Contacts of the strand formed by residues 147 - 152 (chain F) in PDB entry 1XWD


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 147 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122F  LEU*     3.1    33.4    -      -       +      +
    123F  GLN      3.3     5.4    -      -       -      +
    125F  LEU*     5.1     4.3    -      -       +      +
    143F  SER*     3.7    13.5    -      -       -      -
    145F  GLN      3.4    13.0    +      -       -      +
    146F  LYS*     1.3    72.2    -      -       -      +
    148F  LEU*     1.3    68.1    +      -       -      +
    149F  LEU*     3.7     2.6    +      -       +      +
    168F  LEU*     3.8    32.8    -      -       +      +
    169F  SER*     3.9     5.2    -      -       -      -
    172F  SER      3.2     7.5    +      -       -      -
    173F  VAL*     3.3    14.0    -      -       +      +
    174F  ILE*     2.7    33.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 148 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88D  TYR*     3.7    24.7    -      -       +      -
     89D  TYR*     4.5     8.3    -      -       +      +
    123F  GLN      2.8     9.4    +      -       -      +
    124F  TYR*     3.4    35.8    -      -       +      -
    125F  LEU      3.1    24.1    +      -       -      -
    146F  LYS      4.3     0.2    -      -       -      -
    147F  VAL*     1.3    73.3    -      -       -      +
    149F  LEU*     1.3    58.7    +      -       -      +
    150F  ASP*     4.7     1.1    -      -       +      -
    174F  ILE*     3.2    42.4    -      -       +      +
    176F  TRP*     3.5    40.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 149 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125F  LEU*     3.5    42.4    -      -       +      +
    136F  PRO*     5.3     0.7    -      -       +      -
    138F  VAL*     4.6    11.4    -      -       +      -
    147F  VAL*     3.7     2.3    +      -       +      +
    148F  LEU*     1.3    71.9    -      -       -      +
    150F  ASP*     1.3    59.3    +      -       -      +
    151F  ILE*     3.7    27.3    +      -       +      -
    165F  PHE*     3.4    39.7    -      -       +      -
    168F  LEU*     4.2    16.6    -      -       +      -
    174F  ILE      2.8     9.1    +      -       -      +
    175F  LEU*     3.7    15.3    -      -       +      -
    176F  TRP*     2.8    27.9    +      -       -      +
    177F  LEU*     4.4     3.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 150 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88D  TYR      5.1     0.2    -      -       -      +
     91D  LYS*     2.8    23.3    +      -       -      -
    124F  TYR*     3.2    31.6    +      -       +      +
    125F  LEU      2.9     9.4    +      -       -      +
    126F  LEU*     3.2    15.0    -      -       +      +
    127F  ILE      2.8    24.9    +      -       -      -
    148F  LEU*     3.8     0.4    +      -       +      -
    149F  LEU*     1.3    71.3    -      -       -      +
    151F  ILE*     1.3    63.3    +      -       -      +
    152F  GLN*     3.1    23.5    -      -       -      +
    176F  TRP*     3.5    31.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 151 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127F  ILE*     3.4    17.3    -      -       +      +
    132F  ILE*     5.0     1.8    -      -       +      -
    135F  LEU*     3.9    13.2    -      -       +      -
    136F  PRO*     3.5    31.0    -      -       +      -
    149F  LEU*     3.7    37.0    +      -       +      -
    150F  ASP*     1.3    78.1    +      -       -      +
    152F  GLN*     1.3    58.0    +      -       -      +
    154F  ASN*     3.4    19.7    -      -       -      +
    157F  ILE*     3.8    21.1    -      -       +      -
    176F  TRP      2.9    23.1    +      -       -      +
    177F  LEU*     3.5     7.8    -      -       +      -
    178F  ASN      3.4     0.9    -      -       -      +
    180F  ASN*     3.0    23.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 152 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51D  LYS*     5.5     0.2    -      -       -      +
     91D  LYS*     2.8    44.9    +      -       -      +
     89E  SER*     4.1    18.0    +      -       -      -
    127F  ILE      3.2     4.6    +      -       -      -
    128F  SER*     3.2    12.0    +      -       -      +
    129F  ASN      3.2    12.3    +      -       -      -
    150F  ASP*     3.1    15.2    +      -       -      +
    151F  ILE*     1.3    71.1    -      -       -      +
    153F  ASP*     1.3    84.4    +      -       -      +
    154F  ASN*     2.9    13.9    +      -       -      -
    176F  TRP*     5.1     3.1    -      -       -      -
    178F  ASN*     3.3    44.3    +      -       -      +
    179F  LYS*     4.6     2.5    -      -       +      +
    180F  ASN*     3.3     0.7    -      -       -      -
----------------------------------------------------------
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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