Contacts of the strand formed by residues 184 - 191 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  LEU*     3.2    39.0    -      -       +      +
     19B  ILE*     3.6    21.5    -      -       +      -
     20B  ALA*     3.9    11.9    -      -       +      +
     23B  ILE*     5.2     0.2    -      -       +      -
    144B  ASP      2.8    13.4    +      -       -      +
    145B  PHE*     2.9    16.9    -      -       +      +
    146B  ALA      2.8    24.9    +      -       -      -
    183B  ILE*     1.3    70.9    -      -       -      +
    185B  PRO*     1.3    68.7    -      -       +      +
    186B  ILE*     5.8     0.4    -      -       +      -
    226B  GLY      3.3    21.5    -      -       -      +
    227B  THR*     3.9    10.5    -      -       -      +
    228B  LEU*     4.6     9.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146B  ALA      4.4     1.3    -      -       -      +
    174B  TYR*     3.5    24.9    -      -       +      +
    175B  ALA*     3.8    36.3    -      -       +      +
    178B  CYS*     3.8     9.9    -      -       +      -
    179B  GLN*     3.8     8.5    -      -       +      -
    183B  ILE      3.2     8.3    -      -       -      +
    184B  VAL*     1.3    84.7    -      -       -      +
    186B  ILE*     1.3    62.7    +      -       -      +
    187B  VAL*     3.6     2.7    +      -       +      +
    226B  GLY      3.2    17.0    -      -       -      +
    227B  THR*     3.6    12.7    -      -       +      -
    228B  LEU      3.2    21.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  ILE*     3.8    20.4    -      -       +      -
     78B  ILE*     4.1    14.4    -      -       +      -
    145B  PHE*     3.6    36.3    -      -       +      -
    146B  ALA      2.8    18.5    +      -       -      +
    147B  LYS*     4.3     5.4    -      -       +      -
    148B  TRP      3.7     7.4    +      -       -      -
    174B  TYR*     2.9    17.6    +      -       -      -
    184B  VAL*     5.1     0.9    -      -       +      +
    185B  PRO*     1.3    71.9    -      -       -      +
    187B  VAL*     1.3    62.9    +      -       -      +
    188B  GLU*     3.4     4.5    +      -       +      +
    228B  LEU*     3.4    25.1    -      -       +      +
    230B  LYS*     3.4    37.9    -      -       +      +
    269B  THR*     4.5     5.2    -      -       -      +
    301B  SER*     4.9     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  LEU*     3.5    37.2    -      -       +      -
    174B  TYR*     4.4     7.6    -      -       +      -
    175B  ALA*     4.5    19.5    -      -       +      -
    185B  PRO      4.3     6.7    -      -       -      +
    186B  ILE*     1.3    71.6    -      -       -      +
    188B  GLU*     1.3    57.9    +      -       -      +
    189B  PRO*     3.1    10.4    -      -       +      +
    213B  VAL*     3.9    17.9    -      -       +      -
    214B  TYR*     5.7     1.6    -      -       -      +
    217B  LEU*     4.4    20.0    -      -       +      -
    227B  THR*     4.8     7.2    -      -       -      -
    228B  LEU      2.8    16.5    +      -       -      +
    229B  LEU*     3.4     8.7    -      -       +      +
    230B  LYS      3.0    20.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 188 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  LYS*     2.8    36.6    +      -       +      +
    148B  TRP      3.3    14.4    +      -       -      +
    149B  ARG*     3.3    31.3    -      -       +      +
    150B  CYS*     3.0    24.4    +      -       -      +
    171B  LEU*     4.0     4.7    -      -       -      +
    186B  ILE*     3.4     7.2    +      -       +      +
    187B  VAL*     1.3    73.1    -      -       -      +
    189B  PRO*     1.3    58.8    -      -       -      +
    190B  GLU*     3.3    14.7    +      -       -      +
    230B  LYS*     3.3    39.8    -      -       +      +
    271B  LEU*     3.7    12.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 189 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  CYS*     4.2     7.6    -      -       +      +
    152B  LEU*     5.6     5.2    -      -       +      -
    171B  LEU*     3.8    17.9    -      -       +      -
    187B  VAL*     3.1    17.7    -      -       +      +
    188B  GLU*     1.3    82.4    -      -       -      +
    190B  GLU*     1.3    62.1    +      -       -      +
    191B  ILE*     3.4     8.9    +      -       -      +
    209B  VAL*     4.2    11.7    -      -       +      +
    210B  LEU*     4.0    26.5    -      -       +      -
    213B  VAL*     4.1    14.1    -      -       +      -
    229B  LEU*     3.8    10.3    -      -       +      -
    230B  LYS      3.8     6.7    -      -       -      +
    231B  PRO*     4.5     5.3    -      -       +      +
    232B  ASN*     3.6     8.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  ARG*     2.4    31.3    +      -       -      +
    150B  CYS      3.2    16.8    +      -       -      +
    151B  VAL*     3.4     3.6    -      -       -      +
    152B  LEU*     2.8    26.8    +      -       -      +
    188B  GLU*     3.3    17.9    +      -       -      +
    189B  PRO*     1.3    72.3    -      -       -      +
    191B  ILE*     1.3    70.4    +      -       -      +
    192B  LEU*     3.2    23.8    +      -       +      +
    193B  PRO*     4.7     4.7    -      -       -      +
    232B  ASN*     4.0     3.1    -      -       +      +
    271B  LEU*     3.7    39.8    -      -       +      +
    273B  GLY*     5.0     5.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152B  LEU*     3.6    22.0    -      -       +      +
    154B  ILE*     3.5    38.4    -      -       +      -
    189B  PRO      4.2     5.4    -      -       -      +
    190B  GLU*     1.3    75.2    -      -       -      +
    192B  LEU*     1.3    64.9    +      -       -      +
    193B  PRO*     3.7     2.9    -      -       -      +
    202B  CYS*     5.2     4.0    -      -       -      -
    205B  VAL*     3.7     4.9    -      -       +      -
    206B  THR*     3.4    42.4    -      -       +      +
    209B  VAL*     3.6    25.1    -      -       +      -
    232B  ASN*     2.7    37.5    -      -       -      +
----------------------------------------------------------
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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