Contacts of the strand formed by residues 74 - 79 (chain I) 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 I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28I  LYS*     3.7    11.7    +      -       -      -
     29I  GLY      3.5     3.4    -      -       -      +
     31I  LEU*     4.5    16.8    -      -       +      +
     70I  VAL*     2.9    38.7    +      -       +      +
     71I  LYS      4.1     0.7    -      -       -      +
     72I  LYS      3.8     0.6    -      -       -      -
     73I  CYS*     1.3    87.3    -      -       -      +
     75I  GLY*     1.3    59.3    +      -       -      +
     76I  GLY      3.5    23.1    -      -       -      +
     77I  VAL*     4.1     8.5    -      -       +      -
    103I  ILE*     3.6    34.5    -      -       +      +
    300I  PHE*     4.2    17.9    -      -       +      -
    306I  LEU*     4.7     2.7    -      -       +      -
    328I  PHE*     4.7     4.0    -      -       +      -
    332I  ALA*     4.0    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 75 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22I  ARG      4.3     1.9    -      -       -      +
     23I  ILE*     3.6    28.2    -      -       -      -
     28I  LYS*     3.8    20.9    -      -       -      +
     29I  GLY      2.7    11.9    +      -       -      -
     74I  ILE*     1.3    73.6    -      -       -      +
     76I  GLY*     1.3    54.3    +      -       -      -
    102I  GLY      4.9     0.5    -      -       -      +
    103I  ILE*     3.6     4.3    -      -       -      +
    104I  VAL*     2.9    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23I  ILE*     4.4     8.4    -      -       -      +
     29I  GLY      3.4     3.8    +      -       -      -
     30I  ILE*     3.3     8.8    -      -       -      -
     31I  LEU      2.9    23.9    +      -       -      -
     74I  ILE*     3.4     6.2    -      -       -      +
     75I  GLY*     1.3    80.0    -      -       -      +
     77I  VAL*     1.3    64.9    +      -       -      -
    103I  ILE*     3.5     2.7    -      -       -      -
    104I  VAL*     3.2    15.7    -      -       -      -
    145I  PHE*     4.3     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 77 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31I  LEU*     3.3    23.3    -      -       +      +
     33I  ALA*     4.8     0.7    -      -       +      -
     64I  PHE*     3.6    30.5    -      -       +      -
     74I  ILE*     4.1     9.2    -      -       +      -
     76I  GLY*     1.3    78.6    -      -       -      +
     78I  ILE*     1.3    68.1    +      -       -      +
     79I  PHE*     3.5    20.0    -      -       +      -
     98I  ILE*     3.9    17.3    -      -       +      -
    103I  ILE*     3.6    20.0    -      -       +      -
    104I  VAL      2.9     8.0    +      -       -      +
    106I  GLY      2.9    23.9    +      -       -      -
    145I  PHE*     3.9     2.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 78 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30I  ILE*     3.6    27.4    -      -       +      -
     31I  LEU      2.8    12.0    +      -       -      +
     32I  ALA*     4.1     9.4    -      -       +      -
     33I  ALA*     3.0    30.5    +      -       -      +
     34I  ASP*     3.6    23.3    -      -       +      +
     77I  VAL*     1.3    72.0    -      -       -      +
     79I  PHE*     1.3    62.8    +      -       -      +
    106I  GLY      3.5     5.2    -      -       -      +
    107I  ILE      4.3     2.7    -      -       -      -
    108I  LYS      4.1    11.2    -      -       -      +
    145I  PHE*     3.6    15.3    -      -       +      -
    147I  LYS*     4.0    28.0    -      -       +      +
    186I  ILE*     4.1    14.1    -      -       +      -
    230I  LYS*     4.1     3.6    -      -       -      +
    301I  SER*     3.7    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 79 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33I  ALA*     4.3     2.7    -      -       -      -
     34I  ASP*     3.7     4.9    -      -       -      +
     64I  PHE*     3.6    28.7    -      +       -      -
     77I  VAL*     3.5    28.9    -      -       +      -
     78I  ILE*     1.3    74.9    -      -       -      +
     80I  PHE*     1.3    65.5    +      -       -      +
     83I  THR*     3.5    21.5    -      -       +      -
     84I  LEU*     3.7    24.2    -      -       +      -
     94I  PHE*     3.8    20.0    -      -       +      -
     95I  VAL*     4.2    12.1    -      -       +      -
     98I  ILE*     4.1    18.6    -      -       +      -
    105I  VAL*     3.6    24.5    -      -       +      -
    106I  GLY      2.6    19.2    +      -       -      +
    107I  ILE*     3.4     3.7    -      -       +      -
    108I  LYS      3.2    25.1    +      -       -      -
----------------------------------------------------------
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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