Contacts of the strand formed by residues 359 - 364 (chain D) 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 GLY 359 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355D  LYS*     3.5     1.2    -      -       -      +
    356D  TYR      2.6    40.0    +      -       -      -
    358D  ASN*     1.3    72.2    -      -       -      +
    360D  VAL*     1.3    70.8    +      -       -      +
    378D  TRP*     3.8     7.4    -      -       -      -
    379D  ASP      3.5     0.4    -      -       -      -
    380D  PRO*     3.7     3.6    -      -       -      -
    381D  ASN*     2.7    28.0    -      -       -      +
    383D  TRP*     4.0     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 360 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317D  ILE*     4.6     6.5    -      -       +      -
    353D  SER*     5.2     2.7    -      -       -      +
    354D  PHE      3.3    11.2    -      -       -      +
    359D  GLY*     1.3    81.7    -      -       -      +
    361D  TRP*     1.3    60.6    +      -       -      +
    362D  ILE*     3.9    28.7    -      -       +      +
    377D  ILE      3.4     2.3    -      -       -      +
    378D  TRP*     3.1    11.3    -      -       -      -
    379D  ASP*     3.0    41.9    +      -       +      +
    382D  GLY      4.0     6.5    -      -       -      +
    383D  TRP*     3.0    55.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 361 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94D  ILE*     3.6    21.5    +      -       +      +
     95D  ASN*     3.4    32.1    -      -       -      -
     96D  GLY*     4.4     1.3    -      -       -      -
     97D  TRP*     3.2    45.3    -      +       +      -
    352D  PHE*     5.1     0.3    -      -       -      -
    353D  SER*     3.4     7.1    +      -       -      -
    354D  PHE*     3.0    36.1    +      -       +      +
    356D  TYR*     3.8    26.0    -      +       -      -
    360D  VAL*     1.3    71.6    -      -       -      +
    362D  ILE*     1.3    61.0    +      -       -      +
    363D  GLY      4.1     0.3    +      -       -      -
    376D  MET*     4.0    24.3    -      -       +      +
    377D  ILE      3.3    19.1    -      -       -      -
    378D  TRP*     3.6    49.3    -      +       +      -
    392D  VAL*     4.5    15.3    -      -       +      -
    395D  GLN*     4.8     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 362 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300D  ARG*     6.5     0.7    -      -       -      -
    317D  ILE*     4.7     8.5    -      -       +      -
    319D  SER*     4.3    15.5    -      -       -      +
    321D  VAL*     3.7    27.1    -      -       +      +
    323D  GLY*     4.4    13.7    -      -       -      +
    352D  PHE      5.2     0.2    -      -       -      +
    353D  SER*     3.7    17.0    -      -       -      +
    360D  VAL*     3.9    25.4    -      -       +      -
    361D  TRP*     1.3    75.0    -      -       -      +
    363D  GLY*     1.3    74.3    +      -       -      +
    364D  ARG*     4.0    15.2    +      -       +      +
    375D  GLU      3.4     1.9    -      -       -      +
    376D  MET*     3.2     6.9    -      -       -      -
    377D  ILE*     2.7    47.1    +      -       +      +
    379D  ASP*     5.1     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 363 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300D  ARG*     5.1     5.0    +      -       -      -
    323D  GLY*     4.4     4.7    -      -       -      +
    351D  GLY*     5.7     1.2    -      -       -      -
    352D  PHE*     3.9    25.2    +      -       -      +
    361D  TRP      4.1     1.0    +      -       -      -
    362D  ILE*     1.3    80.2    -      -       -      +
    364D  ARG*     1.3    64.3    -      -       -      +
    374D  PHE*     3.6    13.5    -      -       -      -
    375D  GLU      3.5     1.1    -      -       -      -
    376D  MET*     3.4    24.2    -      -       -      +
    407D  SER*     5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 364 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321D  VAL*     3.3    21.1    -      -       -      +
    322D  PHE      2.6    36.7    +      -       -      -
    323D  GLY*     3.9    16.4    -      -       -      +
    327D  ARG*     3.3    25.7    -      -       -      +
    330D  ASP*     2.7    41.2    +      -       -      -
    362D  ILE*     4.3     6.5    -      -       +      -
    363D  GLY*     1.3    76.2    -      -       -      +
    365D  THR*     1.3    64.9    +      -       -      +
    374D  PHE*     3.0    17.4    -      -       -      -
    375D  GLU*     2.8    64.9    +      -       +      +
    377D  ILE*     3.4    11.7    -      -       +      +
    390D  PHE*     5.6     2.0    -      -       -      -
    394D  LYS*     4.7     3.8    -      -       -      +
----------------------------------------------------------
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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