Contacts of the helix formed by residues 332 - 341 (chain Z) in PDB entry 5L4K


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 ALA 332 (chain Z).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296Z  PHE*     4.4    13.2    -      -       +      -
    326Z  LEU*     3.1    15.3    -      -       -      +
    330Z  PHE*     3.8    10.8    -      -       -      -
    331Z  LEU*     1.3    84.2    -      -       -      +
    333Z  LEU*     1.3    62.8    +      -       -      +
    335Z  ARG*     3.4    43.1    -      -       +      +
    336Z  GLU*     3.6    18.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 333 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323Z  ASN*     5.7     0.4    -      -       -      +
    326Z  LEU*     4.1    18.4    -      -       +      +
    327Z  ASN*     5.6     3.8    -      -       -      +
    330Z  PHE*     3.2    31.7    -      -       +      -
    332Z  ALA*     1.3    71.0    -      -       -      +
    334Z  ALA*     1.3    71.9    +      -       +      +
    335Z  ARG      3.2     0.7    -      -       -      -
    337Z  LEU*     3.0    54.7    +      -       +      +
    338Z  ASP*     4.0     1.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 334 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332Z  ALA      3.4     0.4    -      -       -      -
    333Z  LEU*     1.3    90.4    -      -       +      +
    335Z  ARG*     1.3    78.4    +      -       -      +
    338Z  ASP*     3.3    33.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 335 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292Z  LYS*     4.2    19.7    -      -       -      +
    296Z  PHE*     3.9    24.0    -      -       +      -
    300Z  ARG*     3.4    35.3    +      -       -      +
    330Z  PHE*     5.3     4.8    -      -       -      -
    331Z  LEU      4.7     2.0    +      -       -      -
    332Z  ALA*     3.4    29.5    +      -       +      +
    333Z  LEU      3.2     0.6    -      -       -      -
    334Z  ALA*     1.3    97.1    -      -       -      +
    336Z  GLU*     1.3    61.1    +      -       -      +
    339Z  ILE*     2.8    32.6    -      -       -      +
    816Z  TYR*     5.9     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 336 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282Z  PHE*     3.8    24.7    -      -       +      -
    285Z  CYS*     4.6     5.1    -      -       -      -
    296Z  PHE*     4.5     9.7    -      -       +      -
    299Z  GLY*     3.6    22.6    -      -       -      +
    300Z  ARG*     3.7    10.2    +      -       -      +
    303Z  VAL*     3.4    33.3    -      -       -      +
    326Z  LEU*     3.9    16.8    -      -       +      -
    331Z  LEU*     6.1     0.4    -      -       +      +
    332Z  ALA      3.6    16.7    +      -       -      +
    333Z  LEU      3.6     1.0    +      -       -      -
    335Z  ARG*     1.3    80.2    -      -       +      +
    337Z  LEU*     1.3    65.9    +      -       -      +
    338Z  ASP      3.2     1.3    -      -       -      -
    339Z  ILE*     3.0    15.8    +      -       -      +
    340Z  MET*     3.0    25.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 337 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319Z  GLU*     4.3    15.7    -      -       +      +
    323Z  ASN*     3.7    30.7    -      -       +      +
    326Z  LEU*     3.7    17.9    -      -       +      -
    333Z  LEU*     3.0    42.0    +      -       +      +
    336Z  GLU*     1.3    74.9    -      -       -      +
    338Z  ASP*     1.3    57.2    +      -       -      +
    340Z  MET*     3.6    26.7    -      -       +      -
    341Z  GLU*     3.0    41.9    +      -       -      +
    343Z  LYS*     5.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 338 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333Z  LEU*     4.0     3.4    +      -       -      +
    334Z  ALA*     3.3    35.3    +      -       -      +
    336Z  GLU      3.2     0.8    -      -       -      -
    337Z  LEU*     1.3    76.6    -      -       -      +
    339Z  ILE*     1.3    59.1    -      -       +      +
    341Z  GLU      3.3     8.2    -      -       -      +
    343Z  LYS*     3.2    28.3    -      -       +      +
    344Z  VAL*     3.2    38.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 339 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300Z  ARG*     3.9    27.4    -      -       +      +
    303Z  VAL*     4.2     8.3    -      -       +      +
    304Z  PHE*     3.5    71.1    -      -       +      +
    307Z  LEU*     3.7    18.3    -      -       +      +
    335Z  ARG      2.8    27.4    -      -       -      +
    336Z  GLU      3.0     5.3    +      -       -      +
    338Z  ASP*     1.3    83.6    -      -       +      +
    340Z  MET*     1.3    68.5    +      -       -      +
    341Z  GLU      3.3     5.5    -      -       -      +
    342Z  PRO*     4.2     2.4    -      -       -      +
    344Z  VAL*     4.8     7.0    -      -       +      -
    345Z  PRO*     5.0     5.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 340 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303Z  VAL*     3.9    25.6    -      -       +      +
    306Z  GLU*     5.2     5.8    -      -       +      +
    307Z  LEU*     3.8    14.5    -      -       -      +
    315Z  GLU*     4.3    16.3    -      -       -      +
    318Z  THR*     3.8    23.6    -      -       -      +
    319Z  GLU*     3.7    36.3    -      -       +      +
    322Z  SER*     3.8    17.7    -      -       -      -
    336Z  GLU*     3.0    27.1    +      -       +      +
    337Z  LEU*     3.6    32.1    -      -       +      +
    339Z  ILE*     1.3    78.3    -      -       -      +
    341Z  GLU*     1.3    59.0    +      -       -      +
    342Z  PRO*     3.6     7.4    -      -       -      +
    456Z  ARG*     4.1     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 341 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319Z  GLU*     3.2    31.9    -      -       -      +
    337Z  LEU*     3.0    20.0    +      -       -      +
    338Z  ASP      3.3    16.6    -      -       -      +
    339Z  ILE      3.6     1.2    +      -       -      -
    340Z  MET*     1.3    76.2    -      -       -      +
    342Z  PRO*     1.3    57.1    -      -       +      +
    343Z  LYS*     2.6    48.8    +      -       -      +
    455Z  VAL*     3.6    16.5    -      -       -      +
    456Z  ARG*     3.7    15.8    +      -       -      +
    457Z  ASN*     3.9     8.9    +      -       -      +
    459Z  CYS*     3.7    18.5    -      -       -      +
----------------------------------------------------------
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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