Contacts of the strand formed by residues 198 - 205 (chain C) in PDB entry 5UHE


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 THR 198 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189C  GLU*     3.5    25.6    -      -       -      +
    191C  ILE*     3.7    19.5    -      -       +      -
    197C  LYS*     1.3    73.9    -      -       -      +
    199C  LEU*     1.3    66.0    +      -       -      +
    200C  HIS*     4.0    13.0    +      -       -      -
    349C  HIS*     3.8    23.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 199 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189C  GLU*     3.7     4.0    -      -       -      +
    190C  THR*     3.0    54.0    +      -       +      +
    192C  ASP*     4.1    26.2    -      -       +      +
    197C  LYS*     3.4    28.5    +      -       +      +
    198C  THR*     1.3    79.5    -      -       -      +
    200C  HIS*     1.3    63.4    +      -       -      +
    216C  VAL*     3.7    17.9    -      -       +      +
    217C  ASP*     3.2    26.7    -      -       -      +
    218C  LYS*     3.9    11.0    -      -       +      +
    349C  HIS*     4.9     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 200 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188C  ASP      3.7     4.1    +      -       -      +
    189C  GLU*     4.1    16.0    +      -       +      +
    198C  THR*     4.0    21.4    +      -       -      -
    199C  LEU*     1.3    80.5    -      -       -      +
    201C  SER*     1.3    61.1    +      -       -      +
    216C  VAL*     3.1    28.3    +      -       -      +
    345C  LEU*     3.2    28.5    -      -       +      +
    348C  LEU*     3.2    50.6    +      -       +      +
    349C  HIS*     4.0    23.1    +      +       +      -
    367C  THR*     3.8    20.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 201 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186C  TYR      3.9     0.3    -      -       -      +
    187C  PHE*     3.5     3.0    -      -       -      +
    188C  ASP*     2.8    58.7    +      -       -      +
    190C  THR*     4.4    13.0    -      -       -      +
    199C  LEU      4.1     0.4    +      -       -      -
    200C  HIS*     1.3    73.9    -      -       -      +
    202C  VAL*     1.3    63.8    +      -       -      +
    203C  LYS*     5.0    11.4    +      -       -      +
    214C  PHE      3.9     0.7    -      -       -      -
    215C  ASP*     3.3    25.6    -      -       -      +
    216C  VAL      5.3     0.2    -      -       -      -
    345C  LEU*     4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 202 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185C  VAL*     3.5    18.6    -      -       +      -
    186C  TYR      3.4     9.2    -      -       -      +
    187C  PHE*     3.5    38.6    -      -       +      -
    201C  SER*     1.3    76.4    -      -       -      +
    203C  LYS*     1.3    74.6    +      -       -      +
    204C  VAL*     5.1     1.3    -      -       +      -
    213C  GLU*     3.1    16.6    -      -       -      +
    214C  PHE*     2.8    32.5    +      -       +      +
    215C  ASP*     3.5     3.1    -      -       -      +
    341C  THR*     4.0    11.4    -      -       +      -
    345C  LEU*     3.6    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 203 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181C  ARG*     4.8    15.4    -      -       -      +
    184C  GLY      3.8     1.9    -      -       -      +
    185C  VAL*     3.5     1.4    -      -       -      -
    186C  TYR*     3.0    38.7    +      -       +      +
    188C  ASP*     5.4    11.1    +      -       +      +
    201C  SER*     5.0    14.6    +      -       -      +
    202C  VAL*     1.3    79.9    -      -       -      +
    204C  VAL*     1.3    64.1    +      -       -      +
    205C  ILE*     3.9    13.7    +      -       +      +
    211C  TRP*     5.7    12.8    -      -       +      -
    212C  LEU      4.1     4.0    -      -       -      -
    213C  GLU*     3.8    25.1    -      -       +      +
    215C  ASP*     5.3     0.4    -      -       -      -
     14H    G      5.8     3.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 204 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184C  GLY      3.9     5.8    -      -       -      +
    185C  VAL*     4.1    22.9    -      -       +      -
    202C  VAL*     5.1     1.6    -      -       +      -
    203C  LYS*     1.3    74.4    -      -       -      +
    205C  ILE*     1.3    64.3    +      -       -      +
    206C  PRO*     3.6     7.6    -      -       -      +
    211C  TRP*     4.6     4.7    -      -       -      -
    212C  LEU*     2.9    47.4    +      -       +      +
    214C  PHE*     5.2     5.2    -      -       +      -
    306C  TYR*     3.3    23.2    +      -       -      +
    308C  LEU*     5.3     3.8    -      -       +      -
    316C  VAL*     6.0     2.7    -      -       +      -
    333C  LEU*     4.8    17.7    -      -       +      -
    341C  THR*     4.6    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 205 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181C  ARG*     3.4    46.0    -      -       +      +
    182C  SER      4.6     1.3    -      -       -      +
    183C  PRO*     3.6     7.1    -      -       +      +
    184C  GLY*     3.0    33.3    +      -       -      +
    186C  TYR*     3.6    23.8    -      -       +      -
    203C  LYS*     4.1    13.0    -      -       +      +
    204C  VAL*     1.3    76.4    -      -       -      +
    206C  PRO*     1.3    76.3    -      -       +      +
    211C  TRP*     4.8    19.7    -      -       +      +
    308C  LEU*     3.9     6.9    -      -       -      +
     13H    T      5.3    13.5    -      -       +      +
----------------------------------------------------------
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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