Contacts of the strand formed by residues 184 - 191 (chain L) 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 L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16L  LEU*     3.2    39.9    -      -       +      +
     19L  ILE*     3.6    21.3    -      -       +      -
     20L  ALA*     3.9    12.3    -      -       +      +
     23L  ILE*     5.2     0.2    -      -       +      -
    144L  ASP      2.8    13.0    +      -       -      +
    145L  PHE*     2.9    15.7    -      -       +      +
    146L  ALA      2.8    25.8    +      -       -      -
    183L  ILE*     1.3    69.9    -      -       -      +
    185L  PRO*     1.3    67.6    -      -       -      +
    186L  ILE*     5.8     0.2    -      -       +      -
    226L  GLY      3.3    23.6    -      -       -      +
    227L  THR*     3.9    11.7    -      -       -      -
    228L  LEU*     4.6     8.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 185 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146L  ALA      3.9     1.3    -      -       -      +
    174L  TYR*     3.5    24.0    -      -       +      +
    175L  ALA*     3.8    35.7    -      -       +      +
    178L  CYS*     3.8     9.6    -      -       +      -
    179L  GLN*     3.8     8.5    -      -       +      -
    183L  ILE      3.2     7.6    -      -       -      +
    184L  VAL*     1.3    85.5    -      -       -      +
    186L  ILE*     1.3    62.6    +      -       -      +
    187L  VAL*     3.6     2.7    +      -       +      -
    226L  GLY      3.2    17.0    -      -       -      +
    227L  THR*     3.6    12.9    -      -       +      -
    228L  LEU      3.2    20.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 186 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30L  ILE*     3.8    20.4    -      -       +      -
     78L  ILE*     4.1    14.1    -      -       +      -
    145L  PHE*     3.6    35.9    -      -       +      -
    146L  ALA      2.8    18.7    +      -       -      +
    147L  LYS*     4.3     6.3    -      -       +      -
    148L  TRP      3.7     7.4    +      -       -      -
    174L  TYR*     2.9    17.8    +      -       -      -
    184L  VAL*     5.1     0.7    -      -       +      +
    185L  PRO*     1.3    73.1    -      -       -      +
    187L  VAL*     1.3    61.6    +      -       -      +
    188L  GLU*     3.4     4.7    +      -       +      +
    228L  LEU*     3.4    23.8    -      -       +      +
    230L  LYS*     3.4    38.8    -      -       +      +
    269L  THR*     4.5     4.5    -      -       -      +
    301L  SER*     4.9     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 187 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171L  LEU*     3.5    37.2    -      -       +      -
    174L  TYR*     4.4     7.2    -      -       +      -
    175L  ALA*     4.5    19.1    -      -       +      -
    185L  PRO      4.3     6.1    -      -       -      +
    186L  ILE*     1.3    72.3    -      -       -      +
    188L  GLU*     1.3    57.0    +      -       -      +
    189L  PRO*     3.1    10.9    -      -       +      +
    213L  VAL*     3.9    18.4    -      -       +      -
    214L  TYR*     5.7     1.8    -      -       -      +
    217L  LEU*     4.4    19.1    -      -       +      -
    227L  THR*     4.8     8.1    -      -       -      -
    228L  LEU      2.8    16.3    +      -       -      +
    229L  LEU*     3.4     8.2    -      -       +      +
    230L  LYS      3.0    20.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 188 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147L  LYS*     2.8    36.5    +      -       +      +
    148L  TRP      3.3    14.9    +      -       -      +
    149L  ARG*     3.3    30.1    -      -       +      +
    150L  CYS*     3.0    24.3    +      -       -      +
    171L  LEU*     4.0     4.9    -      -       -      +
    186L  ILE*     3.4     6.8    +      -       +      +
    187L  VAL*     1.3    72.8    -      -       -      +
    189L  PRO*     1.3    58.5    -      -       -      +
    190L  GLU*     3.3    14.7    +      -       -      +
    230L  LYS*     3.3    40.5    -      -       +      +
    271L  LEU*     3.7    12.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 189 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150L  CYS*     4.1     7.6    -      -       +      +
    152L  LEU*     5.6     4.7    -      -       +      -
    171L  LEU*     3.8    17.7    -      -       +      -
    187L  VAL*     3.1    17.7    -      -       +      +
    188L  GLU*     1.3    81.1    -      -       -      +
    190L  GLU*     1.3    62.2    +      -       -      +
    191L  ILE*     3.4     8.2    +      -       -      +
    209L  VAL*     4.2    11.2    -      -       +      +
    210L  LEU*     4.0    26.5    -      -       +      -
    213L  VAL*     4.1    14.8    -      -       +      -
    229L  LEU*     3.8     9.9    -      -       +      -
    230L  LYS      3.8     7.0    -      -       -      +
    231L  PRO*     4.5     5.6    -      -       +      +
    232L  ASN*     3.6     9.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 190 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149L  ARG*     2.4    31.9    +      -       +      +
    150L  CYS      3.2    16.6    +      -       -      +
    151L  VAL*     3.4     3.8    -      -       -      +
    152L  LEU*     2.8    27.4    +      -       -      +
    188L  GLU*     3.3    16.9    +      -       -      +
    189L  PRO*     1.3    71.4    -      -       -      +
    191L  ILE*     1.3    69.4    +      -       -      +
    192L  LEU*     3.2    24.5    +      -       +      +
    193L  PRO*     4.7     5.0    -      -       -      +
    232L  ASN*     4.0     3.8    -      -       +      +
    271L  LEU*     3.7    38.6    -      -       +      +
    273L  GLY*     5.0     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 191 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152L  LEU*     3.6    22.7    -      -       +      +
    154L  ILE*     3.5    37.9    -      -       +      -
    189L  PRO      4.2     5.4    -      -       -      +
    190L  GLU*     1.3    73.1    -      -       -      +
    192L  LEU*     1.3    66.4    +      -       -      +
    193L  PRO*     3.7     3.1    -      -       -      +
    202L  CYS*     5.2     4.5    -      -       -      -
    205L  VAL*     3.7     5.2    -      -       +      -
    206L  THR*     3.4    42.8    -      -       +      +
    209L  VAL*     3.6    25.1    -      -       +      -
    232L  ASN*     2.7    37.1    -      -       -      +
----------------------------------------------------------
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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