Contacts of the strand formed by residues 74 - 79 (chain J) in PDB entry 1XFB


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 ILE 74 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28J  LYS*     3.7    11.4    +      -       -      -
     29J  GLY      3.5     2.5    -      -       -      +
     31J  LEU*     4.5    16.2    -      -       +      +
     70J  VAL*     2.9    39.3    +      -       +      +
     71J  LYS      4.1     0.3    -      -       -      +
     72J  LYS      3.8     0.8    -      -       -      -
     73J  CYS*     1.3    86.8    -      -       -      +
     75J  GLY*     1.3    60.4    +      -       -      +
     76J  GLY      3.5    23.6    -      -       -      +
     77J  VAL*     4.1     8.3    -      -       +      -
    103J  ILE*     3.6    34.9    -      -       +      +
    300J  PHE*     4.2    18.8    -      -       +      -
    306J  LEU*     4.7     3.4    -      -       +      -
    328J  PHE*     4.7     4.3    -      -       +      -
    332J  ALA*     4.0    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 75 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22J  ARG      4.3     2.1    -      -       -      +
     23J  ILE*     3.6    27.8    -      -       -      -
     28J  LYS*     3.8    20.7    -      -       -      +
     29J  GLY      2.7    12.7    +      -       -      -
     74J  ILE*     1.3    73.5    -      -       -      +
     76J  GLY*     1.3    55.1    +      -       -      -
    102J  GLY      4.9     0.5    -      -       -      +
    103J  ILE*     3.6     3.7    -      -       -      +
    104J  VAL*     2.9    31.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23J  ILE*     4.4     7.1    -      -       -      +
     29J  GLY      3.4     4.0    +      -       -      -
     30J  ILE*     3.3     9.4    -      -       -      -
     31J  LEU      2.9    23.7    +      -       -      -
     74J  ILE*     3.4     6.4    -      -       -      +
     75J  GLY*     1.3    81.2    -      -       -      +
     77J  VAL*     1.3    63.7    +      -       -      -
    103J  ILE*     3.5     3.3    -      -       -      +
    104J  VAL*     3.2    15.3    -      -       -      -
    145J  PHE*     4.3     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 77 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31J  LEU*     3.3    22.4    -      -       +      +
     33J  ALA*     4.8     0.9    -      -       +      -
     64J  PHE*     3.6    31.0    -      -       +      -
     74J  ILE*     4.1     8.7    -      -       +      -
     76J  GLY*     1.3    79.9    -      -       -      +
     78J  ILE*     1.3    68.0    +      -       -      +
     79J  PHE*     3.5    20.9    -      -       +      -
     98J  ILE*     3.9    16.4    -      -       +      -
    103J  ILE*     3.6    20.6    -      -       +      -
    104J  VAL      2.9     8.6    +      -       -      +
    105J  VAL*     3.8     0.2    -      -       -      -
    106J  GLY      2.9    23.6    +      -       -      -
    145J  PHE*     3.9     2.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 78 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30J  ILE*     3.6    26.7    -      -       +      -
     31J  LEU      2.8    11.4    +      -       -      +
     32J  ALA*     4.1    10.1    -      -       +      -
     33J  ALA*     3.0    30.5    +      -       -      +
     34J  ASP*     3.6    23.3    -      -       +      +
     77J  VAL*     1.3    72.0    -      -       -      +
     79J  PHE*     1.3    64.4    +      -       -      +
    106J  GLY      3.5     4.7    -      -       -      +
    107J  ILE      4.3     3.4    -      -       -      -
    108J  LYS      4.1    10.8    -      -       -      +
    145J  PHE*     3.6    14.8    -      -       +      -
    147J  LYS*     4.0    27.8    -      -       +      -
    186J  ILE*     4.1    13.5    -      -       +      -
    230J  LYS*     4.1     3.4    -      -       -      +
    301J  SER*     3.7    14.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 79 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33J  ALA*     4.3     2.5    -      -       -      -
     34J  ASP*     3.7     4.6    -      -       -      +
     64J  PHE*     3.7    29.2    -      +       -      -
     77J  VAL*     3.5    28.9    -      -       +      -
     78J  ILE*     1.3    75.1    -      -       -      +
     80J  PHE*     1.3    64.9    +      -       -      +
     83J  THR*     3.5    21.8    -      -       +      -
     84J  LEU*     3.7    24.5    -      -       +      -
     94J  PHE*     3.8    19.1    -      -       +      -
     95J  VAL*     4.2    12.6    -      -       +      -
     98J  ILE*     4.1    18.4    -      -       +      -
    105J  VAL*     3.6    25.1    -      -       +      -
    106J  GLY      2.6    19.8    +      -       -      +
    107J  ILE*     3.4     3.4    -      -       +      -
    108J  LYS      3.2    24.9    +      -       -      -
----------------------------------------------------------
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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