Contacts of the strand formed by residues 193 - 196 (chain A) in PDB entry 3UE8


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 PHE 193 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  PHE*     3.7    27.6    -      +       -      -
    128A  ILE*     3.7    22.9    -      -       +      -
    129A  ILE*     3.2    27.4    -      -       +      -
    134A  ASN      4.3     1.2    +      -       -      -
    135A  VAL*     3.4    32.1    -      -       +      -
    136A  LEU*     2.9    27.6    +      -       -      +
    149A  LEU*     3.8    11.2    -      -       +      -
    191A  PRO*     3.4     1.7    -      -       -      +
    192A  LYS*     1.3    77.8    -      -       -      +
    194A  LEU*     1.3    71.4    +      -       -      +
    195A  TYR*     3.7    18.8    -      -       +      -
    225A  PHE*     4.4     6.1    -      -       -      -
    226A  LEU*     3.1    25.6    -      -       +      +
    228A  ILE*     3.7    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  LEU*     3.2    30.3    -      -       +      -
    137A  LEU*     4.3     2.5    -      -       -      +
    138A  ASP      5.8     0.2    -      -       -      +
    159A  VAL*     4.4     7.4    -      -       +      -
    166A  ILE*     5.0    11.2    -      -       +      -
    171A  LEU*     4.1    20.2    -      -       +      -
    193A  PHE*     1.3    76.3    -      -       -      +
    195A  TYR*     1.3    64.8    +      -       -      +
    196A  THR*     4.6    16.2    -      -       +      -
    216A  ILE*     3.6    28.7    -      -       +      -
    225A  PHE*     3.6    20.2    -      -       +      -
    226A  LEU      2.8     8.3    +      -       -      +
    227A  ILE*     3.5    21.9    -      -       +      +
    228A  ILE      3.0    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  LEU*     4.0     6.1    -      -       +      -
    125A  PHE*     3.7    28.0    -      +       -      -
    136A  LEU      2.6    15.3    +      -       -      +
    137A  LEU*     3.6    39.4    -      -       +      -
    138A  ASP*     4.1     5.9    +      -       -      +
    141A  ALA*     4.9     9.4    -      -       +      -
    142A  TYR*     4.3     4.3    -      -       -      +
    145A  THR*     2.8    34.4    -      -       +      +
    149A  LEU*     5.5     0.2    -      -       +      -
    166A  ILE*     5.6     0.3    -      -       -      +
    193A  PHE*     3.7    15.3    -      +       +      -
    194A  LEU*     1.3    77.3    -      -       -      +
    196A  THR*     1.3    67.7    +      -       -      +
    197A  VAL*     4.2    13.9    -      -       +      +
    201A  ASN*     6.2     0.2    -      -       -      -
    228A  ILE*     3.8    15.9    -      -       +      -
    230A  ASP*     2.6    43.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  ASP*     3.4    17.5    +      -       -      -
    166A  ILE*     3.6    15.1    -      -       +      +
    194A  LEU*     4.3    11.6    -      -       +      -
    195A  TYR*     1.3    80.7    -      -       -      +
    197A  VAL*     1.4    71.5    +      -       -      +
    198A  PRO*     3.2    14.2    -      -       +      +
    208A  LEU*     4.1    10.7    -      -       +      +
    227A  ILE*     5.1     1.6    -      -       +      -
    228A  ILE      3.3     8.8    +      -       -      +
    229A  GLU*     5.3     0.4    -      -       -      -
    230A  ASP*     2.9    29.9    +      -       -      +
    246A  PHE*     3.7    30.7    -      -       +      -
----------------------------------------------------------
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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