Contacts of the strand formed by residues 181 - 183 (chain A) in PDB entry 5TWV


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 181 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  ARG      4.3     4.3    -      -       -      +
    178A  ALA*     3.0    36.5    +      -       +      +
    179A  GLU*     2.6    14.6    +      -       -      +
    180A  THR*     1.3    71.7    -      -       -      +
    182A  ILE*     1.3    61.7    +      -       -      +
    183A  PHE*     4.1    11.1    +      -       -      -
    202A  VAL*     5.3     3.4    -      -       +      -
    203A  GLY      3.7     7.6    -      -       -      +
    204A  ASP*     3.8    18.2    -      -       +      +
    210A  ILE*     4.1    33.9    -      -       +      -
    251A  LEU*     5.8     1.8    -      -       +      -
    287A  LEU*     4.0    33.4    -      -       +      +
    298A  THR*     4.9     7.6    -      -       +      -
    300A  ALA*     4.2    10.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  LYS*     6.5     0.2    -      -       -      -
    179A  GLU*     3.9    21.8    -      -       +      +
    180A  THR      3.4     2.2    +      -       -      +
    181A  LEU*     1.3    75.1    -      -       -      +
    183A  PHE*     1.3    67.4    +      -       -      +
    202A  VAL*     3.5     6.2    -      -       -      +
    203A  GLY*     3.0    37.8    +      -       -      +
    205A  LEU*     4.0    31.0    -      -       +      -
    330A  TYR*     6.1     3.8    -      -       +      -
    333A  PHE*     4.0    11.3    -      -       +      -
    401G  ATP      2.9    57.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  LYS*     4.8     2.0    +      -       -      +
    181A  LEU      4.6     7.0    -      -       -      -
    182A  ILE*     1.3    87.1    -      -       -      +
    184A  SER*     1.3    67.4    +      -       -      +
    201A  ARG      4.0     5.2    -      -       -      +
    202A  VAL*     3.8    31.0    -      -       +      -
    215A  ILE*     6.3     0.2    -      -       +      -
    285A  VAL*     4.0    23.1    -      -       +      -
    287A  LEU*     3.7    27.8    -      -       +      -
    300A  ALA*     3.8    30.5    -      -       +      -
    301A  ARG      4.5     0.7    -      -       -      -
    302A  THR*     3.3    39.9    -      -       +      +
    304A  TYR*     3.6    14.4    -      +       -      +
    333A  PHE*     3.8     3.4    -      -       -      -
    401G  ATP      3.5    10.9    +      -       -      -
----------------------------------------------------------
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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