Contacts of the strand formed by residues 845 - 854 (chain C) in PDB entry 5UH6


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 GLY 845 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  ARG*     6.3     0.2    -      -       -      -
    795C  GLU*     3.7     3.1    -      -       -      -
    796C  VAL*     2.9    37.8    +      -       -      +
    844C  SER*     1.3    76.1    -      -       -      +
    846C  LYS*     1.3    62.0    +      -       -      -
    873C  VAL*     3.6     6.1    -      -       -      +
    874C  ALA      3.2    11.4    -      -       -      -
    875C  GLN*     4.7     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 846 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  LEU      4.3     1.8    +      -       -      -
     61A  HIS*     3.7    34.6    -      -       +      +
     62A  GLU*     3.8    10.2    -      -       +      +
     63A  PHE*     4.4    21.5    -      -       +      -
    153A  ARG*     4.7    22.9    -      -       -      +
    161A  ARG      3.9    19.5    +      -       -      -
    162A  ILE*     4.0    14.3    -      -       -      +
    163A  PRO*     4.6     4.2    -      -       -      +
    793C  GLY      4.0    14.8    -      -       -      +
    794C  ALA      3.7    10.3    -      -       -      +
    795C  GLU*     4.6     9.0    -      -       +      -
    845C  GLY*     1.3    74.8    -      -       -      +
    847C  VAL*     1.3    61.2    +      -       -      +
    848C  ILE*     3.2    12.0    +      -       +      +
    873C  VAL*     3.5     2.2    -      -       -      -
    874C  ALA      3.1    28.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 847 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  HIS*     3.6     2.7    -      -       -      -
    790C  VAL*     3.7    19.1    -      -       +      -
    791C  ARG      3.9    10.1    -      -       -      +
    792C  ILE*     3.4     7.1    -      -       -      +
    793C  GLY      3.0    21.2    +      -       -      +
    794C  ALA      2.9    20.1    +      -       -      +
    796C  VAL*     3.6    31.2    -      -       +      -
    802C  LEU*     4.6     0.4    -      -       +      -
    846C  LYS*     1.3    70.2    -      -       -      +
    848C  ILE*     1.3    58.7    +      -       -      +
    849C  GLY      4.2     0.9    -      -       -      +
    850C  ILE*     3.5    31.6    -      -       +      -
    871C  VAL*     3.6    15.5    -      -       +      -
    872C  TYR      3.8     4.3    -      -       -      +
    873C  VAL*     4.3     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 848 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  HIS*     3.5    31.4    +      -       +      +
     63A  PHE*     3.6    37.7    -      -       +      +
    675C  PHE*     4.7    11.4    -      -       +      +
    752C  ILE*     4.0    26.7    -      -       +      -
    792C  ILE*     4.5     0.9    -      -       -      -
    846C  LYS      3.2    12.8    +      -       -      +
    847C  VAL*     1.3    73.3    -      -       -      +
    849C  GLY*     1.3    54.8    +      -       -      -
    872C  TYR*     2.9    30.7    +      -       +      +
    874C  ALA*     3.6    23.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 849 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    792C  ILE*     4.2    12.9    -      -       -      +
    847C  VAL*     3.4     5.7    +      -       -      +
    848C  ILE*     1.3    79.8    -      -       -      +
    850C  ILE*     1.3    70.2    +      -       -      +
    872C  TYR*     3.1    35.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 850 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    787C  ARG*     4.3    13.9    -      -       -      +
    789C  ILE*     3.8    22.2    -      -       +      -
    790C  VAL*     3.9    19.7    -      -       +      +
    792C  ILE*     4.4    21.0    -      -       +      +
    847C  VAL*     3.5    25.1    -      -       +      -
    849C  GLY*     1.3    82.8    -      -       -      +
    851C  ARG*     1.3    67.0    +      -       -      +
    852C  VAL*     3.5    26.7    -      -       +      +
    869C  VAL*     4.9     1.1    -      -       +      -
    870C  ARG      3.5     2.9    -      -       -      +
    871C  VAL*     4.0    12.1    -      -       +      -
    872C  TYR*     5.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 851 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  ASP*     3.0    40.4    +      -       -      +
    125C  LYS*     5.1     7.3    -      -       -      +
    850C  ILE*     1.3    78.4    -      -       -      +
    852C  VAL*     1.3    75.0    +      -       -      +
    853C  PHE*     3.7    41.6    +      -       +      -
    868C  LEU      3.7     3.6    -      -       -      +
    870C  ARG*     3.0    50.0    +      -       +      +
    872C  TYR*     4.3    12.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 852 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    787C  ARG*     3.7    26.0    -      -       -      +
    789C  ILE*     5.2     2.7    -      -       +      -
    850C  ILE*     3.5    25.9    +      -       +      -
    851C  ARG*     1.3    84.2    +      -       -      +
    853C  PHE*     1.3    79.5    +      -       -      +
    854C  SER*     4.4    10.8    -      -       -      +
    859C  ASP*     4.2     4.3    -      -       -      +
    867C  GLU*     4.8     8.7    -      -       -      +
    868C  LEU      3.7     6.3    -      -       -      +
    869C  VAL*     4.7    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 853 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  ASP*     4.1    16.6    -      -       -      -
    125C  LYS*     5.2    11.4    -      -       +      -
    851C  ARG*     3.7    54.7    -      -       +      -
    852C  VAL*     1.3    79.2    -      -       -      +
    854C  SER*     1.3    61.2    +      -       -      +
    859C  ASP*     3.7    25.1    -      -       +      +
    861C  LEU*     3.8    21.5    -      -       +      +
    866C  ASN      3.8     0.9    -      -       -      +
    867C  GLU*     3.5     3.5    -      -       -      +
    868C  LEU*     2.9    59.3    +      -       +      +
    870C  ARG*     4.1    19.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 854 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    852C  VAL*     4.2     7.9    -      -       -      +
    853C  PHE*     1.3    74.7    -      -       -      +
    855C  ARG*     1.3    64.4    +      -       -      +
    856C  GLU*     3.5     8.9    +      -       -      +
    857C  ASP*     3.5    33.3    +      -       -      -
    859C  ASP*     3.1    33.4    +      -       -      +
    861C  LEU*     4.5     1.1    -      -       -      -
    866C  ASN      3.5     2.5    -      -       -      -
    867C  GLU*     2.9    33.3    +      -       -      +
----------------------------------------------------------
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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