Contacts of the strand formed by residues 372 - 379 (chain C) 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 SER 372 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365C  THR*     3.6     1.5    -      -       -      +
    366C  LYS*     2.8    23.0    +      -       -      +
    367C  SER*     3.1    23.4    +      -       -      -
    370C  SER*     2.9    19.7    +      -       -      -
    371C  ARG*     1.3    73.6    -      -       -      +
    373C  GLY*     1.3    63.6    +      -       -      +
    399C  ALA      4.3     0.2    -      -       -      -
    400C  ILE*     3.4    23.7    +      -       -      -
    401C  THR      5.7     0.2    -      -       -      -
    402C  ASP      3.4     7.3    +      -       -      -
    403C  TRP*     3.7    16.3    -      -       -      -
    404C  SER*     3.8     0.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 373 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365C  THR*     3.3     8.3    -      -       -      -
    366C  LYS*     3.6     7.9    -      -       -      -
    372C  SER*     1.3    74.4    -      -       -      +
    374C  PHE*     1.3    63.7    +      -       -      +
    398C  VAL*     2.8    22.4    -      -       -      +
    399C  ALA      3.1    15.5    +      -       -      -
    402C  ASP      2.8    13.9    +      -       -      -
    404C  SER*     3.0    20.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 374 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352C  PHE*     3.9     2.9    -      +       -      -
    363C  GLY*     3.8     9.9    -      -       -      -
    364C  ARG*     3.1    42.2    -      -       -      -
    365C  THR*     4.1     4.9    -      -       +      +
    366C  LYS*     3.6     6.5    +      -       -      +
    373C  GLY*     1.3    76.6    -      -       -      +
    375C  GLU*     1.3    81.0    +      -       -      +
    376C  MET*     4.2     2.0    -      -       -      -
    397C  ILE*     3.0    28.2    +      -       +      -
    398C  VAL*     2.6    44.0    +      -       +      +
    404C  SER*     4.7     4.9    -      -       -      -
    405C  GLY      5.0     4.0    -      -       -      -
    407C  SER*     3.5    37.7    -      -       -      -
    422C  PHE*     3.7    23.8    -      +       -      -
    424C  VAL*     3.8    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 375 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327C  ARG*     5.2     0.2    +      -       -      -
    362C  ILE      3.6     1.4    -      -       -      +
    363C  GLY*     3.5     5.0    -      -       -      -
    364C  ARG*     3.0    66.1    +      -       +      +
    365C  THR      4.3     2.5    -      -       -      +
    366C  LYS*     3.1    31.4    +      -       +      +
    374C  PHE*     1.3    81.9    -      -       -      +
    376C  MET*     1.3    66.0    +      -       -      +
    377C  ILE*     3.2     6.8    -      -       +      +
    394C  LYS*     2.8    44.1    +      -       +      -
    395C  GLN      3.3    12.3    -      -       -      +
    396C  ASP*     4.4     2.2    -      -       -      +
    397C  ILE      4.2     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 376 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97C  TRP*     3.6    54.7    -      -       +      +
    352C  PHE*     4.0    21.8    -      -       +      -
    361C  TRP*     3.8    22.2    -      -       +      -
    362C  ILE      3.5     9.0    -      -       -      +
    363C  GLY*     3.7    16.8    -      -       -      -
    374C  PHE*     4.2     1.8    -      -       -      -
    375C  GLU*     1.3    74.4    -      -       -      +
    377C  ILE*     1.3    62.0    +      -       -      +
    392C  VAL      3.9     0.3    -      -       -      +
    394C  LYS*     3.3     4.9    -      -       -      +
    395C  GLN*     2.7    44.8    +      -       +      +
    397C  ILE*     4.0     8.5    -      -       +      -
    422C  PHE*     3.7    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 377 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321C  VAL*     3.7    18.4    -      -       +      -
    360C  VAL      3.4     1.9    -      -       -      +
    361C  TRP*     3.4     6.9    -      -       -      -
    362C  ILE*     2.7    49.9    +      -       +      +
    364C  ARG*     3.6    20.4    -      -       +      +
    375C  GLU*     3.2    30.1    -      -       +      +
    376C  MET*     1.3    80.5    -      -       -      +
    378C  TRP*     1.3    64.7    +      -       -      +
    379C  ASP*     3.7     3.5    +      -       +      +
    390C  PHE*     3.6    39.0    -      -       +      -
    392C  VAL      3.4     4.3    -      -       -      +
    394C  LYS*     3.8    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 378 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356C  TYR*     3.9    28.0    -      +       +      -
    359C  GLY*     3.8    13.0    -      -       -      -
    360C  VAL*     3.2    43.1    -      -       -      -
    361C  TRP*     3.5    50.1    -      +       +      -
    377C  ILE*     1.3    72.3    -      -       -      +
    379C  ASP*     1.3    58.8    +      -       -      +
    380C  PRO*     3.4    26.2    -      -       +      +
    390C  PHE*     3.4     2.1    -      -       -      +
    391C  SER*     2.9    45.0    +      -       -      -
    392C  VAL*     3.0    23.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 379 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319C  SER*     2.9    27.8    +      -       -      +
    321C  VAL*     3.9     4.6    -      -       +      +
    360C  VAL*     3.2    31.5    +      -       +      +
    362C  ILE*     4.8     6.7    -      -       +      -
    377C  ILE*     3.7     2.3    +      -       +      -
    378C  TRP*     1.3    73.4    -      -       -      +
    380C  PRO*     1.3    92.0    -      -       -      +
    381C  ASN      4.0     0.7    -      -       -      +
    382C  GLY*     3.0    21.7    +      -       -      -
    387C  ASP*     3.6    11.1    -      -       -      +
    389C  SER      3.2    24.7    -      -       -      +
    390C  PHE*     3.9     9.9    -      -       +      -
----------------------------------------------------------
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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