Contacts of the strand formed by residues 70 - 75 (chain F) 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 F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22F  THR*     5.5     0.2    -      -       -      +
     23F  CYS      4.7     1.2    +      -       -      +
     24F  ARG*     3.6    25.6    +      -       +      +
     66F  GLY*     3.8    18.5    -      -       -      -
     67F  SER      3.8     6.5    +      -       -      +
     69F  THR*     1.3    79.1    -      -       -      +
     71F  PHE*     1.3    75.6    +      -       -      +
     72F  THR*     4.1    10.4    +      -       -      -
     18G  ARG*     2.7    43.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 71 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4F  MET*     5.0     2.5    -      -       +      -
     21F  ILE      3.8     0.2    -      -       -      +
     22F  THR*     3.3     5.4    -      -       -      +
     23F  CYS*     2.9    47.0    +      -       +      +
     29F  ILE*     3.7    25.6    -      -       +      -
     31F  SER*     4.6     7.6    -      -       -      -
     33F  LEU*     3.4    43.7    -      -       +      -
     35F  TRP*     4.8     2.0    -      -       +      -
     51F  ALA*     4.8     9.2    -      -       -      -
     65F  SER      3.7     8.3    -      -       -      -
     66F  GLY      3.0    27.6    -      -       -      -
     67F  SER*     3.9    12.8    -      -       -      -
     68F  GLY      3.7    22.9    -      -       -      -
     69F  THR      3.5    14.6    -      -       -      -
     70F  ASP*     1.3    89.7    -      -       -      +
     72F  THR*     1.3    66.6    +      -       -      +
     73F  LEU      4.2     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 72 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20F  THR*     3.4    25.1    -      -       +      -
     21F  ILE      3.1    14.4    -      -       -      +
     22F  THR*     3.6    15.8    -      -       +      +
     35F  TRP*     4.6     1.5    -      -       -      +
     63F  SER      3.3     6.1    -      -       -      +
     64F  GLY*     4.5     0.4    -      -       -      -
     65F  SER*     3.1    44.7    +      -       -      +
     70F  ASP*     4.1     7.6    +      -       -      -
     71F  PHE*     1.3    80.8    +      -       -      +
     73F  LEU*     1.3    71.2    +      -       -      +
     74F  THR*     3.8     6.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 73 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20F  THR      3.7     0.3    -      -       -      -
     21F  ILE*     2.9    61.2    +      -       +      +
     35F  TRP*     3.4    48.2    -      -       +      +
     47F  LEU*     5.2     3.6    -      -       +      -
     48F  ILE*     4.1    14.8    -      -       +      -
     62F  PHE*     4.1    15.9    -      -       +      -
     63F  SER      3.5     3.6    -      -       -      -
     64F  GLY*     4.6     1.6    -      -       -      -
     72F  THR*     1.3    76.4    -      -       -      +
     74F  THR*     1.3    75.7    +      -       -      +
     75F  ILE*     4.0    20.6    -      -       +      -
     86F  TYR*     3.8    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 74 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18F  ARG*     3.9    26.7    -      -       -      -
     19F  VAL      3.5     5.8    -      -       -      +
     20F  THR*     3.9    13.4    -      -       -      +
     61F  ARG      3.3     4.2    -      -       -      +
     62F  PHE*     3.4     2.9    -      -       -      -
     63F  SER*     2.9    51.8    +      -       -      +
     65F  SER*     5.4     1.0    +      -       -      -
     72F  THR*     3.8     8.7    +      -       -      +
     73F  LEU*     1.3    80.7    +      -       -      +
     75F  ILE*     1.3    61.4    +      -       -      +
     76F  SER*     4.4     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 75 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17F  ASP      3.4     3.5    -      -       -      +
     18F  ARG*     3.4     0.7    -      -       -      -
     19F  VAL*     2.7    58.0    +      -       +      +
     21F  ILE*     4.9     0.2    -      -       +      -
     61F  ARG*     3.3    26.0    -      -       +      +
     62F  PHE*     3.7    24.2    -      -       +      -
     73F  LEU*     4.0    13.7    -      -       +      -
     74F  THR*     1.3    75.8    -      -       -      +
     76F  SER*     1.3    62.1    +      -       -      +
     77F  SER      3.4     1.0    +      -       -      -
     78F  LEU*     4.2    28.0    -      -       +      +
     82F  ASP*     4.5     2.9    -      -       -      +
     86F  TYR*     3.6    34.1    -      -       +      +
    104F  VAL*     4.7     2.7    -      -       +      -
----------------------------------------------------------
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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