Contacts of the strand formed by residues 299 - 304 (chain B) in PDB entry 4OBZ


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 299 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294B  VAL      4.0     0.5    -      -       -      +
    295B  SER*     3.3     4.4    -      -       -      -
    296B  GLN*     2.9    49.2    +      -       +      +
    297B  ALA*     3.3    35.9    -      -       -      +
    298B  GLY*     1.3    82.0    -      -       -      +
    300B  THR*     1.4    63.4    +      -       -      +
    301B  LEU*     4.3     2.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 300 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265B  CYS*     4.3    15.1    -      -       +      -
    293B  LYS*     3.5    40.9    +      -       +      +
    294B  VAL      3.7     3.4    -      -       -      +
    295B  SER*     3.1    18.9    +      -       -      +
    298B  GLY      5.6     0.3    -      -       -      -
    299B  LYS*     1.4    74.5    -      -       -      +
    301B  LEU*     1.3    72.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 301 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256B  LEU*     6.2     1.1    -      -       +      -
    262B  MET*     3.7    35.0    -      -       +      -
    263B  ILE      5.5     3.4    -      -       -      +
    265B  CYS*     4.2     2.5    -      -       -      -
    292B  LEU      3.5     0.3    -      -       -      +
    293B  LYS*     3.6     4.7    -      -       -      -
    294B  VAL*     2.9    40.8    +      -       +      +
    296B  GLN*     4.9    14.4    -      -       +      +
    299B  LYS*     4.3     2.4    -      -       +      -
    300B  THR*     1.3    79.5    -      -       -      +
    302B  CYS*     1.3    65.5    +      -       -      +
    303B  LEU      3.9     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 302 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  MET*     3.6     7.0    -      -       -      +
    263B  ILE*     2.9    44.6    +      -       +      +
    265B  CYS*     2.1    50.2    -      -       -      -
    268B  VAL*     4.1    20.0    -      -       +      -
    291B  THR*     5.1     6.7    -      -       -      -
    292B  LEU      3.5     5.4    -      -       -      +
    293B  LYS*     4.6    17.0    -      -       -      -
    301B  LEU*     1.3    76.5    -      -       -      +
    303B  LEU*     1.3    61.9    +      -       -      +
    304B  SER      3.7     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 303 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236B  LEU*     4.3    26.5    -      -       +      -
    256B  LEU*     5.0     0.7    -      -       +      -
    260B  GLU*     4.4    27.8    -      -       +      +
    261B  TYR      3.6    17.3    -      -       -      +
    262B  MET*     3.7    25.4    -      -       +      -
    263B  ILE*     4.9     0.2    -      -       -      -
    291B  THR*     3.4     3.5    -      -       -      -
    292B  LEU*     2.8    54.6    +      -       +      +
    294B  VAL*     4.2    18.6    -      -       +      -
    301B  LEU      3.9     1.0    +      -       -      -
    302B  CYS*     1.3    73.5    -      -       -      +
    304B  SER*     1.3    70.4    +      -       -      +
    305B  GLY      3.5     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 304 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236B  LEU*     4.1     6.4    -      -       -      +
    248B  GLN*     2.7    30.8    +      -       -      -
    251B  ILE*     4.1    11.1    -      -       -      +
    260B  GLU*     6.1     0.2    -      -       -      -
    261B  TYR      3.1    22.6    +      -       -      +
    263B  ILE*     3.7    23.5    -      -       -      +
    290B  TYR*     4.0     3.8    +      -       -      -
    302B  CYS      3.7     2.6    +      -       -      -
    303B  LEU*     1.3    84.4    -      -       -      +
    305B  GLY*     1.3    59.7    +      -       -      +
    306B  PHE*     3.0    19.3    +      -       -      +
----------------------------------------------------------
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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