Contacts of the strand formed by residues 874 - 880 (chain C) in PDB entry 4YOC


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 874 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    794C  VAL*     3.7    28.0    -      -       +      -
    795C  ASP      3.9    12.9    +      -       -      +
    796C  VAL*     3.5     5.9    -      -       -      +
    797C  ILE*     2.9    26.7    +      -       -      +
    865C  LEU*     4.1    22.4    -      -       +      -
    868C  PHE*     3.8    31.4    -      -       +      -
    869C  LYS      3.2    16.3    +      -       -      -
    870C  PRO*     4.0    15.5    +      -       -      +
    872C  GLN      3.2    18.0    +      -       -      -
    873C  PRO*     1.3    70.0    -      -       -      +
    875C  LYS*     1.3    63.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 875 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    797C  ILE*     3.2    31.9    -      -       +      +
    799C  CYS*     3.5    27.1    -      -       -      -
    806C  ASP      4.9     5.0    +      -       -      -
    807C  PRO*     5.3     1.9    +      -       -      +
    842C  SER*     3.9     8.4    -      -       -      -
    847C  ASP*     2.9    41.9    +      -       -      +
    865C  LEU*     4.0     4.8    -      -       -      +
    868C  PHE*     3.4    29.8    -      -       +      -
    873C  PRO*     3.5    11.2    +      -       +      +
    874C  LYS*     1.3    75.2    -      -       -      +
    876C  LEU*     1.3    63.5    +      -       -      +
    877C  TYR*     4.0    18.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 876 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    796C  VAL*     3.8    19.5    -      -       +      -
    797C  ILE      2.8     6.1    +      -       -      -
    798C  PHE*     3.2    20.9    -      -       +      -
    799C  CYS      3.0    22.6    +      -       -      -
    822C  VAL*     5.6     2.5    -      -       +      -
    839C  PHE*     3.5    27.4    -      -       +      -
    840C  PHE      3.8    12.6    -      -       -      +
    841C  LYS*     4.5     8.1    -      -       -      -
    842C  SER      5.0     0.9    -      -       -      +
    853C  LEU*     5.2     0.4    -      -       +      -
    861C  LEU*     5.0     4.5    -      -       +      -
    864C  LEU*     4.1    38.8    -      -       +      +
    865C  LEU*     4.3     8.1    -      -       +      -
    875C  LYS*     1.3    79.4    -      -       -      +
    877C  TYR*     1.3    86.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 877 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    799C  CYS*     3.3    32.5    -      -       +      +
    800C  ASP      5.2     0.2    -      -       -      -
    801C  LYS*     4.8     9.2    -      -       +      -
    839C  PHE*     3.5     0.9    -      -       -      -
    840C  PHE*     2.9    49.6    +      -       +      +
    842C  SER*     4.1    19.7    -      -       -      -
    847C  ASP*     3.0    24.8    +      -       -      -
    848C  GLY*     3.0    39.6    +      -       -      -
    849C  PRO*     3.6    32.8    -      -       +      -
    875C  LYS*     4.0    17.2    -      -       +      -
    876C  LEU*     1.3    85.7    -      -       -      +
    878C  TYR*     1.3    65.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 878 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    798C  PHE*     3.8    20.2    -      +       +      -
    799C  CYS*     2.9    46.3    +      -       -      -
    800C  ASP*     3.3    32.1    +      -       +      +
    801C  LYS*     3.0    25.1    +      -       -      +
    806C  ASP*     4.8     2.9    +      -       -      -
    809C  PHE*     3.7    12.4    -      +       -      -
    826C  VAL*     5.0     3.4    -      -       +      -
    830C  LEU*     3.4    33.5    -      -       +      +
    837C  LEU*     4.0    15.0    -      -       +      -
    838C  GLN      3.1    15.0    -      -       -      +
    839C  PHE*     3.9    18.2    -      +       +      -
    840C  PHE*     4.0     6.9    -      -       -      -
    876C  LEU      4.4     0.2    -      -       -      -
    877C  TYR*     1.3    79.4    -      -       -      +
    879C  GLN*     1.3    67.5    +      -       -      +
    880C  GLN*     4.4     6.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 879 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    800C  ASP*     4.3     4.3    -      -       -      -
    801C  LYS*     4.1    15.8    -      -       +      +
    802C  THR*     4.0    23.0    -      -       +      +
    837C  LEU*     3.6     3.5    -      -       -      +
    838C  GLN*     2.9    55.6    +      -       +      +
    840C  PHE*     3.9    18.5    -      -       +      -
    878C  TYR*     1.3    82.0    -      -       -      +
    880C  GLN*     1.3    64.9    +      -       -      +
    881C  LEU*     3.7    20.1    -      -       +      +
    888C  PHE*     3.7    13.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 880 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    800C  ASP*     4.3    15.0    +      -       -      +
    802C  THR*     5.8     0.4    -      -       -      +
    830C  LEU*     3.7    30.6    +      -       -      +
    832C  THR*     3.7    24.8    +      -       -      +
    836C  LEU*     3.5     8.8    -      -       -      +
    837C  LEU*     4.1    13.7    -      -       +      -
    878C  TYR*     4.4     4.0    -      -       +      -
    879C  GLN*     1.3    79.7    -      -       -      +
    881C  LEU*     1.3    65.4    +      -       -      +
    882C  LYS*     5.6     4.5    -      -       -      +
----------------------------------------------------------
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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