Contacts of the strand formed by residues 279 - 283 (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 279 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228C  SER*     3.8     5.7    +      -       -      -
    277C  GLU      3.7     0.2    +      -       -      -
    278C  CYS*     1.3    70.9    -      -       -      +
    280C  CYS*     1.3    61.4    +      -       -      +
    281C  TYR*     4.6     3.3    -      -       -      -
    288C  THR      3.5     2.1    -      -       -      +
    289C  CYS*     3.2     1.0    -      -       -      -
    290C  VAL*     2.8    34.1    +      -       -      +
    350C  LYS*     3.2    14.4    +      -       -      -
    351C  GLY      2.9    23.9    +      -       -      -
    352C  PHE*     3.6    15.6    -      -       -      +
    408C  GLY*     3.6     9.9    -      -       -      -
    409C  SER*     3.5    21.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 280 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226C  GLN*     3.7    23.9    +      -       -      +
    229C  GLU*     3.8    23.3    +      -       -      +
    231C  ALA*     4.4    12.2    -      -       +      +
    238C  PHE      5.5     1.6    -      -       -      +
    239C  THR*     5.4     2.2    -      -       -      -
    240C  VAL*     4.1     9.2    -      -       -      -
    278C  CYS*     3.8    10.2    -      -       -      -
    279C  SER*     1.3    74.4    -      -       -      +
    281C  TYR*     1.3    62.3    +      -       -      +
    282C  PRO*     4.7     0.2    -      -       -      +
    287C  ILE*     3.6    13.0    -      -       +      -
    288C  THR      3.1     4.5    -      -       -      -
    289C  CYS*     2.0    46.2    -      -       -      -
    305C  PHE*     5.4     0.7    -      -       -      -
    409C  SER*     4.0     6.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 281 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91C  LEU*     3.8    27.4    -      -       +      -
    231C  ALA*     4.2     4.0    -      -       -      -
    279C  SER      4.6     2.9    -      -       -      -
    280C  CYS*     1.3    77.7    -      -       -      +
    282C  PRO*     1.3    80.7    -      -       +      +
    283C  ASN*     3.8    12.7    +      -       +      -
    287C  ILE*     3.5     0.8    -      -       -      +
    288C  THR*     2.9    63.3    +      -       +      +
    290C  VAL*     5.0     1.3    -      -       +      -
    353C  SER      3.5    21.5    -      -       -      -
    354C  PHE*     4.1    15.3    -      +       +      -
    355C  LYS*     2.9    39.4    +      -       -      +
    383C  TRP*     5.6     0.2    -      -       -      -
    409C  SER*     4.5    10.3    -      -       -      +
    411C  VAL*     3.9    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 282 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  GLY      5.0     0.9    -      -       -      +
     91C  LEU*     4.1     0.7    -      -       -      +
    229C  GLU*     5.3     1.6    -      -       -      +
    230C  CYS      5.7     0.2    -      -       -      +
    231C  ALA*     3.8    17.2    -      -       +      -
    232C  CYS      4.3     5.4    -      -       -      +
    233C  VAL*     3.8    26.0    -      -       +      -
    280C  CYS      4.7     0.4    -      -       -      +
    281C  TYR*     1.3    90.1    -      -       +      +
    283C  ASN*     1.3    65.5    +      -       -      +
    286C  GLU      3.4     7.2    -      -       -      +
    287C  ILE*     4.5     1.3    -      -       -      -
    411C  VAL*     3.8    15.5    -      -       +      -
    412C  HIS*     3.6    32.8    -      -       -      +
    418C  ILE*     3.6    23.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 283 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  GLY      4.6     0.2    +      -       -      -
     89C  SER      4.0     4.7    -      -       -      -
     90C  SER*     3.9     5.1    +      -       -      +
     91C  LEU*     3.0    47.3    -      -       -      +
    281C  TYR*     4.0    15.9    -      -       +      +
    282C  PRO*     1.3    75.6    -      -       -      +
    284C  ALA*     1.3    82.3    +      -       -      +
    285C  GLY      3.1     1.4    -      -       -      +
    286C  GLU*     2.7    27.9    +      -       -      +
    288C  THR*     5.2     4.7    -      -       -      +
    355C  LYS      5.3     3.0    +      -       -      -
    418C  ILE*     4.5     0.6    -      -       -      +
----------------------------------------------------------
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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