Contacts of the strand formed by residues 192 - 196 (chain F) in PDB entry 4O9U


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 GLN 192 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352B  TYR*     4.8    20.2    -      -       +      +
    353B  ASP*     5.6     5.1    +      -       -      -
    167F  PRO*     3.6    28.3    -      -       +      +
    168F  ALA      3.2     5.5    +      -       -      +
    169F  LYS*     3.3    34.8    -      -       +      +
    170F  VAL*     2.8    26.5    +      -       -      +
    187F  LYS*     5.8     1.8    -      -       -      +
    190F  GLY      3.8     2.4    +      -       -      -
    191F  ALA*     1.3    69.1    -      -       -      +
    193F  VAL*     1.3    59.6    +      -       -      +
    194F  PHE*     4.3    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 193 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170F  VAL*     3.3    11.2    -      -       +      +
    172F  VAL*     4.0    15.9    -      -       +      -
    183F  ILE*     3.8    33.4    -      -       +      +
    186F  ALA*     3.9    22.9    -      -       +      -
    187F  LYS*     4.1    13.5    -      -       +      +
    191F  ALA*     3.2    21.2    +      -       +      +
    192F  GLN*     1.3    73.7    -      -       -      +
    194F  PHE*     1.3    86.1    +      -       -      +
    211F  ALA*     3.2    23.7    -      -       +      +
    212F  LYS      3.8     3.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 194 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169F  LYS*     4.0    24.2    -      -       +      -
    170F  VAL      2.7    16.0    +      -       -      +
    171F  MET*     3.3     8.1    -      -       +      -
    172F  VAL*     2.8    24.8    +      -       -      -
    192F  GLN*     4.3    13.5    -      -       +      -
    193F  VAL*     1.3    86.4    -      -       -      +
    195F  ALA*     1.3    62.5    +      -       -      +
    211F  ALA*     4.1     2.7    -      -       -      -
    212F  LYS*     3.2    36.3    -      -       +      +
    213F  PRO      5.4     0.2    -      -       -      -
    214F  ILE*     3.7    28.0    -      -       +      -
    249F  MET*     3.6    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 195 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172F  VAL      3.5     4.9    -      -       -      +
    175F  VAL*     3.8    12.7    -      -       +      +
    183F  ILE*     3.7    29.6    -      -       +      -
    194F  PHE*     1.3    77.2    -      -       -      +
    196F  TYR*     1.3    62.1    +      -       -      +
    197F  ASP      4.3     0.5    +      -       -      -
    203F  LEU*     4.6     6.6    -      -       -      +
    206F  ALA*     3.7    20.4    -      -       +      +
    211F  ALA*     4.6     4.1    -      -       +      +
    212F  LYS      4.2     4.8    +      -       -      -
    213F  PRO*     4.0     8.3    -      -       +      +
    214F  ILE*     3.8    19.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 196 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171F  MET*     4.9     3.4    -      -       -      +
    172F  VAL      3.4     7.7    +      -       -      +
    173F  MET*     4.2    21.8    -      -       +      -
    174F  GLY*     2.7    32.7    +      -       -      -
    175F  VAL*     3.6     4.1    +      -       -      +
    195F  ALA*     1.3    73.3    -      -       -      +
    197F  ASP*     1.3    78.0    +      -       -      +
    198F  VAL*     3.8    15.5    -      -       +      +
    203F  LEU*     5.0     1.8    -      -       +      -
    214F  ILE*     4.4    23.8    -      -       +      -
    216F  LEU*     4.7    17.4    +      -       -      -
    218F  ILE*     4.6     9.5    -      -       -      +
    238F  GLN*     3.9    25.9    -      -       +      +
    242F  LEU*     3.6    34.1    -      -       +      -
    266F  LEU*     5.2     1.3    -      -       +      -
    500F  NAD      3.6    27.8    -      +       -      -
----------------------------------------------------------
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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