1.3    73.9    -      -       -      +
    267B  ILE*     1.3    62.4    +      -       -      +
    268B  THR*     4.3     1.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 267 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197B  ARG      3.7     0.9    -      -       -      +
    198B  THR*     3.3     2.7    -      -       -      -
    199B  ILE*     2.8    41.4    +      -       -      +
    201B  MET*     3.4    30.3    -      -       +      -
    211B  PHE*     3.5    31.6    -      -       +      -
    218B  ILE*     5.4     1.3    -      -       +      -
    232B  LEU*     5.3     3.8    -      -       +      -
    238B  ILE*     3.9    19.1    -      -       +      -
    240B  GLU      3.4     9.4    -      -       -      +
    241B  ILE*     4.3     9.0    -      -       +      -
    258B  LEU*     4.1     4.9    -      -       +      -
    265B  VAL*     3.8    16.8    -      -       +      -
    266B  THR*     1.3    78.8    -      -       -      +
    268B  THR*     1.3    64.0    +      -       -      +
    269B  ILE*     3.7    25.8    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 268 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  ARG*     3.4     4.5    -      -       -      +
    196B  GLU*     3.3    40.4    -      -       +      -
    197B  ARG      3.4     2.5    -      -       -      -
    198B  THR*     3.3    21.2    +      -       -      +
    238B  ILE      3.9     0.2    -      -       -      -
    239B  CYS*     2.8    26.9    +      -       -      +
    240B  GLU*     2.9    41.9    +      -       -      +
    266B  THR*     4.3     2.1    +      -       -      +
    267B  ILE*     1.3    73.5    -      -       -      +
    269B  ILE*     1.3    62.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 269 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195B  PHE      4.0     0.3    -      -       -      +
    196B  GLU*     3.5     5.5    -      -       -      +
    197B  ARG*     2.9    49.5    +      -       +      +
    199B  ILE*     4.2    13.9    -      -       +      -
    218B  ILE*     3.8    18.6    -      -       +      -
    232B  LEU*     4.0    23.1    -      -       +      -
    233B  LEU*     4.5    11.2    -      -       +      +
    236B  HIS*     3.5    30.7    -      -       +      -
    237B  ASN      3.2    12.1    -      -       -      +
    238B  ILE*     4.5     1.8    -      -       -      -
    239B  CYS*     4.4     3.6    -      -       -      -
    267B  ILE*     3.7    22.2    -      -       +      +
    268B  THR*     1.3    80.8    -      -       -      +
    270B  MET*     1.3    63.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 270 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137B  PHE*     4.7    11.7    -      -       +      -
    154B  PHE*     4.1    15.5    -      -       -      -
    155B  GLY*     3.4    43.1    -      -       -      +
    193B  ARG*     3.8    14.4    -      -       +      -
    194B  PRO*     3.7    25.1    -      -       +      +
    195B  PHE*     4.1     7.4    -      -       +      +
    236B  HIS*     3.5     4.9    -      -       -      -
    237B  ASN*     2.8    32.6    +      -       +      +
    239B  CYS*     4.0    11.7    -      -       -      -
    269B  ILE*     1.3    77.2    -      -       -      +
    271B  PRO*     1.3    85.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 271 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  PHE*     3.9    17.9    -      -       +      -
    271A  PRO*     5.0     4.3    -      -       +      -
    273A  PHE*     4.0    22.7    -      -       +      -
    195B  PHE*     3.4    35.0    -      -       +      +
    235B  GLU      3.9     0.9    -      -       -      +
    236B  HIS*     3.3    31.3    -      -       +      +
    237B  ASN*     4.5     1.7    +      -       -      -
    270B  MET*     1.3    99.1    -      -       +      +
    272B  ALA*     1.3    62.7    +      -       -      +
----------------------------------------------------------
 Back to top of page


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