Contacts of the strand formed by residues 194 - 199 (chain A) in PDB entry 4BU2


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 LYS 194 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  TYR*     4.9     2.6    +      -       -      +
    169A  THR*     2.8    37.0    +      -       -      +
    175A  GLY*     5.4     1.2    -      -       -      -
    189A  GLN*     4.0    11.4    -      -       -      +
    193A  GLU*     1.3    73.8    -      -       -      +
    195A  HIS*     1.3    63.7    +      -       -      +
    196A  TRP*     3.5    26.6    +      -       +      +
    225A  MSE      3.4     6.5    -      -       -      -
    226A  LEU*     2.9    30.9    +      -       +      -
    242A  ALA*     3.7    14.1    -      -       +      -
    243A  ASP*     3.8    10.1    -      -       -      +
    244A  THR*     3.8     8.1    -      -       -      +
    251A  SER*     3.1    26.7    +      -       -      +
    253A  HIS*     4.3     9.6    +      -       -      +
    701A  AKG      3.1    34.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  LYS*     1.3    69.6    -      -       -      +
    196A  TRP*     1.3    67.0    +      -       -      +
    197A  ARG*     4.1    21.4    +      -       -      +
    223A  GLU*     3.1    34.4    +      -       +      +
    224A  PHE      3.7    12.6    -      -       -      -
    225A  MSE      3.8    22.0    -      -       +      -
    241A  GLN      3.9     0.3    -      -       -      +
    242A  ALA*     3.0     5.5    -      -       -      -
    243A  ASP*     2.7    51.5    +      -       -      +
    245A  PRO*     4.7     1.8    -      -       +      -
    602A   NI      2.4    36.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187A  ILE*     3.4    28.9    -      -       +      +
    189A  GLN*     4.8     1.0    +      -       -      -
    194A  LYS*     3.6    31.0    -      -       +      +
    195A  HIS*     1.3    71.6    -      -       -      +
    197A  ARG*     1.3    69.6    +      -       -      +
    198A  LEU*     4.1    11.9    -      -       +      -
    222A  HIS      4.8     0.2    -      -       -      -
    223A  GLU*     3.3     3.2    -      -       -      +
    224A  PHE*     2.8    57.7    +      +       +      +
    226A  LEU*     3.3    30.8    -      -       +      +
    232A  LEU*     3.8    10.8    -      -       +      -
    234A  PHE*     4.0     8.5    -      +       -      -
    240A  HIS*     3.4    36.8    -      +       +      -
    241A  GLN      3.7    10.8    -      -       -      -
    242A  ALA*     3.7    13.0    -      -       +      -
    253A  HIS*     4.0    19.8    -      +       -      -
    701A  AKG      4.0    15.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  GLN*     5.4     1.6    +      -       -      -
    195A  HIS*     4.1    18.3    +      -       -      +
    196A  TRP*     1.3    79.9    -      -       -      +
    198A  LEU*     1.3    62.4    +      -       -      +
    199A  TYR*     3.3    33.0    +      -       +      +
    214A  GLU*     4.9     5.1    +      -       -      -
    220A  PRO*     4.1    12.4    -      -       +      +
    222A  HIS      3.6     5.6    -      -       -      -
    223A  GLU*     3.8    29.4    -      -       +      +
    240A  HIS*     3.4     1.0    -      -       -      -
    241A  GLN*     3.1    61.5    +      -       +      +
    243A  ASP*     4.0    16.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  PRO*     3.6    35.7    -      -       +      -
    196A  TRP*     4.1    15.0    -      -       +      -
    197A  ARG*     1.3    76.1    -      -       -      +
    199A  TYR*     1.3    61.1    +      -       -      +
    220A  PRO*     3.4     4.5    -      -       -      +
    221A  VAL*     2.9    27.6    +      -       +      -
    222A  HIS*     2.9    25.7    +      -       +      +
    224A  PHE*     4.0    27.1    -      -       +      -
    232A  LEU*     4.4     4.9    -      -       +      -
    234A  PHE*     4.2    14.6    -      -       +      -
    238A  THR*     4.5     7.4    -      -       +      -
    239A  ILE      3.4     4.5    -      -       -      +
    240A  HIS*     3.7    23.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  PRO*     5.4     0.2    -      -       +      -
    197A  ARG*     3.3    39.3    +      -       +      -
    198A  LEU*     1.3    75.6    -      -       -      +
    200A  HIS*     1.3    66.4    +      -       -      +
    201A  PRO*     3.5     4.2    -      -       -      +
    214A  GLU*     4.4     1.0    +      -       -      -
    217A  ILE*     3.4    43.5    -      -       +      +
    218A  GLY      3.6     6.7    -      -       -      -
    219A  ARG      3.8     0.7    -      -       -      -
    220A  PRO*     3.4    41.9    -      -       +      +
    221A  VAL*     4.2     8.5    -      -       -      -
    238A  THR*     4.2     6.1    -      -       -      +
    239A  ILE*     2.8    47.4    +      -       +      +
    240A  HIS*     4.4     0.4    -      -       -      -
    241A  GLN*     2.7    37.1    +      -       +      -
----------------------------------------------------------
 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