Contacts of the strand formed by residues 50 - 55 (chain E) in PDB entry 1XBT


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 CYS 50 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40E  VAL*     3.9    27.1    -      -       +      -
     43E  PHE*     4.2     2.9    -      -       -      -
     44E  GLN*     3.8    41.9    +      -       -      +
     48E  TYR      3.6    16.0    +      -       -      -
     49E  LYS*     1.3    75.6    -      -       -      +
     51E  LEU*     1.3    62.2    +      -       -      +
     52E  VAL*     5.7     0.9    -      -       +      -
     91E  VAL*     3.6     6.8    -      -       -      +
     93E  VAL*     3.3    25.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 51 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40E  VAL*     5.5     0.5    -      -       -      +
     50E  CYS*     1.3    76.7    -      -       -      +
     52E  VAL*     1.3    68.9    +      -       -      +
     53E  ILE*     4.2    18.8    -      -       +      -
     75E  ALA      5.7     1.1    -      -       -      +
     76E  LEU*     3.7    35.0    -      -       +      +
     84E  VAL      4.7     1.6    -      -       -      +
     87E  GLU*     3.9    12.6    -      -       +      +
     88E  ALA*     3.6    40.6    -      -       +      +
     91E  VAL*     4.0    15.9    -      -       +      -
     93E  VAL      2.9     6.9    +      -       -      +
     94E  ILE*     3.3     5.0    -      -       +      -
     95E  GLY      2.7    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 52 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36E  LEU*     4.5     6.3    -      -       +      -
     37E  MET*     3.3    43.1    -      -       +      -
     40E  VAL*     4.2    24.9    -      -       +      -
     50E  CYS*     5.7     0.9    -      -       +      -
     51E  LEU*     1.3    84.1    -      -       -      +
     53E  ILE*     1.3    71.1    +      -       -      +
     54E  LYS*     5.8     1.8    -      -       +      -
     75E  ALA*     3.3    19.1    -      -       +      +
     76E  LEU      2.8    26.2    +      -       -      -
     95E  GLY      3.3    11.4    -      -       -      +
     97E  ASP*     5.2     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 53 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51E  LEU*     4.2    15.5    -      -       +      -
     52E  VAL*     1.3    79.0    -      -       -      +
     54E  LYS*     1.3    62.0    +      -       -      +
     76E  LEU      3.3    11.2    -      -       -      +
     78E  ALA*     4.0    12.8    -      -       +      -
     81E  LEU*     3.8    29.2    -      -       +      -
     84E  VAL*     3.3    31.0    -      -       +      -
     94E  ILE*     3.7    28.0    -      -       +      -
     95E  GLY      2.7    11.0    +      -       -      +
     96E  ILE*     3.5     5.6    -      -       +      -
     97E  ASP*     2.8    29.5    +      -       -      +
    102E  PHE*     4.0    14.6    -      -       +      -
    108E  PHE*     4.2     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 54 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52E  VAL*     4.3     1.8    +      -       +      -
     53E  ILE*     1.3    74.9    -      -       -      +
     55E  TYR*     1.3    72.9    +      -       -      +
     58E  ASP*     3.8    21.3    +      -       -      +
     59E  THR      5.5     0.4    -      -       -      -
     60E  ARG*     4.3    16.1    +      -       -      +
     75E  ALA*     5.4     9.2    -      -       +      +
     76E  LEU      3.0    10.1    +      -       -      +
     77E  PRO*     3.4     6.1    -      -       +      +
     78E  ALA*     2.9    26.9    +      -       -      +
     97E  ASP*     3.8    27.8    +      -       +      +
     98E  GLU*     3.9    20.4    -      -       +      +
    102E  PHE*     3.9     5.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 55 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54E  LYS*     1.3    80.5    -      -       -      +
     56E  ALA*     1.3    63.8    +      -       -      +
     57E  LYS*     3.2    36.4    +      -       +      +
     58E  ASP*     3.2    33.6    +      -       +      +
     77E  PRO*     5.2     0.2    -      -       -      -
     78E  ALA      3.5    11.2    -      -       -      -
     79E  CYS*     4.5    16.6    -      -       -      -
     97E  ASP      3.9     2.8    +      -       -      -
     98E  GLU*     4.3    17.5    -      -       +      +
    101E  PHE*     3.4    53.4    +      +       +      +
    102E  PHE*     3.7    20.9    -      +       +      -
    173E  GLU*     2.7    34.7    +      -       -      -
    175E  ILE*     4.6     2.0    -      -       +      -
----------------------------------------------------------
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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