Contacts of the strand formed by residues 196 - 198 (chain Y) in PDB entry 1T6B


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 VAL 196 (chain Y).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175Y  CYS*     3.3     9.2    -      -       +      +
    181Y  PHE*     4.6     6.1    -      -       +      -
    183Y  GLN*     3.5    31.4    +      -       -      +
    186Y  LEU*     3.8    36.8    -      -       +      +
    187Y  GLU*     4.2     5.2    -      -       +      +
    190Y  ALA*     3.6    22.2    -      -       +      -
    192Y  SER      3.7     8.5    -      -       -      +
    193Y  LYS*     3.1    18.3    +      -       -      +
    194Y  GLU      3.3     1.4    -      -       -      +
    195Y  GLN*     1.3    81.2    -      -       -      +
    197Y  PHE*     1.3    66.9    +      -       -      +
    198Y  PRO*     4.6     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 197 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174Y  TYR*     3.9    22.9    -      +       -      -
    175Y  CYS      3.0     7.4    +      -       -      +
    176Y  VAL*     3.1    14.2    -      -       +      -
    177Y  GLY*     2.6    31.6    +      -       -      -
    181Y  PHE*     4.9     3.1    -      -       -      -
    194Y  GLU      3.3    26.0    -      -       -      -
    195Y  GLN      4.1     5.8    -      -       -      -
    196Y  VAL*     1.3    77.1    -      -       -      +
    198Y  PRO*     1.3    69.6    -      -       +      +
    202Y  GLY*     4.5    11.4    -      -       -      +
    205Y  ALA*     3.6    33.0    -      -       +      -
    206Y  LEU*     4.1    24.7    -      -       +      -
    209Y  ILE*     3.7    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 198 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176Y  VAL*     3.7     2.2    -      -       -      +
    177Y  GLY      3.7     6.3    -      -       -      +
    181Y  PHE*     4.1    25.3    -      -       +      -
    196Y  VAL      4.6     2.5    -      -       -      +
    197Y  PHE*     1.3    90.7    -      -       +      +
    199Y  VAL*     1.3    65.5    +      -       -      +
    200Y  LYS*     3.9    19.3    -      -       +      +
    201Y  GLY      6.0     0.7    -      -       -      -
    202Y  GLY*     3.5    19.7    -      -       -      +
----------------------------------------------------------
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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