Contacts of the strand formed by residues 74 - 79 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  LYS*     3.7    12.5    +      -       -      -
     29A  GLY      3.5     2.5    -      -       -      +
     31A  LEU*     4.5    16.8    -      -       +      +
     70A  VAL*     2.9    39.3    +      -       +      +
     71A  LYS      4.1     0.3    -      -       -      +
     72A  LYS      3.8     0.6    -      -       -      -
     73A  CYS*     1.3    87.7    -      -       -      +
     75A  GLY*     1.3    59.6    +      -       -      +
     76A  GLY      3.5    23.8    -      -       -      +
     77A  VAL*     4.1     8.3    -      -       +      -
    103A  ILE*     3.6    34.8    -      -       +      +
    300A  PHE*     4.2    18.4    -      -       +      -
    306A  LEU*     4.7     2.9    -      -       +      -
    328A  PHE*     4.7     4.3    -      -       +      -
    332A  ALA*     4.0    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ARG      4.3     2.5    -      -       -      +
     23A  ILE*     3.6    27.7    -      -       -      -
     28A  LYS*     3.8    20.4    -      -       -      +
     29A  GLY      2.7    12.3    +      -       -      -
     74A  ILE*     1.3    74.1    -      -       -      +
     76A  GLY*     1.3    54.6    +      -       -      -
    102A  GLY      4.9     0.5    -      -       -      +
    103A  ILE*     3.6     3.8    -      -       -      -
    104A  VAL*     2.9    31.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  ILE*     4.4     6.7    -      -       -      +
     29A  GLY      3.4     3.6    +      -       -      -
     30A  ILE*     3.3     9.4    -      -       -      -
     31A  LEU      2.9    24.1    +      -       -      -
     74A  ILE*     3.4     6.4    -      -       -      +
     75A  GLY*     1.3    80.1    -      -       -      +
     77A  VAL*     1.3    64.8    +      -       -      -
    103A  ILE*     3.5     2.5    -      -       -      -
    104A  VAL*     3.2    15.7    -      -       -      -
    145A  PHE*     4.3     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LEU*     3.3    23.6    -      -       +      +
     33A  ALA*     4.8     0.9    -      -       +      -
     64A  PHE*     3.6    31.2    -      -       +      -
     74A  ILE*     4.1     8.5    -      -       +      -
     76A  GLY*     1.3    79.5    -      -       -      +
     78A  ILE*     1.3    67.8    +      -       -      +
     79A  PHE*     3.5    20.4    -      -       +      -
     98A  ILE*     3.9    16.6    -      -       +      -
    103A  ILE*     3.6    20.4    -      -       +      -
    104A  VAL      2.9     7.4    +      -       -      +
    105A  VAL*     3.8     0.3    -      -       -      -
    106A  GLY      2.9    23.9    +      -       -      -
    145A  PHE*     3.9     1.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ILE*     3.6    27.1    -      -       +      -
     31A  LEU      2.8    11.4    +      -       -      +
     32A  ALA*     4.1     9.2    -      -       +      -
     33A  ALA*     3.0    31.0    +      -       -      +
     34A  ASP*     3.6    23.6    -      -       +      +
     77A  VAL*     1.3    71.4    -      -       -      +
     79A  PHE*     1.3    63.7    +      -       -      +
    106A  GLY      3.5     4.5    -      -       -      +
    107A  ILE      4.3     3.6    -      -       -      -
    108A  LYS      4.1    11.0    -      -       -      +
    145A  PHE*     3.6    15.0    -      -       +      -
    147A  LYS*     4.0    27.8    -      -       +      -
    186A  ILE*     4.1    13.2    -      -       +      -
    230A  LYS*     4.1     4.0    -      -       -      +
    301A  SER*     3.7    13.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ALA*     4.3     2.7    -      -       -      -
     34A  ASP*     3.7     4.5    -      -       -      +
     64A  PHE*     3.7    28.0    -      +       -      -
     77A  VAL*     3.5    28.7    -      -       +      -
     78A  ILE*     1.3    75.3    -      -       -      +
     80A  PHE*     1.3    64.6    +      -       -      +
     83A  THR*     3.5    22.2    -      -       +      -
     84A  LEU*     3.7    25.1    -      -       +      -
     94A  PHE*     3.8    19.7    -      -       +      -
     95A  VAL*     4.2    12.3    -      -       +      -
     98A  ILE*     4.1    18.6    -      -       +      -
    105A  VAL*     3.6    25.1    -      -       +      -
    106A  GLY      2.6    19.4    +      -       -      +
    107A  ILE*     3.4     4.5    -      -       +      -
    108A  LYS      3.2    24.6    +      -       -      -
----------------------------------------------------------
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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