Contacts of the strand formed by residues 471 - 479 (chain A) in PDB entry 4Y05


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 HIS 471 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    403A  GLU*     3.1     7.6    -      -       -      +
    404A  ILE*     2.8    58.6    +      -       +      +
    470A  SER*     1.3    73.2    -      -       -      +
    472A  ALA*     1.3    60.6    +      -       -      +
    473A  CYS*     4.2     0.7    -      -       +      -
    491A  VAL*     4.5    11.4    -      -       +      -
    492A  ASP      3.5     5.4    -      -       -      +
    493A  LEU*     3.6    19.1    -      -       +      +
    494A  ALA*     3.0    39.4    +      -       +      -
    516A  ILE*     4.9     5.7    -      -       +      +
    519A  SER*     2.8    34.8    +      -       -      -
    520A  LEU*     4.4    10.3    -      -       +      -
    544A  LEU*     4.1    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A  TYR*     3.9     9.1    +      -       -      +
    401A  PHE*     4.2    19.3    -      -       +      -
    402A  PHE      3.5     5.8    -      -       -      +
    403A  GLU*     4.2     8.1    -      -       +      +
    412A  LEU*     4.8     3.8    -      -       +      -
    456A  ARG*     5.6     5.2    -      -       +      -
    470A  SER*     4.1     0.4    +      -       -      +
    471A  HIS*     1.3    73.7    -      -       -      +
    473A  CYS*     1.3    59.0    +      -       -      +
    474A  PHE      4.2     0.2    -      -       -      -
    490A  LEU      3.8     1.0    -      -       -      +
    491A  VAL*     3.3     6.7    -      -       -      +
    492A  ASP*     2.9    44.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400A  THR      4.0     0.3    -      -       -      +
    401A  PHE*     3.3     5.8    -      -       -      -
    402A  PHE*     2.8    72.7    +      -       +      -
    404A  ILE*     5.6     1.8    -      -       +      -
    471A  HIS*     5.7     0.7    -      -       +      -
    472A  ALA*     1.3    72.2    -      -       -      +
    474A  PHE*     1.3    61.7    +      -       -      +
    475A  GLN*     3.8    20.2    -      -       -      -
    489A  SER*     4.0    11.7    -      -       -      -
    490A  LEU      3.5     2.7    -      -       -      -
    491A  VAL*     3.8    23.3    -      -       +      -
    544A  LEU*     5.5     5.2    -      -       +      -
    547A  VAL*     5.5     0.2    -      -       -      -
    548A  LEU*     4.2     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A  TYR*     3.6    45.1    -      +       +      -
    378A  SER*     3.6     9.9    -      -       -      -
    399A  VAL*     3.3    28.0    -      -       +      -
    400A  THR      3.4    13.2    -      -       -      -
    401A  PHE*     3.7    20.4    -      +       +      -
    445A  VAL*     3.5    28.5    -      -       +      -
    448A  MET*     5.7     0.7    -      -       +      -
    449A  ILE*     4.1    15.7    -      -       +      -
    472A  ALA      4.2     0.6    -      -       -      -
    473A  CYS*     1.3    73.0    -      -       -      +
    475A  GLN*     1.3    58.3    +      -       -      +
    476A  ILE*     3.6    31.6    -      -       +      -
    489A  SER*     3.6     0.7    -      -       -      -
    490A  LEU*     2.7    42.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 475 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399A  VAL*     3.3    12.6    -      -       -      +
    400A  THR*     2.8    56.3    +      -       -      +
    402A  PHE*     3.6    18.5    -      -       +      -
    434A  LEU*     4.3     4.7    -      -       -      +
    473A  CYS*     3.8    11.4    -      -       -      -
    474A  PHE*     1.3    78.3    -      -       -      +
    476A  ILE*     1.3    62.4    +      -       -      +
    477A  ILE*     4.1    14.8    +      -       +      +
    487A  LYS*     4.1    22.0    +      -       +      +
    488A  PHE      3.2     6.1    -      -       -      +
    489A  SER*     3.2    23.7    +      -       -      +
    547A  VAL*     4.8     5.1    +      -       -      +
    548A  LEU*     4.0    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 476 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336A  ILE*     4.2     8.9    -      -       +      +
    377A  ALA*     4.0    21.8    -      -       +      -
    378A  SER*     4.0    11.4    -      -       -      +
    381A  VAL*     3.9    35.0    -      -       +      -
    397A  VAL*     3.9    24.0    -      -       +      -
    398A  TYR      3.7     2.7    -      -       -      -
    399A  VAL*     4.6     3.1    -      -       +      -
    474A  PHE*     3.6    32.3    -      -       +      -
    475A  GLN*     1.3    71.2    -      -       -      +
    477A  ILE*     1.3    65.3    +      -       -      +
    478A  LEU*     4.3     0.8    +      -       +      -
    486A  GLY      4.2     0.2    -      -       -      +
    487A  LYS*     3.3     3.8    -      -       -      +
    488A  PHE*     2.7    47.4    +      -       +      +
    490A  LEU*     4.3     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 477 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    396A  GLU      3.8     0.3    -      -       -      +
    397A  VAL*     3.6     4.3    -      -       -      -
    398A  TYR*     2.9    42.9    +      -       +      +
    400A  THR*     4.1    16.2    -      -       +      -
    436A  GLU*     3.5    33.4    -      -       +      +
    475A  GLN*     4.3    12.8    -      -       +      +
    476A  ILE*     1.3    77.4    -      -       -      +
    478A  LEU*     1.3    63.7    -      -       -      +
    479A  ARG*     3.9    19.2    +      -       +      +
    484A  MET*     3.0    36.3    -      -       +      -
    486A  GLY      3.6     2.7    -      -       -      -
    487A  LYS*     3.8    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 478 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336A  ILE*     3.5    46.2    -      -       +      +
    337A  PHE*     3.8    33.0    -      -       +      -
    381A  VAL*     4.0    13.2    -      -       +      -
    385A  LYS*     5.3     0.7    -      -       +      -
    395A  LEU*     4.4    11.7    -      -       +      -
    396A  GLU      3.6     3.6    -      -       -      +
    397A  VAL*     3.8    29.2    -      -       +      -
    476A  ILE*     4.2     0.6    -      -       +      -
    477A  ILE*     1.3    74.1    -      -       -      +
    479A  ARG*     1.3    56.7    +      -       -      +
    484A  MET*     3.7     2.4    -      -       -      +
    485A  HIS*     2.7    40.4    +      -       +      -
    486A  GLY      2.7    21.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 479 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    395A  LEU*     3.4     5.2    -      -       -      -
    396A  GLU*     2.9    37.2    +      -       -      +
    398A  TYR*     3.8    34.1    -      -       +      -
    436A  GLU*     2.9    37.3    +      -       -      -
    477A  ILE*     4.0     5.5    -      -       +      +
    478A  LEU*     1.3    77.4    -      -       -      +
    480A  ALA*     1.3    61.5    +      -       -      +
    482A  GLY*     2.9    38.1    +      -       -      +
    483A  ARG      3.2     7.2    -      -       -      +
    484A  MET*     3.3    27.5    -      -       -      +
    703A  SO4      2.9    38.8    +      -       -      -
----------------------------------------------------------
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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