Contacts of the strand formed by residues 419 - 429 (chain F) in PDB entry 2HU4


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 ARG 419 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92F  CYS*     3.7    14.7    -      -       +      +
     94F  ILE*     6.2     0.2    -      -       +      -
    411F  VAL*     3.4     8.6    -      -       -      +
    412F  GLN*     2.3    83.2    +      -       +      +
    413F  THR*     4.5     7.5    -      -       -      +
    415F  LEU*     4.3    24.0    -      -       +      +
    417F  CYS      3.5     3.0    +      -       -      -
    418F  ILE*     1.3    71.7    -      -       -      +
    420F  PRO*     1.3    72.3    -      -       +      +
    421F  CYS*     3.7     5.8    +      -       -      -
    447F  CYS*     4.0    11.2    -      -       -      +
    448F  GLY*     4.4     2.2    -      -       -      +
    449F  VAL*     4.1    32.8    -      -       -      +
    210H  ILE*     4.7     1.8    -      -       -      +
    211H  ILE*     3.1    41.0    +      -       -      +
    212H  THR*     5.5     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 420 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91F  LEU*     4.4     7.4    -      -       +      -
     92F  CYS*     4.3     9.9    -      -       +      +
     94F  ILE*     3.9    22.7    -      -       +      -
     97F  TRP*     3.3     5.8    -      -       +      -
    354F  PHE*     3.6    38.1    -      -       +      -
    356F  TYR*     3.3    25.6    -      -       +      +
    410F  PHE      4.2     1.1    -      -       -      +
    411F  VAL*     5.1     1.6    -      -       +      -
    418F  ILE      3.7     8.1    -      -       -      +
    419F  ARG*     1.3    85.6    -      -       +      +
    421F  CYS*     1.3    55.5    +      -       -      +
    448F  GLY      2.7    31.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 421 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97F  TRP*     4.4     1.8    -      -       -      -
    354F  PHE*     3.4     9.1    -      -       -      -
    410F  PHE*     2.7    54.3    +      -       +      +
    412F  GLN*     2.7    29.6    -      -       -      -
    419F  ARG*     3.9     2.2    -      -       -      -
    420F  PRO*     1.3    76.1    -      -       -      +
    422F  PHE*     1.3    59.2    +      -       -      +
    446F  PHE      3.0    16.4    -      -       -      +
    447F  CYS*     2.1    41.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 422 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97F  TRP*     3.6    40.8    -      +       -      -
    352F  PHE*     3.3    37.2    -      +       +      -
    374F  PHE*     4.0    10.3    -      +       -      -
    376F  MET*     3.7    23.3    -      -       +      -
    397F  ILE*     4.1     8.3    -      -       +      -
    408F  GLY      3.3    10.8    -      -       -      +
    409F  SER*     4.3     0.2    -      -       -      -
    410F  PHE*     3.5     6.7    -      -       -      -
    421F  CYS*     1.3    75.8    -      -       -      +
    423F  TRP*     1.3    71.5    +      -       -      +
    424F  VAL*     3.5    23.3    -      -       +      -
    445F  SER*     3.1     4.0    -      -       -      -
    446F  PHE*     2.9    62.6    +      +       +      -
----------------------------------------------------------
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Residues in contact with TRP 423 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120F  PRO*     3.2    31.2    -      -       +      -
    121F  PHE*     3.4    17.9    -      -       +      +
    122F  ILE*     3.4    40.6    +      -       +      +
    227F  GLU      3.7    10.8    -      -       -      -
    228F  SER*     4.1     2.8    -      -       -      -
    350F  LYS*     3.7    11.7    -      -       +      -
    406F  TYR*     3.4    21.5    -      +       +      -
    407F  SER*     3.3    28.5    -      -       -      -
    408F  GLY*     2.8    64.4    +      -       -      +
    409F  SER      4.2     5.5    +      -       -      +
    410F  PHE*     4.0    11.4    -      +       -      -
    422F  PHE*     1.3    76.3    -      -       -      +
    424F  VAL*     1.3    75.8    +      -       -      +
    425F  GLU*     3.8     8.7    -      -       +      -
    443F  SER*     5.4     5.2    -      -       -      -
    444F  ILE      3.3     9.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 424 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374F  PHE*     4.1    35.7    -      -       +      -
    397F  ILE*     4.5     2.0    -      -       +      -
    404F  SER*     4.6     6.1    -      -       -      -
    405F  GLY      4.8     0.2    -      -       -      +
    406F  TYR      3.6    10.8    -      -       -      +
    407F  SER*     4.5     0.9    -      -       -      -
    422F  PHE*     3.5    26.2    -      -       +      -
    423F  TRP*     1.3    85.6    -      -       -      +
    425F  GLU*     1.3    68.5    +      -       -      +
    426F  LEU*     3.9    14.4    +      -       +      -
    442F  SER      3.5     0.2    -      -       -      +
    443F  SER*     3.1    25.3    -      -       -      -
    444F  ILE*     2.8    35.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 425 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118F  ARG*     2.5    35.9    +      -       -      -
    119F  GLU      2.9    16.5    +      -       -      -
    120F  PRO*     3.1    27.6    -      -       +      +
    404F  SER*     3.0    23.6    -      -       -      +
    405F  GLY*     3.0     5.9    +      -       -      -
    406F  TYR*     2.7    56.6    +      -       +      +
    423F  TRP*     3.8     3.4    -      -       +      -
    424F  VAL*     1.3    71.0    -      -       -      +
    426F  LEU*     1.3    63.7    +      -       -      +
    427F  ILE*     3.8    13.6    -      -       +      +
    441F  GLY*     4.7     5.6    -      -       -      -
    442F  SER      3.2     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 426 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102F  LYS*     4.9     0.9    -      -       -      +
    106F  ILE*     4.0     4.9    -      -       -      +
    398F  VAL*     4.2     8.3    -      -       +      -
    403F  TRP      3.6    19.1    -      -       -      +
    404F  SER*     3.6    10.3    -      -       -      +
    424F  VAL*     4.1    17.9    -      -       +      +
    425F  GLU*     1.3    75.0    -      -       -      +
    427F  ILE*     1.3    63.8    +      -       -      +
    428F  ARG*     3.6     1.9    +      -       -      +
    441F  GLY*     3.2     4.2    -      -       -      -
    442F  SER*     2.7    44.9    +      -       -      +
    444F  ILE*     4.2    22.7    -      -       +      -
    458F  TRP      3.7     8.7    -      -       -      +
    459F  PRO      3.5     6.7    -      -       -      +
    460F  ASP*     3.1    45.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 427 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118F  ARG*     4.0    16.4    -      -       -      +
    371F  ARG*     4.0    29.2    -      -       +      +
    403F  TRP*     3.5    16.5    -      -       -      +
    404F  SER*     2.9    15.3    +      -       -      +
    405F  GLY*     3.8    20.2    -      -       -      -
    425F  GLU*     3.8    27.4    -      -       -      +
    426F  LEU*     1.3    70.9    -      -       -      +
    428F  ARG*     1.3    77.1    +      -       -      +
    429F  GLY      5.5     0.7    -      -       -      +
    430F  ARG      4.6     7.0    -      -       -      +
    431F  PRO*     6.1     1.1    -      -       +      -
    433F  GLU*     4.3     0.2    -      -       -      +
    439F  THR*     4.2    20.4    -      -       +      -
    440F  SER      3.4    10.1    -      -       -      +
    441F  GLY*     4.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 428 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106F  ILE*     3.5    29.8    -      -       +      -
    403F  TRP*     3.5    19.0    -      -       -      -
    426F  LEU      4.2     1.1    -      -       -      +
    427F  ILE*     1.3    87.6    -      -       -      +
    429F  GLY*     1.3    59.9    +      -       -      +
    433F  GLU*     2.9    34.5    +      -       -      +
    438F  TRP*     3.4    10.9    -      -       +      -
    439F  THR*     3.6     0.9    -      -       -      -
    440F  SER      2.7    34.7    +      -       -      +
    460F  ASP*     2.9    37.7    +      -       +      +
    461F  GLY      4.3     1.8    -      -       -      +
    462F  ALA*     2.7    32.9    +      -       -      +
    463F  GLU*     4.5     0.4    -      -       -      +
    464F  LEU*     3.4    27.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 429 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427F  ILE*     5.0     1.1    -      -       -      +
    428F  ARG*     1.3    73.4    -      -       -      +
    430F  ARG*     1.3    67.9    +      -       -      -
    432F  LYS*     3.5     4.2    +      -       -      +
    433F  GLU*     2.8    43.1    +      -       -      +
    436F  THR*     3.3    10.5    -      -       -      -
    438F  TRP*     3.2    12.8    -      -       -      -
    464F  LEU*     3.9     5.9    -      -       -      +
----------------------------------------------------------
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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