Contacts of the strand formed by residues 145 - 152 (chain J) 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 PHE 145 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23J  ILE*     3.6    30.1    -      -       +      -
     30J  ILE*     4.4     7.4    -      -       +      -
     76J  GLY*     4.3     5.6    -      -       -      -
     77J  VAL      3.7    22.2    -      -       -      -
     78J  ILE*     3.6    19.5    -      -       +      -
    104J  VAL*     3.6    20.6    -      -       +      -
    105J  VAL      3.2    20.4    -      -       -      -
    106J  GLY*     2.9    42.9    -      -       -      -
    107J  ILE*     3.2     9.0    +      -       -      +
    143J  ALA      3.7     0.4    -      -       -      -
    144J  ASP*     1.3    80.9    -      -       -      +
    146J  ALA*     1.3    62.2    +      -       -      +
    183J  ILE*     3.7     6.4    -      -       -      +
    184J  VAL*     2.9    20.9    -      -       +      +
    186J  ILE*     3.6    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 146 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107J  ILE*     3.2    17.9    -      -       +      +
    109J  VAL*     3.9    17.7    -      -       +      -
    135J  CYS*     5.7     0.2    -      -       -      -
    145J  PHE*     1.3    77.6    -      -       -      +
    147J  LYS*     1.3    60.8    +      -       -      +
    174J  TYR*     3.2    10.1    -      -       +      +
    178J  CYS*     4.1    11.2    -      -       -      -
    183J  ILE*     3.7    15.0    -      -       +      +
    184J  VAL      2.8     7.3    +      -       -      -
    186J  ILE*     2.8    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 147 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32J  ALA*     5.1     0.6    -      -       -      +
     34J  ASP*     3.2    32.9    +      -       -      +
     78J  ILE*     4.0    28.0    -      -       +      -
    107J  ILE      3.0     5.1    +      -       -      -
    108J  LYS*     3.4    11.9    -      -       +      +
    109J  VAL*     3.0    27.4    +      -       -      +
    110J  ASP*     3.9     2.0    +      -       -      +
    146J  ALA*     1.3    77.8    -      -       -      +
    148J  TRP*     1.3    63.2    +      -       -      +
    149J  ARG*     4.2    16.6    -      -       -      +
    174J  TYR*     3.3     4.5    -      -       -      -
    186J  ILE*     4.0     9.2    -      -       +      +
    188J  GLU*     2.8    28.8    +      -       -      +
    230J  LYS*     3.0    31.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 148 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109J  VAL*     4.0     3.1    -      -       +      -
    110J  ASP*     3.6    23.1    -      -       +      -
    125J  THR*     3.3    36.3    -      -       +      -
    126J  GLN      3.5     0.4    -      -       -      -
    127J  GLY*     3.4    28.3    -      -       -      -
    128J  LEU*     3.4    39.0    -      -       +      -
    131J  LEU*     4.4     4.9    -      -       +      -
    147J  LYS*     1.3    75.2    -      -       -      +
    149J  ARG*     1.3    64.1    +      -       -      +
    150J  CYS*     3.6    12.9    -      -       -      -
    170J  VAL*     3.3    25.7    -      -       +      +
    171J  LEU*     3.6    18.5    -      -       +      +
    174J  TYR*     3.3    49.9    +      +       +      -
    186J  ILE      3.7     1.6    +      -       -      -
    188J  GLU*     3.3    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 149 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108J  LYS*     5.7     2.5    -      -       -      +
    110J  ASP*     3.2    18.4    +      -       -      +
    112J  GLY      5.7     0.2    -      -       -      -
    113J  VAL*     5.6     1.9    +      -       -      +
    125J  THR*     2.8    21.7    +      -       -      +
    147J  LYS*     4.2    11.0    -      -       -      +
    148J  TRP*     1.3    75.8    -      -       -      +
    150J  CYS*     1.3    69.1    +      -       -      +
    151J  VAL*     3.4    31.6    +      -       +      +
    188J  GLU*     3.3    33.0    -      -       +      +
    190J  GLU*     2.4    44.3    +      -       -      +
    192J  LEU*     4.3     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 150 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125J  THR*     3.3    10.5    -      -       -      -
    148J  TRP*     3.6    23.7    +      -       -      -
    149J  ARG*     1.3    78.0    -      -       -      +
    151J  VAL*     1.3    67.4    +      -       -      +
    152J  LEU*     5.6     2.2    -      -       +      -
    167J  ASN*     3.3    36.1    -      -       +      +
    170J  VAL*     4.6     3.1    -      -       -      -
    171J  LEU*     3.6    26.2    -      -       +      -
    188J  GLU      3.0    12.5    +      -       -      +
    189J  PRO*     4.5     6.1    -      -       +      -
    190J  GLU*     3.2    21.5    +      -       -      +
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Residues in contact with VAL 151 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113J  VAL*     4.7    13.6    -      -       +      +
    123J  THR*     3.5    30.8    +      -       -      +
    124J  THR      5.9     0.2    -      -       -      -
    125J  THR*     4.5     1.4    +      -       -      -
    149J  ARG*     3.4    39.9    -      -       +      +
    150J  CYS*     1.3    81.8    -      -       -      +
    152J  LEU*     1.3    73.1    +      -       -      +
    153J  LYS*     5.9     0.2    -      -       +      -
    167J  ASN*     4.2     3.3    +      -       -      +
    190J  GLU      3.4     4.0    -      -       -      +
    192J  LEU*     3.5    40.2    -      -       +      -
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Residues in contact with LEU 152 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122J  GLU*     5.5     1.3    -      -       -      +
    123J  THR      5.2     0.2    -      -       -      +
    150J  CYS*     5.6     2.0    -      -       +      -
    151J  VAL*     1.3    78.9    -      -       -      +
    153J  LYS*     1.3    59.7    +      -       -      +
    159J  PRO*     5.0     9.6    -      -       +      -
    163J  ALA*     3.8    18.8    -      -       +      +
    164J  ILE*     4.6    12.3    -      -       +      -
    167J  ASN*     3.5    34.1    -      -       +      +
    189J  PRO*     5.6     5.2    -      -       +      -
    190J  GLU      2.8    12.8    +      -       -      +
    191J  ILE*     4.2    13.2    -      -       +      -
    192J  LEU*     2.9    31.1    +      -       -      +
    209J  VAL*     3.3    46.7    -      -       +      -
----------------------------------------------------------
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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