Contacts of the strand formed by residues 70 - 75 (chain D) in PDB entry 2BX5


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 ASP 70 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  THR*     5.6     2.8    -      -       -      +
     23D  CYS      4.9     0.9    -      -       -      -
     24D  ARG*     2.4    38.9    +      -       -      +
     65D  SER      4.6     0.2    -      -       -      -
     66D  GLY*     3.5    19.9    -      -       -      -
     67D  SER      3.9     5.4    +      -       -      +
     68D  GLY*     3.6     2.8    -      -       -      -
     69D  THR*     1.3    78.2    -      -       -      +
     71D  PHE*     1.3    68.6    +      -       -      +
     72D  THR*     5.1     2.6    +      -       -      -
     18E  ARG*     3.8    21.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 71 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  MET*     5.1     0.4    -      -       +      -
     22D  THR*     3.5     4.0    -      -       -      -
     23D  CYS      2.9    34.0    +      -       -      +
     25D  ALA*     4.8     2.2    -      -       +      -
     29D  ILE*     3.6    26.0    -      -       +      -
     31D  SER*     4.2     5.6    -      -       -      -
     33D  LEU*     3.5    46.4    -      -       +      -
     35D  TRP*     4.1     3.8    -      -       +      -
     51D  ALA*     4.1    10.3    -      -       +      -
     65D  SER      3.2    16.8    -      -       -      +
     66D  GLY      3.8     8.1    -      -       -      -
     67D  SER*     3.7    17.0    -      -       -      -
     68D  GLY      3.2    40.2    -      -       -      -
     69D  THR      3.4    16.8    -      -       -      -
     70D  ASP*     1.3    75.9    -      -       -      +
     72D  THR*     1.3    69.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 72 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20D  THR*     4.1    10.5    -      -       +      -
     21D  ILE      3.3    10.3    -      -       -      +
     22D  THR*     3.3    21.2    -      -       +      +
     35D  TRP*     3.6     9.9    -      -       -      -
     63D  SER      3.7     0.3    -      -       -      +
     64D  GLY*     3.5     6.1    -      -       -      -
     65D  SER*     3.3    41.9    +      -       -      +
     70D  ASP*     5.1     3.3    +      -       -      -
     71D  PHE*     1.3    83.9    +      -       -      +
     73D  LEU*     1.3    64.3    +      -       -      +
     74D  THR*     4.0    18.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 73 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  VAL*     3.8     1.6    -      -       -      +
     20D  THR*     3.4     3.8    +      -       -      -
     21D  ILE*     2.4    76.3    +      -       +      +
     35D  TRP*     3.4    51.1    -      -       +      -
     47D  LEU*     5.2     3.1    -      -       +      -
     48D  ILE*     3.9    16.8    -      -       +      -
     62D  PHE*     5.2     6.3    -      -       +      -
     63D  SER      3.5     8.5    -      -       -      +
     72D  THR*     1.3    71.5    -      -       -      +
     74D  THR*     1.3    65.9    +      -       -      +
     75D  ILE*     4.0    12.6    +      -       +      +
     86D  TYR*     4.1    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 74 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  ARG*     3.6    37.4    +      -       +      +
     19D  VAL      3.4     5.6    -      -       -      +
     20D  THR*     3.8     9.5    +      -       -      +
     61D  ARG      2.9     5.0    -      -       -      +
     62D  PHE*     3.5     1.9    -      -       -      -
     63D  SER*     2.9    47.7    +      -       -      -
     72D  THR*     4.0    12.2    -      -       -      +
     73D  LEU*     1.3    73.8    -      -       -      +
     75D  ILE*     1.3    75.4    +      -       -      +
     76D  SER*     3.9     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 75 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  ASP      3.9     0.3    -      -       -      +
     18D  ARG*     3.5     0.3    -      -       -      -
     19D  VAL*     3.3    46.2    +      -       +      +
     21D  ILE*     5.7     0.2    -      -       +      -
     61D  ARG*     3.3    15.3    -      -       +      +
     62D  PHE*     4.4    17.5    -      -       +      +
     73D  LEU*     4.0    10.9    -      -       +      -
     74D  THR*     1.3    74.7    -      -       -      +
     76D  SER*     1.3    68.0    +      -       -      +
     77D  SER      3.5    26.0    -      -       -      +
     78D  LEU*     3.6    26.0    -      -       +      -
     82D  ASP*     3.6    15.0    -      -       +      +
     86D  TYR*     4.0    32.8    -      -       +      +
----------------------------------------------------------
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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