Contacts of the strand formed by residues 50 - 55 (chain F) 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 F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40F  VAL*     3.9    25.6    -      -       +      -
     43F  PHE*     4.3     2.7    -      -       -      -
     44F  GLN*     3.8    42.5    +      -       -      +
     48F  TYR      3.5    14.3    +      -       -      -
     49F  LYS*     1.3    83.2    -      -       -      +
     51F  LEU*     1.3    63.9    +      -       -      +
     52F  VAL*     5.8     0.2    -      -       +      -
     91F  VAL*     3.9     7.8    -      -       -      +
     93F  VAL*     3.3    20.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 51 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40F  VAL*     5.5     0.3    -      -       -      +
     50F  CYS*     1.3    75.8    -      -       -      +
     52F  VAL*     1.3    70.3    +      -       -      +
     53F  ILE*     3.9    25.4    -      -       +      -
     75F  ALA      5.7     2.2    -      -       -      +
     76F  LEU*     3.7    28.3    -      -       +      +
     84F  VAL*     4.7     3.1    -      -       +      -
     87F  GLU*     4.1    11.4    -      -       +      -
     88F  ALA*     3.7    34.3    -      -       +      +
     91F  VAL*     3.9    17.0    -      -       +      -
     93F  VAL      2.9     7.5    +      -       -      +
     94F  ILE*     3.3     5.8    -      -       +      +
     95F  GLY      2.8    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 52 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36F  LEU*     4.9     4.3    -      -       +      -
     37F  MET*     3.4    42.0    -      -       +      -
     40F  VAL*     4.1    25.8    -      -       +      -
     50F  CYS*     5.8     0.4    -      -       +      -
     51F  LEU*     1.3    83.1    -      -       -      +
     53F  ILE*     1.3    72.9    +      -       -      +
     54F  LYS*     5.1     2.2    -      -       +      +
     75F  ALA*     3.3    20.4    -      -       +      +
     76F  LEU*     2.9    27.5    +      -       -      +
     95F  GLY*     3.3    11.2    -      -       -      +
     97F  ASP*     5.3     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 53 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51F  LEU*     3.9    17.7    -      -       +      -
     52F  VAL*     1.3    79.1    -      -       -      +
     54F  LYS*     1.3    63.9    +      -       -      +
     76F  LEU*     3.3    11.4    -      -       +      +
     78F  ALA*     4.0    12.3    -      -       +      -
     81F  LEU*     3.9    29.4    -      -       +      -
     84F  VAL*     3.7    27.8    -      -       +      -
     94F  ILE*     3.7    30.5    -      -       +      -
     95F  GLY      2.7    11.0    +      -       -      +
     96F  ILE*     3.5     3.5    -      -       +      +
     97F  ASP*     2.8    29.6    +      -       -      +
    102F  PHE*     3.9    16.2    -      -       +      -
    108F  PHE*     4.4     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 54 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52F  VAL*     4.2     3.5    -      -       +      -
     53F  ILE*     1.3    73.9    -      -       -      +
     55F  TYR*     1.3    68.9    +      -       +      +
     58F  ASP*     3.9    25.0    +      -       -      +
     59F  THR*     5.9     0.4    -      -       -      +
     60F  ARG*     5.0    12.1    +      -       -      +
     75F  ALA*     5.5     8.7    -      -       +      +
     76F  LEU      2.9     9.9    +      -       -      +
     77F  PRO*     3.4     6.4    -      -       +      +
     78F  ALA      2.9    26.0    +      -       -      +
     97F  ASP*     3.9    32.9    +      -       +      +
     98F  GLU*     4.0    15.5    -      -       -      +
    102F  PHE*     3.9     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 55 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54F  LYS*     1.3    78.0    -      -       -      +
     56F  ALA*     1.3    63.6    +      -       -      +
     57F  LYS*     3.0    33.9    +      -       +      -
     58F  ASP*     3.2    30.1    +      -       +      +
     78F  ALA      3.4    12.1    -      -       -      -
     79F  CYS*     4.4    21.5    -      -       -      -
     97F  ASP      3.8     2.8    +      -       -      -
     98F  GLU*     4.2    20.4    -      -       +      +
    101F  PHE*     3.4    54.7    +      +       +      -
    102F  PHE*     3.7    21.9    -      +       +      -
    173F  GLU*     2.6    35.8    +      -       -      -
    175F  ILE*     4.4     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