Contacts of the helix formed by residues 429 - 434 (chain E) in PDB entry 5U8T


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 429 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36E  ILE*     3.6    28.5    -      -       +      -
    425E  VAL*     3.4    23.6    -      -       +      +
    426E  GLU*     2.4    28.8    +      -       -      +
    428E  LEU*     1.3    74.6    -      -       -      +
    430E  ALA*     1.3    52.5    +      -       -      +
    431E  LEU      3.5     0.2    -      -       -      -
    432E  LEU*     3.4    17.2    -      -       +      +
    433E  GLU*     2.6    29.1    -      -       -      +
    543E  LEU*     4.8     4.9    -      -       +      +
    547E  ARG*     3.9    28.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 430 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    426E  GLU      3.0     3.2    +      -       -      +
    427E  ALA*     3.0    17.9    +      -       -      +
    429E  THR*     1.3    76.1    -      -       -      +
    431E  LEU*     1.3    57.0    +      -       -      +
    432E  LEU      2.9    10.4    +      -       -      -
    433E  GLU*     3.0    23.3    -      -       -      +
    434E  VAL*     3.1    15.8    -      -       -      +
    495E  GLY*     3.4    29.6    -      -       -      +
    498E  LEU*     4.2     5.4    -      -       +      -
    502E  LEU*     3.5    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 431 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427E  ALA*     3.1    13.9    -      -       +      +
    428E  LEU*     3.5     3.3    +      -       -      +
    430E  ALA*     1.3    74.4    -      -       -      +
    432E  LEU*     1.3    60.2    +      -       -      +
    434E  VAL      3.2     9.6    -      -       -      +
    435E  GLY*     5.5     1.8    -      -       -      -
    476E  ASN*     2.3    46.4    +      -       -      +
    479E  LEU*     4.0    17.5    -      -       +      +
    480E  SER*     3.5    31.4    -      -       -      +
    483E  ALA*     3.4    32.5    -      -       +      -
    491E  LEU*     5.0     3.6    -      -       +      +
    492E  LEU*     5.3     3.6    -      -       +      +
    494E  ARG*     5.3     2.5    -      -       +      -
    495E  GLY*     3.6    31.9    -      -       -      +
    498E  LEU*     4.7     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 432 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34E  LEU*     3.5    35.9    -      -       +      +
     36E  ILE*     4.6    12.6    -      -       +      -
     39E  LEU*     5.4     7.2    -      -       +      -
    428E  LEU      3.2    17.3    -      -       -      +
    429E  THR*     3.4    22.4    -      -       +      +
    430E  ALA      2.9     0.4    -      -       -      -
    431E  LEU*     1.3    84.8    -      -       -      +
    433E  GLU*     1.3    67.2    +      -       -      +
    473E  TRP*     3.9    30.3    -      -       -      +
    476E  ASN*     4.7     2.2    +      -       -      +
    477E  PHE*     4.9    12.3    -      -       +      -
    480E  SER*     4.3    15.9    -      -       -      +
    541E  ASN*     4.8     2.9    -      -       -      +
    543E  LEU*     3.4    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 433 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429E  THR      2.6    22.3    -      -       -      +
    430E  ALA      3.0    15.3    -      -       -      +
    432E  LEU*     1.3    70.3    -      -       -      +
    434E  VAL*     1.3    61.4    +      -       +      +
    472E  ARG*     4.0    21.5    +      -       -      -
    473E  TRP*     4.7     5.0    +      -       -      +
    476E  ASN*     4.8     0.4    -      -       -      -
    502E  LEU*     3.1    41.5    -      -       +      +
    538E  LEU*     4.7    19.6    -      -       +      +
    541E  ASN*     3.2    40.3    +      -       +      +
    544E  THR*     3.7    11.4    -      -       +      +
    547E  ARG*     3.7     5.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 434 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    430E  ALA      3.1    15.9    -      -       -      +
    431E  LEU*     3.2    15.8    -      -       -      +
    432E  LEU      3.5     1.2    -      -       -      -
    433E  GLU*     1.3    82.5    -      -       +      +
    435E  GLY*     1.3    62.1    +      -       -      +
    436E  ASN*     3.5     5.6    -      -       -      +
    472E  ARG*     4.9     4.0    -      -       -      +
    476E  ASN*     2.3    26.8    +      -       -      +
    498E  LEU*     3.9    24.5    -      -       +      -
    501E  ASP*     5.4     6.5    -      -       -      +
    502E  LEU*     3.8    24.7    -      -       +      -
    538E  LEU*     5.4    12.6    -      -       +      -
----------------------------------------------------------
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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