Contacts of the strand formed by residues 346 - 350 (chain A) in PDB entry 2XJF


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 ILE 346 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  ILE*     4.4     1.6    -      -       -      -
     48A  CYS*     3.4    12.8    -      -       +      +
    246A  PHE*     3.9    20.2    -      -       +      -
    335A  ILE*     4.8     8.3    -      -       +      -
    336A  CYS*     3.8    20.0    -      -       -      -
    341A  ALA*     4.0    15.3    -      -       +      -
    342A  LYS      3.7    13.7    -      -       -      +
    343A  GLY      3.0     6.4    +      -       -      +
    345A  ASP*     1.3    80.6    -      -       -      +
    347A  LEU*     1.3    71.5    +      -       -      +
    348A  TYR      4.0     0.4    -      -       -      +
    366A  TRP*     3.6    52.9    -      -       +      +
    367A  ARG*     2.9    34.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  LEU*     4.1    15.9    -      -       +      -
     43A  MET*     4.3    20.4    -      -       -      -
     46A  ILE*     3.8    22.8    -      -       +      +
     48A  CYS      2.9     9.0    +      -       -      +
     49A  PHE*     3.5    20.1    -      -       +      -
     50A  GLY      2.9    24.9    +      -       -      +
    346A  ILE*     1.3    72.0    -      -       -      +
    348A  TYR*     1.3    57.2    +      -       -      +
    349A  ILE*     3.9    11.0    +      -       +      +
    367A  ARG*     3.5     1.8    -      -       -      -
    368A  THR      3.7    38.6    -      -       -      +
    369A  PHE*     3.8     9.4    -      -       +      +
    460A  LEU*     4.5     7.6    -      -       +      -
    468A  LEU*     4.4    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLY*     3.6    18.2    -      -       -      +
     51A  PHE      3.9    18.2    -      -       -      -
     52A  A5N      3.8    11.3    +      -       -      +
    246A  PHE*     4.1     9.9    -      +       -      -
    248A  ALA*     3.4    23.6    +      -       +      +
    292A  LYS*     3.4    18.7    +      -       +      -
    295A  PHE*     6.5     0.2    -      +       -      -
    296A  PHE*     4.2     9.0    -      +       -      -
    346A  ILE*     3.8     1.5    -      -       +      -
    347A  LEU*     1.3    72.3    -      -       -      +
    349A  ILE*     1.3    63.1    +      -       -      +
    356A  ASP*     3.6    38.2    +      -       +      -
    357A  ILE*     4.0     7.7    -      -       +      +
    360A  SER*     4.1    17.9    -      -       -      +
    366A  TRP*     3.5    34.8    -      +       +      -
    367A  ARG      2.8    14.7    +      -       -      +
    368A  THR*     3.5     3.7    -      -       -      -
    369A  PHE      2.9    26.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  PHE*     4.9     2.9    -      -       +      -
     50A  GLY      2.7    16.5    +      -       -      +
     51A  PHE*     3.5    32.5    -      -       +      -
     52A  A5N      3.0    26.3    +      -       -      -
     56A  THR*     3.6    17.2    -      -       +      +
    239A  MET*     4.1    15.7    -      -       +      -
    347A  LEU*     4.0    15.0    -      -       +      +
    348A  TYR*     1.3    79.4    -      -       -      +
    350A  GLY*     1.3    59.8    +      -       -      +
    369A  PHE*     3.5    20.2    -      -       +      -
    371A  VAL*     3.9     7.0    -      -       +      -
    465A  PHE*     3.6    27.1    -      -       +      -
    468A  LEU*     4.1    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  A5N      4.2     1.8    -      -       -      -
     56A  THR*     3.6    11.4    -      -       -      -
    349A  ILE*     1.3    74.7    -      -       -      +
    351A  ASP*     1.3    60.6    +      -       -      -
    352A  HIS      3.7     1.6    -      -       -      -
    356A  ASP*     3.5    18.6    -      -       -      -
    357A  ILE*     4.0     8.3    -      -       -      +
    369A  PHE      3.2     7.3    +      -       -      -
    370A  LEU*     3.4     9.1    -      -       -      +
    371A  VAL*     2.8    26.5    +      -       -      -
----------------------------------------------------------
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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