Contacts of the strand formed by residues 29 - 33 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  ILE      4.8     2.5    -      -       -      -
     28D  LYS*     1.3    74.5    -      -       -      +
     30D  ILE*     1.3    64.2    +      -       -      -
     73D  CYS      2.8    11.2    +      -       -      -
     74D  ILE*     3.5     3.9    -      -       -      -
     75D  GLY*     2.7    24.1    +      -       -      -
     76D  GLY      3.4     3.3    +      -       -      -
    299D  THR*     3.5    10.3    -      -       -      -
    300D  PHE*     3.2    26.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 30 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  ILE*     3.6    33.4    -      -       +      -
     24D  VAL*     6.0     0.4    -      -       +      -
     29D  GLY*     1.3    75.7    -      -       -      +
     31D  LEU*     1.3    64.8    +      -       -      +
     74D  ILE*     4.9     0.4    -      -       -      -
     76D  GLY*     3.3    12.8    -      -       -      +
     78D  ILE*     3.6    34.1    -      -       +      -
    145D  PHE*     4.4     3.4    -      -       +      -
    186D  ILE*     3.8    26.5    -      -       +      -
    228D  LEU*     4.5     0.7    -      -       +      -
    269D  THR*     3.9    22.0    -      -       +      -
    299D  THR*     5.7     0.2    -      -       -      +
    300D  PHE*     2.8    25.3    +      -       -      +
    301D  SER*     3.4    10.7    -      -       -      +
    302D  TYR      3.3    24.3    +      -       -      +
    306D  LEU*     3.7     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 31 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  GLY      4.3     0.4    +      -       -      -
     30D  ILE*     1.3    72.0    -      -       -      +
     32D  ALA*     1.3    62.4    +      -       -      +
     33D  ALA*     3.4     6.3    +      -       +      +
     63D  LEU*     4.2    20.0    -      -       +      -
     64D  PHE*     4.3    11.2    -      -       +      -
     74D  ILE*     4.5    12.2    -      -       +      +
     76D  GLY      2.9    11.8    +      -       -      +
     77D  VAL*     3.3    25.7    -      -       +      +
     78D  ILE      2.8    25.8    +      -       -      -
    302D  TYR      4.2     0.7    -      -       -      +
    306D  LEU*     3.7    26.0    -      -       +      -
    307D  GLN*     3.8    23.3    -      -       +      +
    328D  PHE*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 32 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30D  ILE      3.6     0.6    +      -       -      -
     31D  LEU*     1.3    71.8    -      -       -      +
     33D  ALA*     1.3    54.8    -      -       -      +
     34D  ASP*     3.4    21.7    +      -       -      +
     35D  GLU*     3.7     4.9    -      -       -      +
     78D  ILE*     4.1    11.9    -      -       +      -
    147D  LYS*     5.1     0.4    -      -       -      +
    230D  LYS*     4.1    20.6    -      -       -      +
    301D  SER*     4.4     3.4    -      -       -      +
    302D  TYR      2.9    26.8    +      -       -      +
    303D  GLY*     3.5    10.6    -      -       -      +
    307D  GLN*     3.3    17.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 33 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31D  LEU*     3.4    16.0    +      -       +      -
     32D  ALA*     1.3    73.7    -      -       -      +
     34D  ASP*     1.3    55.8    +      -       -      +
     35D  GLU*     3.0    15.7    +      -       -      +
     60D  ARG*     3.1    25.6    +      -       -      +
     63D  LEU*     4.4    13.7    -      -       +      -
     64D  PHE*     4.4    22.9    -      -       +      -
     77D  VAL*     4.8     0.7    -      -       +      -
     78D  ILE      3.0    16.5    +      -       -      +
     79D  PHE*     4.3     0.7    -      -       -      -
     80D  PHE      3.7     7.6    +      -       -      -
     83D  THR*     4.9     1.9    +      -       -      +
    307D  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