Contacts of the strand formed by residues 198 - 202 (chain A) in PDB entry 5TOL


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 PHE 198 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  THR*     4.1     8.1    -      -       +      -
    169A  LEU*     3.8    34.5    -      -       +      -
    185A  PHE*     3.8    32.3    -      +       +      -
    197A  LEU*     1.3    78.5    -      -       -      +
    199A  SER*     1.3    63.9    +      -       -      +
    200A  LEU*     4.1    10.5    -      -       +      -
    222A  MET*     4.0    17.0    -      -       +      -
    223A  ILE      3.1    14.4    -      -       -      +
    224A  ILE*     4.1     4.5    -      -       -      -
    226A  GLY      4.4     2.2    -      -       -      -
    247A  TYR*     3.4    24.9    -      -       -      -
    392A  VAL*     4.5     0.4    -      -       -      +
    393A  PHE*     2.8    69.9    +      +       +      +
    395A  ARG*     4.0     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  PHE*     1.3    75.9    -      -       -      +
    200A  LEU*     1.3    65.0    +      -       -      +
    221A  SER      3.7     0.5    -      -       -      +
    222A  MET*     3.3     6.9    -      -       -      +
    223A  ILE*     2.9    35.0    +      -       -      +
    226A  GLY      2.8    16.9    +      -       -      -
    390A  TYR*     2.7    37.2    +      -       -      -
    391A  VAL      3.3    11.9    -      -       -      -
    392A  VAL*     4.1    13.5    -      -       -      -
    393A  PHE*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  LEU*     4.2     9.4    -      -       +      -
     79A  VAL*     4.0    23.6    -      -       +      -
     81A  THR*     3.6    30.3    -      -       +      -
    198A  PHE*     4.1     7.0    -      -       +      -
    199A  SER*     1.3    74.5    -      -       -      +
    201A  GLN*     1.3    58.1    +      -       -      +
    202A  LEU*     3.9     8.9    +      -       +      -
    221A  SER      3.5     2.5    -      -       -      +
    222A  MET*     3.6    36.1    -      -       +      -
    277A  SER*     4.1     6.1    -      -       -      +
    386A  MET*     4.0    17.6    -      -       +      +
    389A  PHE      3.9     3.5    -      -       -      +
    390A  TYR*     3.8     4.8    -      -       -      -
    391A  VAL*     2.9    34.5    +      -       -      +
    393A  PHE*     3.8    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  SER      4.3     0.2    -      -       -      -
    200A  LEU*     1.3    72.8    -      -       -      +
    202A  LEU*     1.3    60.8    +      -       -      +
    203A  CYS*     3.7     8.8    -      -       -      -
    220A  GLY*     3.0     8.3    -      -       -      -
    221A  SER*     2.8    46.2    +      -       -      +
    231A  LEU*     2.9    57.9    +      -       +      +
    389A  PHE      4.5     3.6    -      -       -      +
    390A  TYR*     3.9    16.4    -      -       +      -
    405A  SER*     3.1    25.4    +      -       -      +
    406A  ALA*     3.6     6.9    -      -       -      +
    407A  CYS*     3.5    24.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  LEU*     3.7    29.6    -      -       +      -
     62A  TYR*     3.7    43.5    -      -       +      +
     79A  VAL*     5.8     1.6    -      -       +      -
    200A  LEU*     3.9    18.5    +      -       +      -
    201A  GLN*     1.3    74.9    -      -       -      +
    203A  CYS*     1.3    60.3    +      -       -      +
    277A  SER*     4.0    28.9    -      -       -      +
    383A  ALA*     5.1     6.5    -      -       -      -
    386A  MET*     3.9    31.6    +      -       +      +
    387A  GLU*     3.2    33.0    -      -       +      +
    389A  PHE      4.7     0.4    +      -       -      +
    405A  SER*     5.1     0.3    +      -       -      -
    407A  CYS*     4.4     2.8    -      -       -      -
----------------------------------------------------------
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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