Contacts of the strand formed by residues 184 - 188 (chain I) in PDB entry 6ASX


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 LEU 184 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174I  ALA      3.9     0.3    -      -       -      +
    175I  ARG*     3.6     1.0    -      -       -      -
    176I  ILE*     3.1    54.8    +      -       +      +
    182I  SER      5.0     0.4    -      -       -      +
    183I  TRP*     1.3    78.9    -      -       -      +
    185I  ASP*     1.3    68.7    +      -       -      +
    186I  PHE*     4.0    21.1    -      -       +      -
    196I  VAL*     3.7    27.6    -      -       +      -
    197I  ARG      3.7     4.3    -      -       -      +
    198I  ILE*     3.9    10.5    -      -       +      -
    209I  ILE*     4.7     7.0    -      -       +      -
    389I  PHE*     3.6    37.7    -      -       +      -
    420I  LEU*     4.7     6.1    -      -       +      -
    425I  ILE*     4.9    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 185 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173I  ASN*     6.0     3.1    -      -       +      +
    174I  ALA      3.3     4.0    -      -       -      +
    175I  ARG*     3.3    38.5    +      -       +      +
    183I  TRP*     5.2     7.0    -      -       -      +
    184I  LEU*     1.3    86.6    +      -       -      +
    186I  PHE*     1.3    65.6    +      -       -      +
    187I  GLU*     5.4     5.8    -      -       +      +
    195I  PHE      3.6     1.1    -      -       -      +
    196I  VAL*     3.1     6.4    -      -       -      +
    197I  ARG*     2.9    50.4    +      -       +      +
    200I  ARG*     3.8    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 186 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173I  ASN*     3.2     4.9    -      -       -      +
    174I  ALA*     2.9    37.1    +      -       +      +
    176I  ILE*     5.2     2.5    -      -       +      -
    184I  LEU*     4.0    22.7    -      -       +      -
    185I  ASP*     1.3    80.1    -      -       -      +
    187I  GLU*     1.3    61.0    +      -       -      +
    194I  LEU*     4.6     7.4    -      -       +      -
    195I  PHE      3.5     3.1    -      -       -      +
    196I  VAL*     3.5    33.0    -      -       +      -
    206I  ALA*     5.2     6.1    -      -       +      -
    209I  ILE*     4.9     7.9    -      -       +      -
    425I  ILE*     3.9    24.5    -      -       +      -
    428I  VAL*     4.1    25.6    -      -       +      -
    429I  MET*     3.6    35.7    -      -       +      -
    432I  LEU*     3.7    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 187 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171I  LEU*     6.5     0.4    -      -       +      -
    172I  TYR      4.4     1.6    -      -       -      -
    173I  ASN*     3.7    27.8    +      -       +      +
    185I  ASP*     5.3     5.0    -      -       +      +
    186I  PHE*     1.3    76.6    -      -       -      +
    188I  PHE*     1.3    68.7    +      -       -      +
    193I  ASN      3.7     0.2    -      -       -      +
    194I  LEU*     3.3     9.3    -      -       -      +
    195I  PHE*     2.9    43.0    +      -       +      +
    197I  ARG*     2.8    44.6    +      -       +      -
    200I  ARG*     4.9     5.5    +      -       -      -
    203I  LYS*     3.6    21.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 188 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171I  LEU*     3.6    32.1    -      -       +      +
    172I  TYR*     3.2    38.6    +      -       +      +
    187I  GLU*     1.3    80.6    -      -       -      +
    189I  ASP*     1.3    73.4    +      -       -      +
    192I  ASP*     5.0     3.4    -      -       -      +
    193I  ASN      3.2    17.0    -      -       -      -
    194I  LEU*     3.6    27.1    -      -       +      -
    195I  PHE*     5.5     0.4    -      -       -      -
    346I  TYR*     4.3    30.7    -      +       +      -
    432I  LEU*     3.8    22.9    -      -       +      -
    433I  ILE*     4.7     9.4    -      -       +      -
    436I  ARG*     4.0    35.7    -      -       +      +
----------------------------------------------------------
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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