Contacts of the strand formed by residues 74 - 79 (chain F) 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 F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28F  LYS*     3.7    11.9    +      -       -      -
     29F  GLY      3.5     2.7    -      -       -      +
     31F  LEU*     4.5    16.6    -      -       +      +
     70F  VAL*     2.9    39.2    +      -       +      +
     71F  LYS      4.1     0.2    -      -       -      +
     72F  LYS      3.8     0.6    -      -       -      -
     73F  CYS*     1.3    86.4    -      -       -      +
     75F  GLY*     1.3    60.1    +      -       -      +
     76F  GLY      3.5    23.6    -      -       -      +
     77F  VAL*     4.1     7.9    -      -       +      -
    103F  ILE*     3.6    35.5    -      -       +      +
    300F  PHE*     4.2    18.8    -      -       +      -
    306F  LEU*     4.7     2.7    -      -       +      -
    328F  PHE*     4.7     4.5    -      -       +      -
    332F  ALA*     4.0    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 75 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22F  ARG      4.3     1.9    -      -       -      +
     23F  ILE*     3.6    28.1    -      -       -      -
     28F  LYS*     3.8    20.7    -      -       -      +
     29F  GLY      2.7    12.3    +      -       -      -
     74F  ILE*     1.3    74.1    -      -       -      +
     76F  GLY*     1.3    53.8    +      -       -      -
    102F  GLY      4.9     0.5    -      -       -      +
    103F  ILE*     3.6     3.1    -      -       -      +
    104F  VAL*     2.9    31.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23F  ILE*     4.4     6.9    -      -       -      +
     29F  GLY      3.4     3.6    +      -       -      -
     30F  ILE*     3.3     9.2    -      -       -      -
     31F  LEU      2.9    24.1    +      -       -      -
     74F  ILE*     3.4     6.2    -      -       -      +
     75F  GLY*     1.3    80.8    -      -       -      +
     77F  VAL*     1.3    66.0    +      -       -      -
    103F  ILE*     3.5     2.5    -      -       -      -
    104F  VAL*     3.2    15.0    -      -       -      -
    145F  PHE*     4.3     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 77 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31F  LEU*     3.3    23.6    -      -       +      +
     33F  ALA*     4.8     0.9    -      -       +      -
     64F  PHE*     3.6    31.2    -      -       +      -
     74F  ILE*     4.1     8.1    -      -       +      -
     76F  GLY*     1.3    78.6    -      -       -      +
     78F  ILE*     1.3    67.7    +      -       -      +
     79F  PHE*     3.5    21.6    -      -       +      -
     98F  ILE*     3.9    16.2    -      -       +      -
    103F  ILE*     3.6    20.6    -      -       +      -
    104F  VAL      2.9     7.7    +      -       -      +
    106F  GLY      2.9    23.6    +      -       -      -
    145F  PHE*     3.9     2.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 78 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30F  ILE*     3.6    27.4    -      -       +      -
     31F  LEU      2.8    11.6    +      -       -      +
     32F  ALA*     4.1     9.4    -      -       +      -
     33F  ALA*     3.0    31.2    +      -       -      +
     34F  ASP*     3.6    23.1    -      -       +      +
     77F  VAL*     1.3    71.8    -      -       -      +
     79F  PHE*     1.3    64.2    +      -       -      +
    106F  GLY      3.5     4.9    -      -       -      +
    107F  ILE      4.3     3.1    -      -       -      +
    108F  LYS      4.1    11.4    -      -       -      +
    145F  PHE*     3.6    15.0    -      -       +      -
    147F  LYS*     4.0    28.5    -      -       +      +
    186F  ILE*     4.1    13.9    -      -       +      -
    230F  LYS*     4.1     3.4    -      -       -      +
    301F  SER*     3.7    13.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 79 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33F  ALA*     4.3     2.9    -      -       -      -
     34F  ASP*     3.7     5.0    -      -       -      +
     64F  PHE*     3.6    29.2    -      +       -      -
     77F  VAL*     3.5    29.6    -      -       +      -
     78F  ILE*     1.3    74.0    -      -       -      +
     80F  PHE*     1.3    64.9    +      -       -      +
     83F  THR*     3.5    21.5    -      -       +      -
     84F  LEU*     3.7    23.8    -      -       +      -
     94F  PHE*     3.8    20.0    -      -       +      -
     95F  VAL*     4.2    12.1    -      -       +      -
     98F  ILE*     4.1    18.4    -      -       +      -
    105F  VAL*     3.6    24.2    -      -       +      -
    106F  GLY      2.6    19.6    +      -       -      +
    107F  ILE*     3.4     4.3    -      -       +      -
    108F  LYS      3.2    24.4    +      -       -      -
----------------------------------------------------------
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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