Contacts of the strand formed by residues 419 - 429 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92E  CYS*     3.6    13.6    -      -       +      +
    411E  VAL*     3.5     7.3    -      -       -      +
    412E  GLN*     2.8    69.2    +      -       +      +
    413E  THR*     4.6     8.4    -      -       -      +
    415E  LEU*     3.9    28.0    -      -       +      +
    417E  CYS      3.6     1.2    +      -       -      -
    418E  ILE*     1.3    72.9    -      -       -      +
    420E  PRO*     1.3    67.1    -      -       +      +
    421E  CYS*     3.7    12.2    +      -       -      -
    447E  CYS*     4.1     7.0    -      -       -      +
    448E  GLY*     4.1     7.6    -      -       -      +
    449E  VAL*     4.3    26.1    -      -       -      +
    210G  ILE*     4.8     1.8    -      -       -      +
    211G  ILE*     2.9    46.2    +      -       -      +
    212G  THR*     5.2     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 420 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91E  LEU*     4.2     8.7    -      -       +      -
     92E  CYS*     4.3     6.5    -      -       +      +
     94E  ILE*     4.0    22.2    -      -       +      -
     97E  TRP*     3.2     6.9    -      -       +      -
    354E  PHE*     3.5    39.5    -      -       +      -
    356E  TYR*     3.3    25.6    -      -       -      +
    410E  PHE      4.2     1.6    -      -       -      +
    411E  VAL*     5.1     1.8    -      -       +      -
    418E  ILE      3.5     8.7    -      -       -      +
    419E  ARG*     1.3    85.8    -      -       +      +
    421E  CYS*     1.3    60.0    +      -       -      +
    448E  GLY      2.9    23.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 421 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97E  TRP*     4.3     1.3    -      -       -      -
    354E  PHE*     3.5     9.8    -      -       -      -
    410E  PHE*     3.0    45.8    +      -       +      +
    412E  GLN*     2.8    29.2    -      -       -      -
    419E  ARG*     3.9     3.6    -      -       -      -
    420E  PRO*     1.3    77.5    -      -       -      +
    422E  PHE*     1.3    64.0    +      -       -      +
    446E  PHE      3.0    17.0    -      -       -      +
    447E  CYS*     2.1    43.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 422 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97E  TRP*     3.7    39.0    -      +       -      -
    352E  PHE*     3.3    37.9    -      +       +      -
    354E  PHE*     4.7     0.2    -      -       +      -
    374E  PHE*     3.9     9.9    -      +       -      -
    376E  MET*     3.7    23.8    -      -       +      -
    397E  ILE*     4.0     9.2    -      -       +      -
    408E  GLY      3.3    10.5    -      -       -      +
    410E  PHE*     3.7     7.2    -      -       -      -
    421E  CYS*     1.3    75.7    -      -       -      +
    423E  TRP*     1.3    69.6    +      -       -      +
    424E  VAL*     3.6    21.8    -      -       +      -
    445E  SER*     3.4     1.9    -      -       -      -
    446E  PHE*     2.9    64.6    +      +       +      +
----------------------------------------------------------
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Residues in contact with TRP 423 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120E  PRO*     3.2    27.8    -      -       +      -
    121E  PHE*     3.4    22.8    -      -       +      +
    122E  ILE*     3.5    42.7    +      -       +      +
    227E  GLU      3.8     1.8    -      -       -      -
    228E  SER*     4.1     3.1    -      -       -      -
    229E  GLU      5.6     0.2    -      -       -      +
    350E  LYS*     3.6    21.3    -      -       +      -
    406E  TYR*     3.6    17.0    -      +       +      -
    407E  SER*     3.3    26.8    -      -       -      -
    408E  GLY*     2.9    60.0    +      -       -      +
    409E  SER      4.2     4.8    +      -       -      +
    410E  PHE*     4.0    12.6    -      +       +      -
    422E  PHE*     1.3    77.9    -      -       -      +
    424E  VAL*     1.3    81.5    +      -       -      +
    425E  GLU*     4.0     7.2    -      -       +      -
    443E  SER*     5.6     4.3    -      -       -      -
    444E  ILE      3.4     8.7    -      -       -      +
    445E  SER*     4.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 424 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374E  PHE*     3.9    37.2    -      -       +      -
    397E  ILE*     4.7     0.2    -      -       +      -
    398E  VAL*     5.1     0.2    -      -       +      -
    404E  SER*     4.6     6.1    -      -       -      -
    406E  TYR      3.7     7.4    -      -       -      +
    407E  SER*     4.1     0.9    -      -       -      -
    422E  PHE*     3.6    24.2    -      -       +      -
    423E  TRP*     1.3    87.9    -      -       -      +
    425E  GLU*     1.3    68.2    +      -       -      +
    426E  LEU*     3.6    21.9    -      -       +      +
    443E  SER*     3.1     7.8    -      -       -      -
    444E  ILE*     3.0    49.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 425 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118E  ARG*     2.7    33.3    +      -       -      -
    119E  GLU      2.9    17.9    +      -       -      -
    120E  PRO*     3.1    25.5    -      -       +      +
    404E  SER*     3.0    23.6    -      -       -      +
    405E  GLY*     3.2     4.5    +      -       -      -
    406E  TYR*     2.9    40.8    +      -       -      +
    423E  TRP*     3.9     5.5    -      -       +      -
    424E  VAL*     1.3    75.0    -      -       -      +
    426E  LEU*     1.3    65.3    +      -       -      +
    427E  ILE*     3.5    19.4    -      -       +      +
    441E  GLY*     4.5     5.9    -      -       -      -
    442E  SER      3.2     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 426 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102E  LYS*     5.0     0.9    -      -       -      +
    106E  ILE*     4.4     0.2    -      -       -      +
    398E  VAL*     4.7     5.4    -      -       +      -
    403E  TRP      4.2    16.2    -      -       -      +
    404E  SER*     3.6     7.0    -      -       -      +
    424E  VAL*     3.6    21.5    -      -       +      +
    425E  GLU*     1.3    79.9    -      -       -      +
    427E  ILE*     1.3    63.0    +      -       -      +
    428E  ARG*     3.5     9.0    +      -       +      +
    441E  GLY*     3.3     4.3    -      -       -      -
    442E  SER*     2.9    41.8    +      -       -      +
    443E  SER*     4.5     0.9    -      -       -      +
    444E  ILE*     4.0    21.3    -      -       +      -
    458E  TRP      3.8     8.5    -      -       -      +
    459E  PRO*     3.5     9.2    -      -       +      +
    460E  ASP*     3.2    44.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 427 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118E  ARG*     3.9    22.2    -      -       -      +
    371E  ARG*     4.1    21.3    -      -       +      +
    403E  TRP*     3.5    17.5    -      -       -      +
    404E  SER      2.8    15.4    +      -       -      +
    405E  GLY*     3.7    17.3    -      -       -      -
    406E  TYR      4.3     0.7    -      -       -      +
    425E  GLU*     3.5    32.1    -      -       -      +
    426E  LEU*     1.3    69.6    -      -       -      +
    428E  ARG*     1.3    72.8    +      -       -      +
    429E  GLY      4.4     0.8    +      -       -      +
    430E  ARG      4.5     7.2    -      -       -      +
    431E  PRO*     6.0     1.3    -      -       +      -
    433E  GLU*     4.4     0.5    -      -       -      +
    439E  THR*     4.2    21.8    -      -       +      -
    440E  SER      3.5     9.4    -      -       -      +
    441E  GLY*     4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 428 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106E  ILE*     3.6    25.1    -      -       +      -
    403E  TRP*     3.6    18.0    -      -       -      -
    426E  LEU*     4.0     3.8    -      -       -      +
    427E  ILE*     1.3    85.6    -      -       -      +
    429E  GLY*     1.3    59.9    +      -       -      +
    433E  GLU*     2.6    37.7    +      -       -      +
    438E  TRP*     3.6     7.4    -      -       +      -
    439E  THR*     3.5     2.9    -      -       -      +
    440E  SER      2.8    32.5    +      -       -      +
    460E  ASP*     2.9    41.3    +      -       -      +
    461E  GLY*     4.5     2.0    -      -       -      +
    462E  ALA*     2.8    32.5    +      -       -      +
    464E  LEU*     3.3    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 429 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427E  ILE*     4.4     1.6    +      -       -      +
    428E  ARG*     1.3    74.4    -      -       -      +
    430E  ARG*     1.3    67.8    +      -       -      -
    432E  LYS*     3.3     4.9    +      -       -      +
    433E  GLU*     2.7    42.8    +      -       -      +
    436E  THR*     3.2    20.2    -      -       -      -
    438E  TRP*     3.3     6.1    -      -       -      -
    464E  LEU*     3.7     5.7    -      -       -      +
----------------------------------------------------------
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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