Contacts of the strand formed by residues 846 - 853 (chain C) in PDB entry 5D4D


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 LYS 846 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445C  GLU*     4.0    17.4    +      -       -      -
    557C  ARG*     4.4    10.3    +      -       -      +
    560C  MET*     4.0    24.2    -      -       -      +
    564C  MET*     3.6    32.9    -      -       +      -
    686C  ASP*     3.7    19.7    -      -       -      +
    688C  ILE*     5.0     2.9    -      -       -      -
    838C  LYS*     4.1    11.2    -      -       -      -
    839C  LEU      3.3     6.7    -      -       -      +
    840C  ALA*     3.9     3.8    -      -       +      -
    844C  GLY      4.1     7.2    -      -       -      +
    845C  ASN*     1.3    83.3    +      -       -      +
    847C  GLY*     1.3    58.3    +      -       -      +
    741D  ASP*     3.7    28.4    +      -       +      +
   2005D    C      2.6    31.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 847 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    686C  ASP      3.2    16.4    -      -       -      -
    688C  ILE*     4.3     8.1    -      -       -      +
    838C  LYS*     3.5     5.4    -      -       -      +
    839C  LEU*     2.8    35.7    +      -       -      +
    846C  LYS*     1.3    76.3    -      -       -      +
    848C  VAL*     1.3    65.1    +      -       -      -
    740D  PHE      3.5     8.3    -      -       -      -
    741D  ASP*     4.1     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 848 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    686C  ASP      4.0     0.8    +      -       -      -
    687C  ALA*     3.5     1.7    -      -       -      -
    688C  ILE*     2.8    23.9    +      -       -      -
    836C  GLY*     3.8    21.5    -      -       -      +
    837C  ASP      3.3     7.9    -      -       -      +
    838C  LYS*     4.5     7.4    -      -       +      -
    847C  GLY*     1.3    75.6    -      -       -      +
    849C  VAL*     1.3    61.9    +      -       -      +
    850C  ALA      3.2     0.7    +      -       -      -
    630D  VAL*     4.2     6.3    -      -       +      -
    631D  ILE      3.8    10.1    -      -       -      +
    632D  VAL*     3.5    24.7    -      -       +      -
    740D  PHE*     2.9    33.3    +      -       +      +
    741D  ASP      4.4     0.4    -      -       -      -
    742D  GLY*     3.7    25.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 849 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    688C  ILE*     3.3     7.2    -      -       +      +
    690C  ILE*     3.8    26.2    -      -       +      -
    833C  LEU*     4.4     7.2    -      -       +      -
    834C  GLN      3.8    19.3    -      -       -      +
    835C  VAL*     3.1    10.8    -      -       -      +
    836C  GLY      3.0    20.1    +      -       -      +
    837C  ASP      3.1    12.9    +      -       -      +
    839C  LEU*     4.0    28.9    -      -       +      -
    848C  VAL*     1.3    70.5    -      -       -      +
    850C  ALA*     1.3    58.4    -      -       -      +
    851C  LYS      3.9     6.7    -      -       -      +
    852C  ILE*     3.7    28.9    -      -       +      -
    632D  VAL*     3.4     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 850 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682C  TYR*     3.5    28.3    -      -       +      +
    687C  ALA*     3.8    10.8    -      -       +      -
    688C  ILE      2.9     6.3    +      -       -      -
    835C  VAL*     4.2     9.4    -      -       -      +
    848C  VAL      3.2     1.0    +      -       -      -
    849C  VAL*     1.3    75.1    -      -       -      +
    851C  LYS*     1.3    65.7    +      -       -      +
    632D  VAL*     3.6    29.9    -      -       +      +
    633D  VAL*     3.6    20.5    -      -       +      +
    727D  GLN*     5.4     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 851 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183B  ASP*     4.7    14.1    +      -       -      -
    682C  TYR*     3.6    60.5    +      -       +      -
    688C  ILE      3.8     2.2    +      -       -      -
    689C  VAL*     3.6     8.4    -      -       +      +
    690C  ILE*     3.0    26.3    +      -       -      +
    835C  VAL*     4.6     2.0    -      -       -      -
    849C  VAL*     3.5     2.3    -      -       -      +
    850C  ALA*     1.3    83.3    -      -       -      +
    852C  ILE*     1.3    70.8    +      -       -      +
    853C  LEU*     3.6    32.3    -      -       +      -
    636D  GLN*     5.4     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 852 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    690C  ILE*     3.3    29.2    -      -       +      +
    691C  SER      4.2     1.3    -      -       -      -
    692C  GLU*     3.6    36.3    -      -       +      +
    695C  LEU*     4.2    15.3    -      -       +      -
    833C  LEU      4.0     6.3    -      -       -      +
    834C  GLN*     4.0    28.0    -      -       +      -
    835C  VAL*     4.2    15.6    -      -       +      +
    849C  VAL*     3.7     6.3    -      -       +      -
    851C  LYS*     1.3    81.6    -      -       -      +
    853C  LEU*     1.3    62.3    +      -       -      +
    854C  PRO*     4.0     5.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 853 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679C  PHE*     3.5    40.8    -      -       +      -
    682C  TYR*     5.7     0.9    -      -       +      -
    689C  VAL*     3.7    22.0    -      -       +      -
    690C  ILE      3.0     6.9    +      -       -      -
    691C  SER*     3.5     2.6    -      -       -      -
    692C  GLU*     2.6    33.9    +      -       -      +
    851C  LYS*     3.6    30.7    -      -       +      -
    852C  ILE*     1.3    72.3    -      -       -      +
    854C  PRO*     1.3    75.7    -      -       +      +
    857C  ASP*     4.3    19.1    -      -       +      +
    858C  MET*     3.8    24.0    -      -       -      -
    870C  ILE*     4.6     0.9    -      -       +      -
----------------------------------------------------------
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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