Contacts of the strand formed by residues 17 - 23 (chain A) in PDB entry 1BXO


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 TYR 17 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ASN*     3.7    23.6    -      -       +      -
      9A  THR      3.4     4.0    -      -       -      +
     10A  PRO*     3.5    29.2    -      -       +      -
     14A  ASP*     3.4    16.1    -      -       +      +
     16A  GLU*     1.3    77.0    -      -       -      +
     18A  ILE*     1.3    63.8    +      -       -      +
     19A  THR*     5.0     1.5    +      -       -      -
     30A  LEU      3.9     0.3    -      -       -      +
     31A  ASN*     3.6    28.1    +      -       -      +
     32A  PHE      4.1     4.1    +      -       -      +
    157A  LEU*     3.9    26.5    -      -       +      -
    158A  LYS      2.8    39.7    +      -       -      -
    165A  TYR*     5.4     5.8    -      -       +      +
    214A  THR      5.2     4.1    +      -       -      +
    300A  ASP*     3.5    35.4    -      -       +      -
    304A  LYS*     3.3    23.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  THR      4.0     0.7    -      -       -      +
      8A  ASN*     3.3     3.1    -      -       -      -
      9A  THR*     2.9    37.9    +      -       -      +
     11A  THR*     3.8    22.7    -      -       +      -
     16A  GLU*     4.3    11.4    -      -       +      +
     17A  TYR*     1.3    81.2    -      -       -      +
     19A  THR*     1.3    65.0    +      -       -      +
     20A  PRO*     4.7     1.2    -      -       -      +
     29A  ASN*     3.3    40.4    -      -       +      +
     30A  LEU      3.4     5.8    -      -       -      +
     31A  ASN*     4.5     3.6    -      -       +      +
    117A  ASN      3.6    20.0    -      -       -      +
    118A  ASN*     3.7    20.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ALA*     3.8    22.7    -      -       +      -
      7A  THR      3.6    13.2    -      -       -      +
      8A  ASN*     3.2    20.4    -      -       -      +
     17A  TYR      5.0     1.0    +      -       -      -
     18A  ILE*     1.3    76.4    +      -       -      +
     20A  PRO*     1.4    74.7    -      -       +      +
     21A  VAL*     3.7     5.7    +      -       -      +
     29A  ASN*     4.5     2.9    -      -       -      -
     30A  LEU      2.9    26.6    +      -       -      +
     32A  PHE*     3.6    35.7    -      -       +      +
    165A  TYR*     4.0    11.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ALA*     5.5     0.5    -      -       -      +
      7A  THR*     3.5    18.8    -      -       -      +
     18A  ILE      4.7     0.9    -      -       -      +
     19A  THR*     1.4    93.3    -      -       +      +
     21A  VAL*     1.3    63.6    +      -       -      +
     27A  THR*     3.8    17.7    -      -       +      -
     28A  LEU      3.4     7.4    -      -       -      +
     29A  ASN*     3.8    15.3    -      -       -      +
     91A  THR      4.5     2.3    -      -       -      +
     92A  VAL*     4.8     6.1    -      -       -      -
     93A  GLY      5.1     3.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  THR      3.8     4.0    -      -       -      +
     20A  PRO*     1.3    82.2    -      -       -      +
     22A  THR*     1.3    66.6    +      -       -      +
     23A  ILE*     3.8    14.4    +      -       +      +
     26A  THR      3.6     1.0    -      -       -      +
     27A  THR*     3.4     1.9    -      -       -      +
     28A  LEU*     2.9    32.0    +      -       -      +
     30A  LEU*     3.9    22.9    -      -       +      -
     32A  PHE*     3.5    33.7    -      -       +      -
     90A  VAL*     3.6    30.5    -      -       +      -
     91A  THR      3.5     9.2    -      -       -      +
     92A  VAL*     4.0     6.7    -      -       +      -
    122A  LEU*     4.1     3.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  VAL*     1.3    70.4    -      -       -      +
     23A  ILE*     1.3    61.9    +      -       -      +
     25A  GLY*     3.7    34.3    -      -       -      +
     26A  THR      3.5     3.6    -      -       -      +
     27A  THR*     2.8    23.1    +      -       -      +
     89A  SER      3.6     1.6    -      -       -      +
     90A  VAL*     3.4     4.2    -      -       -      -
     91A  THR*     2.8    50.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  VAL*     4.0    22.7    -      -       +      +
     22A  THR*     1.3    75.2    -      -       -      +
     24A  GLY*     1.3    70.4    +      -       -      +
     25A  GLY      3.1     0.2    -      -       -      -
     26A  THR*     2.8    27.0    +      -       -      +
     28A  LEU*     3.3    35.9    -      -       +      -
     30A  LEU*     4.4     4.7    -      -       +      -
     39A  LEU*     4.8     3.4    -      -       +      -
     41A  VAL*     4.0    14.8    -      -       +      -
     57A  TYR*     3.7    32.8    -      -       +      -
     88A  ASP*     4.3     2.7    -      -       +      -
     89A  SER      3.3     8.5    -      -       -      +
     90A  VAL*     4.1    10.8    -      -       +      -
    102A  VAL*     3.9    22.0    -      -       +      -
----------------------------------------------------------
 Back to top of page


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