Contacts of the helix formed by residues 39 - 50 (chain D) in PDB entry 4HXD


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 ASN 39 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  ASP*     3.1    10.3    +      -       -      +
     38D  GLY*     1.3    77.6    +      -       -      +
     40D  CYS*     1.3    62.8    +      -       -      +
     41D  PHE*     3.0     4.9    +      -       -      -
     42D  TYR*     3.0    21.1    +      -       -      +
     43D  HIS*     3.1    32.7    +      -       +      +
     58D  PHE*     3.7    31.7    -      -       +      -
     62D  LYS*     4.5     8.9    -      -       -      +
     96D  ASP*     3.4    11.1    -      -       -      +
     97D  ASN*     2.9    42.4    -      -       -      +
     98D  GLU      4.0     7.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 40 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75C  GLY      4.1     0.2    -      -       -      -
    101C  4LJ      1.8    62.4    -      -       +      -
     34D  GLN*     4.0     3.6    -      -       +      +
     35D  PRO      3.3    19.5    -      -       -      +
     37D  ASP*     3.6     2.5    +      -       -      -
     38D  GLY      3.5     0.6    -      -       -      -
     39D  ASN*     1.3    76.7    -      -       -      +
     41D  PHE*     1.3    53.1    +      -       -      +
     43D  HIS*     3.8     9.0    -      -       -      +
     44D  SER*     2.7    37.2    +      -       -      -
    151D  HIS*     3.8    10.3    -      -       +      -
    152D  PHE      3.4    23.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 41 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75C  GLY      3.5    19.0    +      -       -      +
     38D  GLY      6.0     0.2    -      -       -      +
     39D  ASN      3.0     0.8    +      -       -      -
     40D  CYS*     1.3    79.6    -      -       -      +
     42D  TYR*     1.3    96.2    +      +       +      +
     44D  SER*     2.9    20.1    +      -       -      -
     45D  ILE*     3.0    39.3    +      -       +      +
    100D  GLY*     4.0     9.4    -      -       -      +
    101D  GLY*     3.4    35.2    -      -       -      -
    104D  GLU*     3.8    14.8    -      -       +      -
    105D  ALA*     4.0     6.7    -      -       +      -
    108D  LEU*     4.5     1.3    -      -       +      -
    118D  LEU*     4.5     9.2    -      -       +      -
    144D  LEU*     4.0    16.4    -      -       +      -
    152D  PHE*     3.8    28.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 42 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  GLY      5.5     0.2    -      -       -      -
     39D  ASN*     3.0    14.1    +      -       -      +
     41D  PHE*     1.3   102.8    -      +       +      +
     43D  HIS*     1.3    60.3    +      -       -      +
     45D  ILE*     3.4     3.3    +      -       -      +
     46D  ALA*     2.9    30.1    +      -       -      +
     58D  PHE*     3.6    25.6    -      -       +      +
     61D  VAL*     3.5    22.0    -      -       +      +
     62D  LYS*     3.6    43.7    -      -       +      -
     65D  LEU*     3.5    18.2    -      -       +      +
     93D  ALA*     4.8     4.7    +      -       -      +
     98D  GLU      4.0    18.6    -      -       -      -
     99D  TRP      4.4     2.5    +      -       -      -
    100D  GLY*     3.8     9.8    -      -       -      -
    104D  GLU*     3.1    25.6    -      -       +      +
    108D  LEU*     4.6     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 43 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34D  GLN*     3.4    17.5    -      -       -      +
     35D  PRO*     4.3    12.4    -      -       +      +
     37D  ASP*     3.4    24.0    +      -       -      -
     39D  ASN*     3.1    38.0    +      -       +      +
     40D  CYS*     3.8     9.4    -      -       -      +
     42D  TYR*     1.3    73.4    -      -       -      +
     44D  SER*     1.3    65.3    +      -       -      +
     46D  ALA*     3.3     4.1    +      -       -      +
     47D  GLU*     3.1    24.1    +      -       -      +
     53D  LYS*     3.2    26.9    +      -       -      +
     55D  PRO*     3.2    28.9    -      -       +      -
     58D  PHE*     3.3    26.2    +      +       +      +
----------------------------------------------------------
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Residues in contact with SER 44 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34D  GLN*     3.1    16.0    -      -       -      +
     40D  CYS      2.7    18.4    +      -       -      -
     41D  PHE*     2.9    13.7    +      -       -      -
     43D  HIS*     1.3    76.4    -      -       -      +
     45D  ILE*     1.3    61.3    +      -       -      +
     47D  GLU*     3.2    16.6    +      -       -      +
     48D  LEU*     3.6    12.5    +      -       -      +
    144D  LEU*     3.9    25.4    -      -       -      -
    152D  PHE      2.8    22.5    +      -       -      -
    153D  ASP      3.5     7.3    -      -       -      -
    154D  ALA*     4.0     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 45 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  PHE*     3.0    44.3    +      -       +      +
     42D  TYR      3.9     6.3    -      -       -      +
     44D  SER*     1.3    76.2    -      -       -      +
     46D  ALA*     1.3    62.9    +      -       -      +
     47D  GLU      3.2     0.7    +      -       -      -
     48D  LEU*     3.2     4.1    +      -       -      +
     49D  PHE*     3.0    26.6    +      -       +      +
     61D  VAL*     3.8    21.5    -      -       +      -
    108D  LEU*     4.0    15.9    -      -       +      -
    112D  LEU*     5.3     7.6    -      -       +      -
    116D  ILE*     4.5    20.0    -      -       +      -
    142D  LEU*     4.3    19.0    -      -       +      +
    144D  LEU*     3.8    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 46 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42D  TYR      2.9    18.1    +      -       -      +
     43D  HIS*     3.3     6.9    +      -       -      +
     45D  ILE*     1.3    76.6    -      -       -      +
     47D  GLU*     1.3    60.5    +      -       -      +
     49D  PHE*     4.7     0.7    -      -       -      -
     50D  PHE*     3.2    44.9    +      -       +      +
     53D  LYS*     4.2     7.8    -      -       +      +
     57D  SER*     3.7    29.2    -      -       -      -
     58D  PHE*     3.9     9.4    -      -       -      +
     61D  VAL*     4.3     2.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 47 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  ILE*     4.1    22.8    -      -       +      +
     34D  GLN*     3.9    19.4    +      -       -      +
     43D  HIS      3.1    11.4    +      -       -      +
     44D  SER      3.5    11.0    -      -       -      +
     45D  ILE      3.2     0.4    -      -       -      -
     46D  ALA*     1.3    76.6    -      -       -      +
     48D  LEU*     1.3    61.6    +      -       +      +
     50D  PHE      4.1     7.4    -      -       -      +
     53D  LYS*     4.1    29.3    +      -       +      +
    154D  ALA*     4.2    11.4    -      -       +      -
    156D  ARG*     2.9    39.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 48 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  ILE*     4.8     0.2    -      -       +      -
     44D  SER      3.9     8.7    -      -       -      +
     45D  ILE      3.2     3.6    +      -       -      +
     47D  GLU*     1.3    79.9    -      -       +      +
     49D  PHE*     1.3    62.5    +      -       -      +
     50D  PHE      3.6     3.6    -      -       -      +
    142D  LEU*     4.0    25.7    -      -       +      +
    143D  ASN      3.3    42.8    -      -       -      +
    144D  LEU*     3.9    14.8    -      -       +      -
    154D  ALA*     4.1    13.5    -      -       +      -
    155D  LEU      3.4    19.7    -      -       -      +
    156D  ARG*     3.9    35.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 49 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  GLN*     6.5     1.8    -      -       +      -
     45D  ILE*     3.0    22.9    +      -       +      +
     46D  ALA*     4.5     2.5    -      -       -      +
     48D  LEU*     1.3    79.8    -      -       -      +
     50D  PHE*     1.3    92.9    +      +       +      +
     61D  VAL*     6.1     2.7    -      -       +      -
     64D  HIS*     4.7     9.9    -      +       -      -
    112D  LEU*     3.9    40.4    -      -       +      -
    114D  THR*     4.4    14.6    -      -       +      -
    142D  LEU*     4.4    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 50 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46D  ALA*     3.2    40.3    +      -       +      +
     47D  GLU      4.1    12.0    -      -       -      +
     48D  LEU      4.4     2.9    -      -       -      +
     49D  PHE*     1.3   110.5    -      +       -      +
     51D  ASP*     1.3    64.9    +      -       -      +
     52D  VAL*     3.4    18.7    -      -       -      +
     57D  SER*     3.8    30.5    -      -       -      -
     60D  LYS*     3.8    42.8    -      -       +      -
     61D  VAL*     4.5     9.9    -      -       +      -
     64D  HIS*     5.3     1.8    -      +       -      -
    156D  ARG*     5.4     1.2    +      -       -      -
----------------------------------------------------------
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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