Contacts of the helix formed by residues 479 - 494 (chain C) in PDB entry 1Z6T


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 ASP 479 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    396C  PRO*     4.2     8.1    -      -       +      -
    398C  LYS*     3.5    22.8    -      -       +      +
    399C  VAL*     3.8    17.9    -      -       +      -
    402C  ILE*     3.2    12.5    -      -       -      +
    468C  HIS*     2.9    24.4    +      -       -      -
    477C  GLN*     3.7    20.6    -      -       -      +
    478C  GLU*     1.3    73.1    +      -       -      +
    480C  CYS*     1.3    64.7    +      -       -      +
    481C  MET      3.4     2.9    -      -       -      -
    482C  TYR*     3.2     7.0    +      -       -      +
    483C  TRP*     3.0    41.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 480 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    473C  LEU*     4.4     5.7    -      -       -      +
    474C  SER      3.4    36.1    -      -       -      +
    475C  PRO*     3.7     6.1    -      -       +      +
    477C  GLN*     3.2    23.0    +      -       +      +
    478C  GLU      3.4     0.6    -      -       -      -
    479C  ASP*     1.3    80.2    +      -       -      +
    481C  MET*     1.3    81.6    +      -       +      +
    483C  TRP*     3.2     9.5    +      -       -      +
    484C  TYR*     3.1    44.8    +      -       -      -
    516C  LEU*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 481 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216C  LEU*     5.9     2.9    -      -       -      -
    475C  PRO*     4.8     8.7    -      -       +      -
    477C  GLN      5.0     0.2    +      -       -      -
    478C  GLU      5.0     2.3    +      -       -      +
    479C  ASP      3.4     0.4    -      -       -      -
    480C  CYS*     1.3   110.2    -      -       +      +
    482C  TYR*     1.3    60.3    +      -       -      +
    483C  TRP      3.2     0.2    -      -       -      -
    484C  TYR*     3.5    18.6    -      -       +      +
    485C  ASN*     2.9    48.9    +      -       -      +
    516C  LEU*     3.6    17.9    -      -       +      -
    517C  VAL*     4.7    17.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 482 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388C  ILE      5.0     1.6    +      -       -      -
    389C  LEU*     5.3     5.4    -      -       -      +
    390C  GLN*     4.0     6.6    +      -       -      -
    393C  VAL*     4.0     9.4    -      -       +      -
    394C  LYS      5.5     0.7    -      -       -      -
    395C  VAL*     3.6    31.9    -      -       +      +
    396C  PRO*     4.6    10.8    -      -       +      -
    399C  VAL*     3.8    35.7    -      -       +      +
    460C  ILE*     4.5     3.2    -      -       +      +
    478C  GLU      5.5     0.6    +      -       -      -
    479C  ASP*     3.2    14.6    +      -       -      +
    481C  MET*     1.3    78.4    -      -       -      +
    483C  TRP*     1.3    81.8    +      +       -      +
    485C  ASN*     4.8     0.7    -      -       -      +
    486C  PHE*     2.9    55.6    +      +       +      +
    490C  HIS*     2.7    34.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 483 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399C  VAL*     4.3    14.8    -      -       +      -
    402C  ILE*     4.1    20.4    -      -       +      -
    460C  ILE*     3.8    35.0    -      -       +      -
    461C  ILE*     5.5     1.1    -      -       +      -
    464C  PHE*     3.5    43.5    -      +       +      -
    468C  HIS*     3.8    10.5    -      +       -      -
    473C  LEU*     4.0    22.7    -      -       +      -
    479C  ASP*     3.0    49.9    +      -       -      +
    480C  CYS      3.2     4.9    +      -       -      +
    482C  TYR*     1.3    97.3    -      +       -      +
    484C  TYR*     1.3    61.9    +      -       -      +
    487C  LEU*     2.8    52.8    +      -       +      +
    490C  HIS*     4.6     7.4    -      +       -      -
    509C  TRP*     4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 484 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    470C  PRO      4.4     3.1    +      -       -      -
    473C  LEU*     3.8    31.9    +      -       +      +
    474C  SER*     5.6     0.2    -      -       -      -
    480C  CYS*     3.1    47.2    +      -       -      +
    481C  MET*     3.5    17.9    -      -       +      +
    483C  TRP*     1.3    76.1    -      -       -      +
    485C  ASN*     1.3    60.5    +      -       -      +
    487C  LEU*     4.7     0.9    +      -       -      +
    488C  ALA      5.6     0.2    +      -       -      -
    509C  TRP*     3.4    38.5    -      +       -      -
    512C  ALA*     3.5    19.9    +      -       +      +
    513C  LYS*     2.6    67.1    +      -       +      +
    516C  LEU*     3.5    19.1    -      -       +      +
    517C  VAL*     5.9     4.5    -      -       +      -
    525C  GLU*     4.2     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 485 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197C  MET*     3.6    33.7    -      -       -      +
    481C  MET*     2.9    37.5    +      -       -      +
    482C  TYR*     4.8     0.4    -      -       -      +
    484C  TYR*     1.3    83.0    -      -       -      +
    486C  PHE*     1.3    87.2    +      -       +      +
    489C  TYR*     4.8     2.6    -      -       -      +
    513C  LYS*     5.0     1.6    +      -       -      -
    517C  VAL*     5.2    10.6    -      -       -      +
    521C  HIS*     3.1    28.5    +      -       -      -
    525C  GLU*     3.7     6.0    -      -       -      +
    529C  TYR*     5.2     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 486 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197C  MET*     4.5    18.8    -      -       +      -
    390C  GLN*     3.4    31.6    -      -       -      +
    393C  VAL*     3.7    35.7    -      -       +      -
    482C  TYR*     2.9    53.8    +      +       +      +
    483C  TRP*     4.9     0.9    -      -       -      -
    485C  ASN*     1.3   106.6    -      -       +      +
    487C  LEU*     1.3    68.7    +      -       -      +
    488C  ALA      3.3     2.2    -      -       -      -
    489C  TYR*     3.2    12.3    +      -       +      -
    490C  HIS*     3.0    29.1    +      -       +      -
    521C  HIS*     5.7     0.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 487 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461C  ILE*     3.6    24.3    -      -       +      +
    464C  PHE*     3.6    44.2    -      -       +      -
    470C  PRO*     4.5     5.2    -      -       +      -
    473C  LEU*     5.1     0.9    -      -       +      -
    482C  TYR      4.2     0.2    +      -       -      -
    483C  TRP*     2.8    37.0    +      -       +      +
    484C  TYR      4.7     0.6    +      -       -      +
    486C  PHE*     1.3    77.5    -      -       -      +
    488C  ALA*     1.3    62.1    +      -       -      +
    490C  HIS*     3.3     1.0    +      -       -      -
    491C  MET*     3.1    41.6    +      -       +      +
    503C  LEU*     3.9    31.2    -      -       +      -
    509C  TRP*     4.5    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 488 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484C  TYR      5.6     0.6    +      -       -      -
    486C  PHE      3.3     0.4    -      -       -      -
    487C  LEU*     1.3    76.0    -      -       -      +
    489C  TYR*     1.3    61.3    +      -       -      +
    491C  MET*     3.3     1.8    +      -       -      -
    492C  ALA*     2.9    32.6    +      -       -      +
    500C  LEU*     3.7    19.9    -      -       +      +
    503C  LEU*     4.0    11.8    -      -       +      +
    504C  MET*     4.1    10.1    -      -       +      -
    509C  TRP*     6.2     1.5    -      -       +      +
    525C  GLU*     3.4    26.4    +      -       -      +
    529C  TYR*     3.6    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 489 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388C  ILE      4.8     0.7    +      -       -      -
    390C  GLN*     3.6    48.3    -      -       +      +
    457C  HIS*     3.8    28.3    +      +       -      -
    485C  ASN      4.8     0.7    -      -       -      +
    486C  PHE*     3.2    21.7    +      +       +      +
    488C  ALA*     1.3    79.6    -      -       -      +
    490C  HIS*     1.3    67.1    +      +       -      +
    492C  ALA*     3.8     1.2    -      -       -      +
    493C  SER*     2.7    51.0    +      -       -      -
    525C  GLU*     4.6     0.6    +      -       -      -
    529C  TYR*     3.2    33.4    +      +       -      +
----------------------------------------------------------
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Residues in contact with HIS 490 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388C  ILE*     3.7    36.6    -      -       +      -
    390C  GLN*     4.4     0.4    +      -       -      -
    457C  HIS*     2.9    33.7    +      +       -      +
    460C  ILE*     3.6    20.8    -      -       +      +
    461C  ILE*     3.7    20.0    -      -       +      -
    482C  TYR*     2.7    39.5    +      +       -      -
    483C  TRP*     4.6     5.2    -      +       -      -
    486C  PHE*     3.0    28.4    +      -       +      +
    489C  TYR*     1.3    87.0    -      +       -      +
    491C  MET*     1.3    58.5    +      -       -      +
    494C  ALA*     2.9    30.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 491 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461C  ILE*     3.5    28.9    -      -       +      -
    464C  PHE*     5.8     2.7    -      -       +      -
    465C  GLN*     4.7     5.8    -      -       +      +
    470C  PRO*     5.9     2.7    -      -       +      -
    487C  LEU*     3.1    37.3    +      -       +      +
    488C  ALA      3.7     3.6    -      -       -      +
    490C  HIS*     1.3    74.4    -      -       -      +
    492C  ALA*     1.3    59.1    +      -       -      +
    494C  ALA*     3.4     3.4    +      -       -      -
    495C  LYS      3.2     2.6    +      -       -      -
    496C  MET*     2.8    42.7    +      -       +      +
    499C  GLU*     3.6    43.7    -      -       +      +
    500C  LEU*     3.7    13.0    -      -       +      -
    503C  LEU*     3.9    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 492 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488C  ALA      2.9    17.5    +      -       -      +
    489C  TYR      3.8     2.5    -      -       -      +
    491C  MET*     1.3    73.4    -      -       -      +
    493C  SER*     1.3    60.7    +      -       -      +
    495C  LYS*     3.0    29.5    +      -       -      +
    500C  LEU*     4.4     4.2    -      -       +      +
    529C  TYR*     3.6    39.9    -      -       +      -
    531C  HIS*     6.3     0.2    -      -       -      +
    532C  ILE*     3.9    22.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 493 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454C  GLN*     4.0    16.1    -      -       -      +
    457C  HIS*     3.4    34.3    -      -       -      -
    489C  TYR*     2.7    43.9    +      -       -      -
    490C  HIS      3.8     0.2    -      -       -      -
    492C  ALA*     1.3    77.7    -      -       -      +
    494C  ALA*     1.3    58.2    +      -       -      +
    495C  LYS*     3.2     7.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 494 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454C  GLN*     3.5    26.5    +      -       -      +
    457C  HIS*     3.7     1.1    -      -       -      +
    458C  LYS*     3.3    39.2    -      -       +      +
    490C  HIS      2.9    19.0    +      -       -      +
    491C  MET      3.4     0.9    +      -       -      +
    492C  ALA      3.2     0.6    -      -       -      -
    493C  SER*     1.3    73.9    -      -       -      +
    495C  LYS*     1.3    67.4    +      -       -      +
    496C  MET*     3.3    21.8    +      -       +      +
----------------------------------------------------------
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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