Contacts of the helix formed by residues 348 - 354 (chain H) in PDB entry 3LUE


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 348 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22H  ALA*     4.3     2.2    -      -       -      -
     23H  GLY*     3.8    22.3    +      -       -      -
    344H  SER      2.8    19.4    +      -       -      -
    345H  ILE*     2.6    23.4    +      -       -      -
    346H  LEU      2.8     2.8    +      -       -      -
    347H  ALA*     1.3    74.2    -      -       -      +
    349H  LEU*     1.3    66.7    +      -       -      +
    350H  SER      3.7     1.4    +      -       -      -
     95Q  ASP*     4.0    16.4    +      -       -      +
    101Q  PHE*     5.4     0.5    -      -       -      -
    102Q  HIS*     5.2     6.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 349 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49F  GLN*     3.6    31.2    -      -       +      +
    143H  TYR*     4.0     9.2    -      -       +      +
    345H  ILE*     3.2    22.0    +      -       +      +
    346H  LEU*     3.0    23.7    +      -       +      +
    347H  ALA      4.7     0.9    -      -       -      +
    348H  SER*     1.3    80.5    -      -       -      +
    350H  SER*     1.3    60.4    +      -       -      +
    351H  THR*     3.0    19.5    -      -       -      +
    352H  PHE*     3.1    18.2    +      -       -      +
    353H  GLN*     4.1     2.3    +      -       -      +
     95Q  ASP*     4.6     6.7    -      -       -      +
    101Q  PHE      4.4     6.5    -      -       -      +
    102Q  HIS*     6.0     0.2    -      -       -      -
    104Q  ILE*     6.3     0.4    -      -       +      -
    105Q  ALA*     3.1    37.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 350 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348H  SER      3.7     2.6    +      -       -      -
    349H  LEU*     1.3    71.1    -      -       -      +
    351H  THR*     1.3    62.6    +      -       -      +
    352H  PHE      3.4     0.5    +      -       -      -
    353H  GLN*     3.5     8.2    +      -       -      +
    354H  GLN*     3.1    23.1    +      -       -      -
     95Q  ASP*     5.3     2.0    +      -       -      -
    109Q  LYS*     4.9    16.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 351 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41F  GLN*     2.7    49.5    +      -       +      +
     49F  GLN*     4.2    10.2    +      -       -      +
    346H  LEU*     6.0     1.1    -      -       +      -
    349H  LEU*     3.8    21.2    -      -       +      +
    350H  SER*     1.3    75.8    +      -       -      +
    352H  PHE*     1.3    62.5    +      -       +      +
    354H  GLN*     3.0    28.9    +      -       -      +
    355H  MET*     4.0     1.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 352 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104H  LEU*     3.5    16.2    -      -       +      -
    133H  TYR*     3.5    32.3    -      +       +      -
    346H  LEU*     3.3    43.5    -      -       +      +
    347H  ALA*     3.7    10.5    -      -       -      +
    349H  LEU*     3.1    14.5    +      -       +      +
    351H  THR*     1.3    73.4    -      -       -      +
    353H  GLN*     1.3    63.2    +      -       -      +
    354H  GLN      2.9     6.9    +      -       -      -
    355H  MET*     2.9    56.8    +      -       +      +
    356H  TRP*     3.2    55.3    +      +       -      -
----------------------------------------------------------
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Residues in contact with GLN 353 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102H  PRO*     4.2    13.5    -      -       -      +
    131H  ALA*     4.9     5.7    -      -       -      +
    349H  LEU      4.1     2.4    +      -       -      +
    350H  SER*     3.5     7.6    +      -       -      +
    351H  THR      3.3     1.6    +      -       -      -
    352H  PHE*     1.3    75.4    -      -       -      +
    354H  GLN*     1.3    72.8    +      -       -      +
    355H  MET      3.3     3.6    +      -       -      -
    356H  TRP*     2.9    57.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 354 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350H  SER*     3.1    23.4    +      -       -      -
    351H  THR*     3.0    19.3    -      -       -      +
    352H  PHE      2.9     0.2    -      -       -      -
    353H  GLN*     1.3    88.6    -      -       -      +
    355H  MET*     1.3    69.0    +      -       -      +
----------------------------------------------------------
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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