Contacts of the strand formed by residues 29 - 33 (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 GLY 29 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23J  ILE      4.8     1.8    -      -       -      -
     24J  VAL*     6.5     0.2    -      -       -      -
     28J  LYS*     1.3    74.3    -      -       -      +
     30J  ILE*     1.3    63.8    +      -       -      -
     73J  CYS      2.7    10.7    +      -       -      -
     74J  ILE*     3.5     4.4    -      -       -      -
     75J  GLY*     2.7    24.9    +      -       -      -
     76J  GLY      3.4     3.3    +      -       -      -
    299J  THR*     3.5    11.0    -      -       -      -
    300J  PHE*     3.2    25.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 30 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23J  ILE*     3.6    33.7    -      -       +      +
     29J  GLY*     1.3    75.7    -      -       -      +
     31J  LEU*     1.3    65.0    +      -       -      +
     74J  ILE*     4.9     0.4    -      -       -      -
     76J  GLY*     3.3    14.8    -      -       -      +
     78J  ILE*     3.6    34.5    -      -       +      -
    145J  PHE*     4.4     2.7    -      -       +      -
    186J  ILE*     3.8    26.0    -      -       +      -
    228J  LEU*     4.5     1.1    -      -       +      -
    269J  THR*     3.9    21.5    -      -       +      -
    299J  THR*     5.7     0.2    -      -       -      +
    300J  PHE*     2.8    24.7    +      -       -      +
    301J  SER*     3.4    10.9    -      -       -      +
    302J  TYR      3.3    24.3    +      -       -      +
    306J  LEU*     3.7     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 31 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29J  GLY      4.3     0.2    +      -       -      -
     30J  ILE*     1.3    71.4    -      -       -      +
     32J  ALA*     1.3    63.0    +      -       -      +
     33J  ALA*     3.4     6.1    +      -       +      +
     63J  LEU*     4.2    20.2    -      -       +      -
     64J  PHE*     4.3    11.0    -      -       +      -
     74J  ILE*     4.5    12.8    -      -       +      +
     76J  GLY      2.9    12.0    +      -       -      +
     77J  VAL*     3.3    25.1    -      -       +      +
     78J  ILE      2.8    27.0    +      -       -      -
    302J  TYR      4.2     0.2    -      -       -      +
    306J  LEU*     3.7    26.2    -      -       +      -
    307J  GLN*     3.8    22.9    -      -       +      +
    328J  PHE*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 32 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30J  ILE      3.6     1.0    +      -       -      -
     31J  LEU*     1.3    70.9    -      -       -      +
     33J  ALA*     1.3    56.4    +      -       -      +
     34J  ASP*     3.4    20.4    +      -       -      +
     35J  GLU*     3.7     5.0    -      -       -      +
     78J  ILE*     4.1    12.8    -      -       +      -
    147J  LYS*     5.1     0.4    -      -       -      +
    230J  LYS*     4.1    20.6    -      -       -      +
    301J  SER*     4.4     2.9    -      -       -      +
    302J  TYR      2.9    26.6    +      -       -      +
    303J  GLY*     3.5    11.2    -      -       -      +
    307J  GLN*     3.3    16.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 33 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31J  LEU*     3.4    15.8    +      -       +      -
     32J  ALA*     1.3    72.2    -      -       -      +
     34J  ASP*     1.3    55.7    +      -       -      +
     35J  GLU*     3.0    15.8    +      -       -      +
     60J  ARG*     3.1    25.7    +      -       -      +
     63J  LEU*     4.4    13.9    -      -       +      -
     64J  PHE*     4.4    22.2    -      -       +      -
     77J  VAL*     4.8     0.4    -      -       +      -
     78J  ILE      3.0    17.3    +      -       -      +
     79J  PHE*     4.3     0.7    -      -       -      -
     80J  PHE      3.7     8.1    +      -       -      -
     83J  THR*     4.9     2.1    +      -       -      +
    307J  GLN*     4.2     1.6    -      -       -      +
----------------------------------------------------------
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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