Contacts of the strand formed by residues 439 - 447 (chain E) 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 THR 439 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116E  VAL*     3.3    15.6    -      -       -      +
    117E  ILE      3.8     2.8    -      -       -      +
    118E  ARG*     4.2    22.9    -      -       +      +
    136E  GLN*     5.3     0.5    -      -       -      +
    148E  THR*     3.1    24.2    +      -       -      +
    149E  VAL*     3.3    21.3    -      -       +      +
    427E  ILE*     4.2    17.0    -      -       +      -
    428E  ARG      3.5     5.8    -      -       -      -
    430E  ARG      2.8    35.4    +      -       -      +
    438E  TRP*     1.3    73.7    +      -       -      +
    440E  SER*     1.3    67.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 440 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106E  ILE*     3.7     8.7    -      -       -      +
    115E  PHE      4.1     2.3    +      -       -      -
    116E  VAL*     3.5    10.7    -      -       -      -
    117E  ILE*     2.7    37.2    +      -       -      +
    118E  ARG*     4.5     4.3    -      -       -      -
    140E  LEU*     3.9    21.8    -      -       -      +
    427E  ILE*     3.5     4.1    -      -       -      +
    428E  ARG      2.8    32.7    +      -       -      +
    438E  TRP*     3.8     6.0    -      -       -      -
    439E  THR*     1.3    77.8    -      -       -      +
    441E  GLY*     1.3    64.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 441 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105E  SER*     3.3    11.8    +      -       -      -
    106E  ILE*     4.1     5.9    -      -       -      +
    117E  ILE*     3.4    31.0    +      -       -      +
    118E  ARG*     4.7     0.4    -      -       -      +
    120E  PRO*     5.8     0.4    -      -       -      -
    425E  GLU*     4.5    11.4    -      -       -      -
    426E  LEU      3.3    13.0    -      -       -      -
    427E  ILE*     4.3     1.8    -      -       -      -
    440E  SER*     1.3    84.2    +      -       -      +
    442E  SER*     1.3    61.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 442 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102E  LYS*     6.0     0.9    -      -       -      -
    103E  ASP*     3.6     3.5    +      -       -      -
    104E  ASN*     4.0     4.0    -      -       -      -
    105E  SER*     2.8    32.3    +      -       -      -
    106E  ILE*     3.5     2.6    +      -       -      +
    117E  ILE*     5.9     0.7    -      -       -      -
    120E  PRO*     4.4     3.3    -      -       -      +
    425E  GLU*     3.2     9.9    -      -       -      +
    426E  LEU*     2.9    40.2    +      -       -      -
    441E  GLY*     1.3    73.2    -      -       -      -
    443E  SER*     1.3    64.6    -      -       -      +
    460E  ASP*     3.0    28.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 443 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101E  SER*     4.7     2.6    +      -       -      -
    102E  LYS*     3.4     4.3    -      -       -      +
    103E  ASP*     2.5    50.6    +      -       -      +
    104E  ASN      4.9     0.2    +      -       -      -
    120E  PRO*     4.7    17.0    -      -       -      -
    122E  ILE*     5.7     5.8    -      -       -      +
    131E  THR*     4.8    10.4    +      -       -      +
    423E  TRP*     5.6     5.6    -      -       -      -
    424E  VAL      3.1    11.7    -      -       -      -
    426E  LEU*     4.7     0.9    -      -       -      -
    442E  SER*     1.3    81.2    -      -       -      +
    444E  ILE*     1.3    69.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 444 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99E  VAL*     5.9     1.6    -      -       +      -
    101E  SER*     3.3     9.6    -      -       -      +
    102E  LYS*     3.9    21.5    -      -       +      -
    122E  ILE*     5.5     0.2    -      -       -      -
    397E  ILE*     3.7    17.3    -      -       +      -
    398E  VAL*     3.7    23.3    -      -       +      -
    423E  TRP*     3.4     2.6    -      -       -      +
    424E  VAL*     3.0    45.7    +      -       +      +
    426E  LEU*     4.0    14.8    -      -       +      -
    443E  SER*     1.3    81.0    -      -       -      +
    445E  SER*     1.3    62.8    +      -       -      +
    446E  PHE*     4.0    13.5    -      -       +      -
    458E  TRP*     3.4    33.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 445 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99E  VAL*     3.6     2.3    -      -       -      +
    100E  TYR*     2.6    39.9    +      -       -      +
    101E  SER*     2.6    38.1    +      -       -      +
    122E  ILE*     3.4    25.5    -      -       -      +
    410E  PHE*     4.3     6.1    -      -       -      -
    422E  PHE      3.4    11.4    -      -       -      -
    423E  TRP*     4.1     0.4    -      -       -      -
    444E  ILE*     1.3    76.5    -      -       -      +
    446E  PHE*     1.3    65.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 446 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97E  TRP*     3.9    18.2    -      -       +      -
     98E  ALA      3.0    11.4    -      -       -      +
     99E  VAL*     3.5    33.4    -      -       +      -
    100E  TYR*     3.9     2.7    -      -       -      +
    395E  GLN*     5.4     1.1    -      -       -      -
    397E  ILE*     3.8    32.5    -      -       +      -
    410E  PHE*     4.2     0.5    -      -       -      -
    421E  CYS*     3.0     5.9    -      -       -      +
    422E  PHE*     2.9    62.7    +      +       +      -
    444E  ILE*     4.0    21.1    -      -       +      -
    445E  SER*     1.3    81.2    -      -       -      +
    447E  CYS*     1.3    64.5    +      -       -      +
    458E  TRP*     3.6    40.8    -      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 447 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97E  TRP*     3.6     7.0    -      -       -      -
     98E  ALA*     2.9    25.4    +      -       -      +
    100E  TYR*     4.1    18.4    -      -       -      +
    410E  PHE*     4.3     0.9    -      -       -      -
    412E  GLN*     2.6    20.6    -      -       -      -
    419E  ARG*     4.1    11.2    -      -       -      +
    420E  PRO      3.8     0.7    -      -       -      -
    421E  CYS*     2.1    44.0    -      -       -      +
    446E  PHE*     1.3    75.2    -      -       -      +
    448E  GLY*     1.3    70.4    +      -       -      +
    449E  VAL*     4.0     3.4    -      -       +      +
    211G  ILE*     3.9    17.9    -      -       +      -
----------------------------------------------------------
 Back to top of page


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