Contacts of the helix formed by residues 509 - 523 (chain X) in PDB entry 5A31


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 CYS 509 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317X  ARG      5.2    10.1    -      -       -      +
    476X  ILE*     6.0     4.9    -      -       +      -
    507X  SER      4.3     5.4    -      -       -      +
    508X  ASP*     1.3    78.4    -      -       -      +
    510X  VAL*     1.3    82.3    +      -       +      +
    511X  LEU      3.5     0.3    +      -       -      -
    512X  HIS*     3.5    15.6    +      -       -      +
    513X  ARG*     3.8     3.5    +      -       -      +
    535X  ALA*     4.4     6.6    -      -       -      +
    538X  LEU*     3.9    10.5    -      -       -      +
    539X  ASP*     4.2    26.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 510 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    476X  ILE*     4.1    16.8    -      -       +      -
    480X  VAL*     3.8    26.0    -      -       +      -
    509X  CYS*     1.3    88.1    -      -       -      +
    511X  LEU*     1.3    64.2    +      -       -      +
    513X  ARG*     3.1    34.0    +      -       +      +
    514X  ILE*     2.9    29.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 511 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    474X  ASP      5.7     0.4    -      -       -      +
    476X  ILE*     4.3    16.4    -      -       +      +
    479X  VAL*     4.4     8.7    -      -       +      -
    480X  VAL*     3.5    29.8    -      -       +      -
    499X  LEU*     4.1    22.6    -      -       +      +
    502X  ALA*     3.4    29.4    -      -       +      -
    503X  LEU*     3.6    20.1    -      -       +      +
    507X  SER*     3.3    24.5    -      -       -      +
    508X  ASP      3.0    14.5    +      -       -      +
    510X  VAL*     1.3    82.3    -      -       -      +
    512X  HIS*     1.3    57.7    +      -       -      +
    514X  ILE*     3.2     5.2    +      -       +      +
    515X  LEU*     2.9    29.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 512 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    503X  LEU*     3.8    20.6    -      -       +      +
    506X  GLN*     4.2    12.4    +      -       -      +
    508X  ASP*     3.0    51.1    +      -       +      -
    509X  CYS      3.5     7.7    +      -       -      +
    510X  VAL      3.3     0.8    -      -       -      -
    511X  LEU*     1.3    76.3    -      -       -      +
    513X  ARG*     1.3    63.1    -      -       -      +
    515X  LEU*     3.3     2.0    +      -       -      +
    516X  GLY*     3.0    18.9    +      -       -      -
    531X  GLN*     3.4    45.8    +      -       -      +
    534X  ILE*     3.3    33.3    -      -       +      +
    535X  ALA      4.4     4.5    -      -       -      +
    538X  LEU*     3.9     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 513 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509X  CYS      3.8     1.4    +      -       -      -
    510X  VAL*     3.1    30.2    +      -       +      +
    512X  HIS*     1.3    77.7    -      -       -      +
    514X  ILE*     1.3    82.8    +      -       -      +
    516X  GLY*     3.3     3.7    +      -       -      -
    517X  ASP*     3.1    43.6    +      -       -      +
    531X  GLN      5.3     1.3    -      -       -      -
    532X  TYR*     4.6    20.9    -      -       +      -
    535X  ALA*     4.2    19.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 514 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    480X  VAL*     4.4    23.8    -      -       +      +
    483X  ALA*     4.1    21.8    -      -       +      -
    499X  LEU*     3.5    19.1    -      -       +      -
    510X  VAL*     2.9    26.1    +      -       +      +
    511X  LEU*     3.2     7.2    +      -       -      +
    513X  ARG*     1.3   103.5    -      -       -      +
    515X  LEU*     1.3    63.4    +      -       -      +
    517X  ASP*     3.2    12.0    +      -       +      +
    518X  PHE*     3.1    31.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 515 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    496X  ILE*     4.2    10.3    -      -       +      +
    499X  LEU*     3.3    27.7    -      -       +      +
    500X  ARG*     3.5    35.2    -      -       +      +
    503X  LEU*     3.2    31.2    -      -       +      -
    511X  LEU      2.9    14.1    +      -       -      +
    512X  HIS      3.3     3.6    +      -       -      +
    514X  ILE*     1.3    75.2    -      -       -      +
    516X  GLY*     1.3    63.2    +      -       -      +
    518X  PHE*     3.2     3.5    +      -       -      -
    519X  LEU*     3.0    53.6    +      -       +      +
    531X  GLN*     4.1    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 516 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    512X  HIS      3.0    11.8    +      -       -      -
    513X  ARG      3.3     4.4    +      -       -      -
    515X  LEU*     1.3    76.6    -      -       -      +
    517X  ASP*     1.3    60.6    +      -       -      +
    519X  LEU      3.4     1.0    +      -       -      -
    520X  VAL*     3.3    26.0    +      -       -      +
    528X  ALA*     3.7     8.3    -      -       -      +
    531X  GLN*     3.7    21.6    -      -       -      +
    532X  TYR*     3.6    19.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 517 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    513X  ARG*     3.1    46.2    +      -       -      +
    514X  ILE*     3.2    15.8    +      -       +      +
    516X  GLY*     1.3    74.4    -      -       -      +
    518X  PHE*     1.3    71.0    +      -       +      +
    520X  VAL*     3.1    26.1    -      -       -      +
    521X  ALA*     3.5     4.2    +      -       -      +
    532X  TYR*     2.6    26.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 518 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    483X  ALA*     3.4    30.5    -      -       +      -
    486X  LEU*     4.0     9.4    -      -       +      -
    487X  SER*     3.8    26.0    -      -       -      -
    492X  TYR*     3.4    36.1    -      +       -      +
    495X  GLY*     3.5    30.1    -      -       -      -
    496X  ILE*     3.6    18.3    -      -       +      +
    499X  LEU*     4.9     4.7    -      -       +      -
    514X  ILE*     3.1    26.9    +      -       +      +
    515X  LEU*     3.7     6.7    -      -       -      +
    517X  ASP*     1.3    82.4    -      -       +      +
    519X  LEU*     1.3    61.9    +      -       -      +
    521X  ALA*     2.9    25.5    +      -       -      +
    522X  VAL*     3.0    13.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 519 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    496X  ILE*     3.4    25.1    -      -       +      -
    500X  ARG*     3.9    10.8    -      -       -      +
    515X  LEU*     3.0    29.1    +      -       +      +
    516X  GLY      3.8     4.5    -      -       -      +
    517X  ASP      3.3     0.2    -      -       -      -
    518X  PHE*     1.3    78.6    -      -       -      +
    520X  VAL*     1.3    56.6    +      -       -      +
    522X  VAL*     3.0     4.7    +      -       +      +
    523X  ASN      2.9    22.0    +      -       -      -
    524X  GLU*     3.3    35.5    +      -       +      +
    527X  GLU*     3.3    42.2    -      -       +      +
    528X  ALA*     3.4    10.5    -      -       -      +
    531X  GLN*     3.6    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 520 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516X  GLY      3.3    15.4    +      -       -      +
    517X  ASP*     3.1    19.5    -      -       -      +
    518X  PHE      3.2     0.8    -      -       -      -
    519X  LEU*     1.3    76.0    -      -       -      +
    521X  ALA*     1.3    59.0    +      -       -      +
    523X  ASN*     2.9    22.3    +      -       -      +
    525X  TYR*     4.0    30.0    +      -       +      +
    528X  ALA*     3.6    15.7    -      -       +      -
    532X  TYR*     4.7    11.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 521 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    492X  TYR*     3.3    49.2    -      -       +      -
    493X  GLU*     4.6     5.9    -      -       -      +
    517X  ASP      3.5     4.0    +      -       -      +
    518X  PHE      2.9    14.1    +      -       -      +
    520X  VAL*     1.3    79.6    -      -       +      +
    522X  VAL*     1.3    61.0    +      -       -      +
    523X  ASN*     3.1     4.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 522 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    492X  TYR*     5.5     0.9    -      -       +      +
    493X  GLU*     3.3    28.0    -      -       -      +
    496X  ILE*     3.1    36.8    -      -       +      -
    518X  PHE      3.0     4.0    +      -       -      +
    519X  LEU*     3.0    11.8    +      -       +      +
    521X  ALA*     1.3    74.4    -      -       -      +
    523X  ASN*     1.3    67.3    +      -       -      +
    524X  GLU*     4.1    23.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 523 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    519X  LEU      2.9     3.8    +      -       -      -
    520X  VAL      2.9    16.2    +      -       -      +
    521X  ALA      4.5     2.2    +      -       -      +
    522X  VAL*     1.3    82.2    -      -       -      +
    524X  GLU*     1.3    58.6    +      -       -      +
    525X  TYR*     3.1    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