Contacts of the strand formed by residues 184 - 191 (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 VAL 184 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  LEU*     3.2    39.5    -      -       +      +
     19A  ILE*     3.6    21.1    -      -       +      -
     20A  ALA*     3.9    12.8    -      -       +      +
     23A  ILE*     5.2     0.2    -      -       +      -
    144A  ASP      2.8    13.4    +      -       -      +
    145A  PHE*     2.9    15.4    -      -       +      +
    146A  ALA      2.8    26.2    +      -       -      -
    183A  ILE*     1.3    70.4    -      -       -      +
    185A  PRO*     1.3    67.1    -      -       +      +
    186A  ILE*     5.8     0.4    -      -       +      -
    226A  GLY      3.3    22.2    -      -       -      +
    227A  THR*     3.9    11.7    -      -       -      +
    228A  LEU*     4.6     8.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  ALA      3.9     1.8    -      -       -      +
    174A  TYR*     3.5    24.2    -      -       +      +
    175A  ALA*     3.8    36.1    -      -       +      +
    178A  CYS*     3.8     9.2    -      -       +      -
    179A  GLN*     3.8     8.7    -      -       +      -
    183A  ILE      3.2     8.3    -      -       -      +
    184A  VAL*     1.3    85.8    -      -       -      +
    186A  ILE*     1.3    63.2    +      -       -      +
    187A  VAL*     3.6     2.7    +      -       +      +
    226A  GLY      3.2    16.4    -      -       -      +
    227A  THR*     3.6    13.3    -      -       +      -
    228A  LEU      3.2    20.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ILE*     3.8    20.2    -      -       +      -
     78A  ILE*     4.1    14.1    -      -       +      -
    145A  PHE*     3.6    35.7    -      -       +      -
    146A  ALA      2.8    18.1    +      -       -      +
    147A  LYS*     4.3     5.8    -      -       +      -
    148A  TRP      3.7     7.1    +      -       -      -
    174A  TYR*     2.9    18.0    +      -       -      -
    184A  VAL*     5.1     0.9    -      -       +      +
    185A  PRO*     1.3    72.1    -      -       -      +
    187A  VAL*     1.3    61.5    +      -       -      +
    188A  GLU*     3.4     5.0    +      -       +      +
    228A  LEU*     3.4    25.1    -      -       +      +
    230A  LYS*     3.4    39.0    -      -       +      +
    269A  THR*     4.5     4.3    -      -       -      +
    301A  SER*     4.9     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  LEU*     3.5    38.1    -      -       +      -
    174A  TYR*     4.4     7.4    -      -       +      -
    175A  ALA*     4.5    19.5    -      -       +      -
    185A  PRO      4.3     7.2    -      -       -      +
    186A  ILE*     1.3    72.3    -      -       -      +
    188A  GLU*     1.3    56.5    +      -       -      +
    189A  PRO*     3.1     9.9    -      -       +      +
    213A  VAL*     3.9    17.9    -      -       +      -
    214A  TYR*     5.7     1.6    -      -       -      +
    217A  LEU*     4.4    19.3    -      -       +      -
    227A  THR*     4.8     7.2    -      -       -      -
    228A  LEU      2.8    15.9    +      -       -      +
    229A  LEU*     3.4     8.5    -      -       +      +
    230A  LYS      3.0    21.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  LYS*     2.8    36.3    +      -       +      +
    148A  TRP      3.3    15.1    +      -       -      +
    149A  ARG*     3.3    30.5    -      -       +      +
    150A  CYS*     3.0    24.4    +      -       -      +
    171A  LEU*     4.0     4.5    -      -       -      +
    186A  ILE*     3.4     6.9    +      -       +      +
    187A  VAL*     1.3    73.7    -      -       -      +
    189A  PRO*     1.3    58.1    -      -       -      +
    190A  GLU*     3.3    14.0    +      -       -      +
    230A  LYS*     3.3    40.6    -      -       +      +
    271A  LEU*     3.7    12.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  CYS*     4.2     7.4    -      -       +      +
    152A  LEU*     5.6     5.2    -      -       +      -
    171A  LEU*     3.8    18.6    -      -       +      -
    187A  VAL*     3.1    18.2    -      -       +      +
    188A  GLU*     1.3    80.6    -      -       -      +
    190A  GLU*     1.3    61.6    +      -       -      +
    191A  ILE*     3.4     8.9    +      -       -      +
    209A  VAL*     4.2    11.7    -      -       +      +
    210A  LEU*     4.0    26.7    -      -       +      -
    213A  VAL*     4.1    14.6    -      -       +      -
    229A  LEU*     3.8     9.6    -      -       +      -
    230A  LYS      3.8     7.2    -      -       -      +
    231A  PRO*     4.5     5.7    -      -       +      +
    232A  ASN*     3.6     8.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  ARG*     2.4    31.9    +      -       +      +
    150A  CYS      3.2    17.3    +      -       -      +
    151A  VAL*     3.4     3.2    -      -       -      +
    152A  LEU*     2.8    27.8    +      -       -      +
    188A  GLU*     3.3    17.1    +      -       +      +
    189A  PRO*     1.3    73.3    -      -       -      +
    191A  ILE*     1.3    69.5    +      -       -      +
    192A  LEU*     3.2    24.1    +      -       +      +
    193A  PRO*     4.7     4.3    -      -       -      +
    232A  ASN*     4.0     3.4    -      -       +      +
    271A  LEU*     3.7    38.5    -      -       +      +
    273A  GLY*     5.0     6.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  LEU*     3.6    22.4    -      -       +      +
    154A  ILE*     3.5    38.8    -      -       +      -
    189A  PRO      4.2     5.4    -      -       -      +
    190A  GLU*     1.3    75.0    -      -       -      +
    192A  LEU*     1.3    64.2    +      -       -      +
    193A  PRO*     3.7     2.6    -      -       -      +
    202A  CYS*     5.2     3.7    -      -       -      -
    205A  VAL*     3.7     5.2    -      -       +      -
    206A  THR*     3.4    42.2    -      -       +      +
    209A  VAL*     3.6    24.2    -      -       +      -
    232A  ASN*     2.7    38.3    -      -       -      +
----------------------------------------------------------
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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