Contacts of the strand formed by residues 392 - 403 (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 VAL 392 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95C  ASN      5.2     8.1    -      -       -      +
    361C  TRP*     4.6    13.0    -      -       +      -
    376C  MET      4.4     0.7    -      -       -      -
    377C  ILE*     3.4     9.7    -      -       -      +
    378C  TRP*     3.0    44.3    +      -       +      -
    390C  PHE*     3.9     2.8    -      -       -      -
    391C  SER*     1.3    89.1    -      -       -      +
    394C  LYS*     1.3    79.2    +      -       -      +
    395C  GLN*     5.4     3.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 394 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364C  ARG*     4.7     4.2    -      -       -      +
    366C  LYS*     4.4     1.1    -      -       -      +
    375C  GLU*     2.8    42.3    +      -       +      +
    376C  MET      3.3     7.2    -      -       -      +
    377C  ILE*     3.8    15.5    -      -       +      +
    390C  PHE*     4.2    24.1    -      -       +      -
    392C  VAL*     1.3    83.9    -      -       -      +
    395C  GLN*     1.3    62.5    +      -       -      +
    396C  ASP*     4.1    18.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 395 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  GLY*     3.7     4.6    -      -       -      -
     97C  TRP*     2.9    64.9    -      -       -      +
    361C  TRP*     5.0     4.4    -      -       +      -
    375C  GLU*     3.3     1.4    -      -       -      -
    376C  MET*     2.7    44.5    +      -       +      +
    392C  VAL*     4.8     4.7    -      -       +      +
    394C  LYS*     1.3    75.1    -      -       -      +
    396C  ASP*     1.3    75.0    +      -       -      +
    397C  ILE*     3.3     9.8    -      -       +      +
    446C  PHE*     5.4     0.9    -      -       -      -
    453C  THR*     3.6    13.4    +      -       -      -
    454C  VAL*     3.3    15.0    -      -       -      +
    455C  GLY*     3.9    12.8    -      -       -      +
    458C  TRP*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 396 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366C  LYS*     2.6    32.5    +      -       -      +
    374C  PHE      4.1     3.8    -      -       -      -
    375C  GLU*     4.4     0.2    -      -       -      +
    394C  LYS*     4.1    17.1    +      -       -      +
    395C  GLN*     1.3    73.7    -      -       -      +
    397C  ILE*     1.3    67.2    -      -       -      +
    398C  VAL      5.1     1.3    -      -       -      +
    399C  ALA*     6.0     0.7    -      -       -      +
    455C  GLY*     3.3    11.9    -      -       -      -
    456C  TRP*     3.3    34.2    +      -       -      +
    458C  TRP*     4.3     2.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 397 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97C  TRP*     5.3     0.7    -      -       +      -
    374C  PHE*     3.0    31.2    +      -       +      +
    376C  MET*     4.0    17.7    -      -       +      +
    395C  GLN*     3.3    28.0    -      -       +      +
    396C  ASP*     1.3    96.0    -      -       -      +
    398C  VAL*     1.3    75.6    +      -       +      +
    422C  PHE*     4.1    11.2    -      -       +      -
    424C  VAL*     4.5     1.1    -      -       +      -
    444C  ILE*     3.9    17.0    -      -       +      -
    446C  PHE*     3.7    30.5    -      -       +      -
    456C  TRP      3.3     8.3    -      -       -      +
    458C  TRP*     3.0    31.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 398 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366C  LYS*     3.0     9.7    -      -       -      +
    373C  GLY*     2.8    12.6    -      -       -      -
    374C  PHE*     2.6    41.1    +      -       +      +
    396C  ASP*     5.8     1.1    -      -       -      -
    397C  ILE*     1.3    97.5    -      -       +      +
    399C  ALA*     1.3    71.7    +      -       -      +
    402C  ASP*     3.9    20.0    -      -       +      +
    403C  TRP      4.3     9.6    -      -       -      +
    404C  SER*     4.8     1.8    -      -       -      -
    424C  VAL*     5.2     1.1    -      -       +      -
    426C  LEU*     4.3     9.6    -      -       +      -
    444C  ILE*     3.9     7.6    -      -       +      -
    456C  TRP      5.0     0.7    -      -       -      -
    457C  SER*     3.9     3.8    -      -       -      +
    458C  TRP      3.7    20.0    -      -       -      +
    459C  PRO*     4.6     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 399 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366C  LYS*     4.1     6.3    -      -       -      +
    373C  GLY*     3.1    12.2    -      -       -      -
    396C  ASP*     6.4     0.4    -      -       -      -
    398C  VAL*     1.3    75.2    -      -       -      +
    400C  ILE*     1.3    63.5    +      -       +      +
    401C  THR*     3.0    19.7    -      -       +      +
    402C  ASP*     3.0    18.3    +      -       -      +
    456C  TRP      5.0     0.4    +      -       -      -
    457C  SER*     3.0    28.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 400 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366C  LYS*     3.7    39.4    -      -       +      +
    367C  SER*     4.2    20.4    -      -       -      +
    372C  SER*     3.4    17.6    +      -       -      -
    373C  GLY*     4.1     8.1    -      -       -      -
    399C  ALA*     1.3    72.8    -      -       +      +
    401C  THR*     1.3    62.5    +      -       +      +
    402C  ASP      3.2     2.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 401 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372C  SER*     5.6     0.2    -      -       -      -
    399C  ALA*     3.7    12.7    -      -       +      +
    400C  ILE*     1.3    81.8    -      -       +      +
    402C  ASP*     1.3    74.9    +      -       -      +
    403C  TRP*     5.8     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 402 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372C  SER*     3.4     5.2    -      -       -      -
    373C  GLY*     2.8    29.1    +      -       -      -
    398C  VAL*     3.9     5.9    -      -       +      +
    399C  ALA*     3.0    14.1    +      -       -      +
    400C  ILE      3.2     0.4    -      -       -      -
    401C  THR*     1.3    95.0    +      -       -      +
    403C  TRP*     1.3    66.2    +      -       -      +
    457C  SER*     4.7     0.7    +      -       -      -
    459C  PRO*     3.4    39.6    -      -       +      +
    460C  ASP      5.3     0.3    +      -       -      -
    461C  GLY*     5.4     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 403 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370C  SER*     4.2    13.7    -      -       -      -
    371C  ARG*     3.5    22.7    -      -       +      +
    372C  SER*     3.7    17.0    -      -       -      -
    398C  VAL*     4.3     4.4    -      -       -      +
    401C  THR      5.8     2.0    +      -       -      -
    402C  ASP*     1.3    80.4    +      -       -      +
    404C  SER*     1.3    59.4    +      -       -      +
    426C  LEU*     3.5    18.7    -      -       -      +
    427C  ILE      3.3    23.3    -      -       -      +
    428C  ARG*     3.5    30.7    -      -       -      +
    432C  LYS*     3.5    48.0    -      -       +      -
    433C  GLU*     3.4    26.5    +      -       +      +
    460C  ASP*     5.0     5.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 404 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365C  THR*     3.7     8.1    -      -       -      +
    371C  ARG*     2.9    27.1    +      -       -      +
    373C  GLY*     3.0    31.7    +      -       -      -
    374C  PHE*     4.7     2.7    -      -       -      -
    398C  VAL*     4.8     2.2    -      -       -      -
    403C  TRP*     1.3    75.3    -      -       -      +
    405C  GLY*     1.3    68.0    +      -       -      -
    424C  VAL*     4.5    10.5    -      -       -      -
    425C  GLU      3.0    11.9    -      -       -      -
    426C  LEU*     3.8    10.5    -      -       -      +
    427C  ILE*     3.0    27.0    +      -       -      +
----------------------------------------------------------
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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