Contacts of the strand formed by residues 29 - 33 (chain E) 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 GLY 29 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23E  ILE      4.8     2.0    -      -       -      -
     28E  LYS*     1.3    73.9    -      -       -      +
     30E  ILE*     1.3    64.1    +      -       -      -
     73E  CYS      2.8    10.3    +      -       -      -
     74E  ILE*     3.5     4.8    -      -       -      -
     75E  GLY*     2.7    24.7    +      -       -      -
     76E  GLY      3.4     3.3    +      -       -      -
    299E  THR*     3.5    10.5    -      -       -      -
    300E  PHE*     3.2    25.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 30 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23E  ILE*     3.6    33.2    -      -       +      -
     24E  VAL*     6.0     0.4    -      -       +      -
     29E  GLY*     1.3    76.8    -      -       -      +
     31E  LEU*     1.3    65.0    +      -       -      +
     74E  ILE*     4.9     0.4    -      -       -      -
     76E  GLY*     3.3    13.2    -      -       -      +
     78E  ILE*     3.6    34.3    -      -       +      -
    145E  PHE*     4.4     2.9    -      -       +      -
    186E  ILE*     3.8    26.0    -      -       +      -
    228E  LEU*     4.5     0.7    -      -       +      -
    269E  THR*     3.9    22.4    -      -       +      -
    300E  PHE*     2.8    25.3    +      -       -      +
    301E  SER*     3.4    10.3    -      -       -      +
    302E  TYR      3.3    23.9    +      -       -      +
    306E  LEU*     3.7     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 31 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  ILE*     1.3    71.5    -      -       -      +
     32E  ALA*     1.3    62.0    +      -       -      +
     33E  ALA*     3.4     6.3    +      -       +      +
     63E  LEU*     4.2    19.1    -      -       +      -
     64E  PHE*     4.3    11.0    -      -       +      -
     74E  ILE*     4.5    12.8    -      -       +      +
     76E  GLY      2.9    12.0    +      -       -      +
     77E  VAL*     3.3    25.2    -      -       +      -
     78E  ILE      2.8    26.7    +      -       -      -
    302E  TYR      4.2     0.2    -      -       -      +
    306E  LEU*     3.7    27.1    -      -       +      -
    307E  GLN*     3.8    22.7    -      -       +      +
    328E  PHE*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 32 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  ILE      3.6     0.8    +      -       -      -
     31E  LEU*     1.3    72.2    -      -       -      +
     33E  ALA*     1.3    56.2    +      -       -      +
     34E  ASP*     3.4    21.0    +      -       -      +
     35E  GLU*     3.7     4.7    -      -       -      +
     78E  ILE*     4.1    12.6    -      -       +      -
    147E  LYS*     5.1     0.9    -      -       -      +
    230E  LYS*     4.1    20.6    -      -       -      +
    301E  SER*     4.4     3.6    -      -       -      +
    302E  TYR      2.9    26.6    +      -       -      +
    303E  GLY*     3.5    11.2    -      -       -      +
    307E  GLN*     3.3    17.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 33 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31E  LEU*     3.4    16.0    +      -       +      -
     32E  ALA*     1.3    72.5    -      -       -      +
     34E  ASP*     1.3    55.4    +      -       -      +
     35E  GLU*     3.0    16.6    +      -       -      +
     60E  ARG*     3.1    24.5    +      -       -      +
     63E  LEU*     4.4    14.8    -      -       +      -
     64E  PHE*     4.4    22.0    -      -       +      -
     77E  VAL*     4.8     0.4    -      -       +      -
     78E  ILE      3.0    16.9    +      -       -      +
     79E  PHE*     4.3     0.5    -      -       -      -
     80E  PHE      3.7     8.3    +      -       -      -
     83E  THR*     4.9     1.7    +      -       -      +
    307E  GLN*     4.2     1.3    -      -       -      +
----------------------------------------------------------
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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