Contacts of the strand formed by residues 196 - 201 (chain A) in PDB entry 3HA6


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 196 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  GLU      4.3     0.7    -      -       -      +
    182A  VAL*     3.8    36.8    -      -       +      +
    185A  GLN*     4.1    27.4    +      -       +      +
    186A  SER*     3.6    35.8    -      -       -      +
    189A  ARG*     5.3     0.3    +      -       -      -
    194A  LEU      3.7     1.6    +      -       -      -
    195A  ARG*     1.3    77.1    +      -       -      +
    197A  TYR*     1.3    65.4    +      -       -      +
    198A  GLY      3.2    22.7    +      -       -      +
    199A  TYR*     5.3     0.4    -      -       +      -
    208A  LEU*     3.9    23.1    -      -       +      -
    209A  ILE      3.4    24.5    -      -       -      +
    210A  LEU*     3.8    15.3    -      -       +      -
     13B  PRO*     5.1     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  TRP*     4.9     5.1    +      -       +      -
    157A  PHE*     4.1    18.1    -      +       -      -
    159A  LEU*     3.5    34.3    -      -       +      -
    195A  ARG*     3.5    50.9    +      -       +      +
    196A  LEU*     1.3    71.0    -      -       -      +
    198A  GLY*     1.3    57.7    +      -       -      +
    209A  ILE*     2.9    20.8    +      -       +      +
    211A  GLU*     3.5    36.2    -      -       +      +
     13B  PRO*     3.7    16.5    -      -       -      +
     15B  ASP      5.5     0.3    -      -       -      +
     17B  ILE*     4.9    16.4    -      -       +      +
     19B  PHE*     3.9    27.8    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLY 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  TRP*     4.2     7.2    -      -       -      -
    182A  VAL*     6.3     0.4    -      -       -      -
    196A  LEU*     3.2    12.2    -      -       -      +
    197A  TYR*     1.3    81.4    -      -       -      +
    199A  TYR*     1.3    60.6    +      -       -      -
    209A  ILE*     2.8    36.7    +      -       -      +
     13B  PRO*     3.1    20.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  TRP*     3.8     2.9    -      -       -      -
    182A  VAL*     3.8    24.5    -      -       +      -
    196A  LEU*     5.3     0.2    -      -       +      -
    198A  GLY*     1.3    75.8    -      -       -      +
    200A  PHE*     1.3    76.1    +      -       -      +
    201A  HIS*     4.1    14.6    +      +       -      -
    206A  VAL*     4.4     9.4    -      -       +      -
    207A  TYR      3.3    13.5    -      -       -      +
    208A  LEU*     4.7     8.1    -      -       +      -
    209A  ILE*     4.6     1.1    -      -       -      -
      8B  TYR*     2.8    21.1    +      -       +      -
      9B  SER*     3.5     2.8    -      -       -      -
     10B  TYR*     2.7    57.5    +      +       +      -
     12B  ALA*     3.8    14.6    -      -       +      -
     13B  PRO      2.9    13.5    +      -       -      -
     14B  SER*     3.3    39.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  TRP*     3.4    38.6    -      -       +      +
    129A  ALA*     4.0     1.1    -      -       -      -
    130A  LEU*     3.5    31.4    -      -       +      -
    133A  PHE*     3.5    34.3    -      +       -      -
    161A  LEU*     4.1     2.9    -      -       +      -
    199A  TYR*     1.3    80.9    -      -       -      +
    201A  HIS*     1.3    67.5    +      -       -      +
    206A  VAL*     3.7     2.3    -      -       -      +
    207A  TYR*     2.7    78.7    +      +       +      +
    209A  ILE*     3.8    16.4    -      -       +      -
     14B  SER*     5.5     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  LYS*     2.9    27.4    +      -       -      -
    199A  TYR*     4.1     8.3    +      +       -      -
    200A  PHE*     1.3    86.4    -      -       -      +
    202A  ASP*     1.3    61.2    +      -       -      +
    205A  ARG      3.2    15.5    -      -       -      +
    206A  VAL*     4.0    10.3    -      -       +      -
    207A  TYR*     4.2     5.4    -      -       -      -
      7B  SER      3.5    21.6    +      -       -      -
      8B  TYR*     3.3    27.6    +      -       +      +
      9B  SER*     5.1     1.6    -      -       -      -
----------------------------------------------------------
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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