Contacts of the strand formed by residues 279 - 283 (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 SER 279 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228D  SER*     3.7     6.7    +      -       -      -
    277D  GLU      3.8     0.2    +      -       -      -
    278D  CYS*     1.3    71.6    -      -       -      +
    280D  CYS*     1.3    60.5    +      -       -      +
    281D  TYR*     4.8     3.1    -      -       -      -
    288D  THR      3.6     1.6    -      -       -      +
    289D  CYS*     3.1     1.9    -      -       -      -
    290D  VAL*     3.0    30.9    +      -       -      +
    350D  LYS*     3.5    13.0    +      -       -      -
    351D  GLY      2.6    29.2    +      -       -      -
    352D  PHE*     3.7    11.4    -      -       -      -
    408D  GLY*     3.7     9.9    -      -       -      -
    409D  SER*     3.5    22.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 280 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226D  GLN*     3.7    23.3    +      -       -      +
    229D  GLU*     4.1    20.5    +      -       -      +
    231D  ALA*     3.9    15.1    -      -       +      +
    238D  PHE      5.4     1.8    -      -       -      +
    239D  THR*     5.5     1.6    -      -       -      -
    240D  VAL*     4.0     9.9    -      -       -      -
    278D  CYS*     3.9    10.3    -      -       -      -
    279D  SER*     1.3    75.2    -      -       -      +
    281D  TYR*     1.3    62.7    +      -       -      +
    287D  ILE*     3.7    11.7    -      -       +      -
    288D  THR      3.2     3.6    -      -       -      -
    289D  CYS*     2.0    46.9    -      -       -      -
    305D  PHE*     5.7     0.4    -      -       -      -
    409D  SER*     4.1     5.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 281 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91D  LEU*     3.9    22.4    -      -       +      -
    229D  GLU*     5.4     0.2    -      -       -      +
    231D  ALA*     4.1     4.7    -      -       -      -
    279D  SER      4.8     2.5    -      -       -      -
    280D  CYS*     1.3    76.0    -      -       -      +
    282D  PRO*     1.3    81.9    -      -       +      +
    283D  ASN*     4.2    11.0    -      -       +      -
    287D  ILE*     3.5     1.2    -      -       -      -
    288D  THR*     2.9    68.5    +      -       +      +
    290D  VAL*     5.0     2.7    -      -       +      -
    353D  SER      3.3    21.4    +      -       -      -
    354D  PHE*     3.5    26.0    -      +       +      -
    355D  LYS*     2.9    32.3    +      -       -      +
    409D  SER*     4.3     9.4    -      -       -      +
    411D  VAL*     3.7    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 282 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87D  GLY      5.0     1.6    -      -       -      +
     91D  LEU*     4.2     0.5    -      -       -      +
    229D  GLU*     5.4     2.0    -      -       -      +
    231D  ALA*     3.9    16.2    -      -       +      -
    232D  CYS      4.0     7.2    -      -       -      +
    233D  VAL*     3.8    25.4    -      -       +      -
    281D  TYR*     1.3    93.9    -      -       +      +
    283D  ASN*     1.3    65.7    +      -       -      +
    286D  GLU      3.3     7.0    -      -       -      +
    287D  ILE*     4.6     0.4    -      -       -      -
    411D  VAL*     3.8    13.0    -      -       +      -
    412D  HIS*     3.7    31.4    -      -       -      +
    418D  ILE*     3.8    24.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 283 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87D  GLY      4.6     0.2    +      -       -      -
     89D  SER      3.9     5.2    -      -       -      -
     90D  SER*     3.7     6.4    +      -       -      +
     91D  LEU*     3.0    44.8    -      -       -      +
    281D  TYR*     3.9    15.7    +      -       +      +
    282D  PRO*     1.3    77.4    -      -       -      +
    284D  ALA*     1.3    80.0    +      -       -      +
    285D  GLY      3.2     1.9    -      -       -      +
    286D  GLU*     2.8    25.9    +      -       -      +
    288D  THR*     5.3     4.9    -      -       -      +
    355D  LYS      5.7     1.4    +      -       -      -
    418D  ILE*     4.5     1.5    -      -       -      +
----------------------------------------------------------
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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