Contacts of the helix formed by residues 298 - 311 (chain Q) in PDB entry 4UJ3


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 ASP 298 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296Q  GLU      3.3     5.7    +      -       -      +
    297Q  ALA*     1.3    68.0    -      -       -      +
    299Q  LEU*     1.3    64.4    +      -       -      +
    300Q  SER*     2.9    28.4    +      -       -      -
    301Q  LEU*     3.1    30.1    +      -       +      +
    302Q  TYR*     3.0    22.1    +      -       -      +
    438Q  PHE*     4.5     4.5    -      -       -      -
    442Q  MET*     4.9     5.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 299 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296Q  GLU*     6.0     1.8    -      -       -      +
    297Q  ALA*     3.2    12.3    +      -       +      +
    298Q  ASP*     1.3    72.2    +      -       -      +
    300Q  SER*     1.3    63.3    +      -       -      +
    302Q  TYR*     3.9     9.1    -      -       +      +
    303Q  ASN*     3.1    38.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 300 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298Q  ASP*     2.9    13.6    +      -       -      -
    299Q  LEU*     1.3    82.2    -      -       -      +
    301Q  LEU*     1.3    67.1    +      -       -      +
    303Q  ASN*     3.7     3.9    +      -       -      +
    304Q  GLU*     3.3    20.2    +      -       -      +
    323Q  LYS*     6.0     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 301 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298Q  ASP*     3.1    27.4    +      -       +      +
    300Q  SER*     1.3    82.4    -      -       -      +
    302Q  TYR*     1.3    59.6    +      -       -      +
    304Q  GLU*     3.3    25.7    +      -       -      +
    305Q  PHE*     2.9    30.8    +      -       -      +
    320Q  PHE*     5.4     0.3    -      -       -      -
    323Q  LYS*     3.5    27.6    -      -       +      -
    438Q  PHE*     3.8    13.0    -      -       +      -
    442Q  MET*     3.7    23.3    -      -       +      -
    445Q  ARG*     4.1    16.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 302 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297Q  ALA*     4.5    11.9    -      -       +      -
    298Q  ASP      3.0    16.0    +      -       -      +
    299Q  LEU*     3.9    11.9    -      -       +      +
    300Q  SER      3.4     0.2    -      -       -      -
    301Q  LEU*     1.3    77.8    -      -       -      +
    303Q  ASN*     1.3    64.9    +      -       -      +
    305Q  PHE*     3.3     2.2    +      +       -      +
    306Q  ARG*     2.7    74.0    +      -       +      +
    434Q  VAL*     4.1     5.5    -      -       +      +
    435Q  ASP*     2.7    31.4    +      -       -      -
    438Q  PHE*     3.6    45.0    -      +       +      -
----------------------------------------------------------
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Residues in contact with ASN 303 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299Q  LEU*     3.1    24.9    +      -       -      +
    300Q  SER*     4.1     4.4    -      -       -      +
    302Q  TYR*     1.3    86.3    -      -       -      +
    304Q  GLU*     1.3    60.3    +      -       -      +
    306Q  ARG*     3.7     7.7    -      -       -      +
    307Q  LEU*     2.9    39.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 304 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300Q  SER      3.3    13.1    +      -       -      +
    301Q  LEU*     3.4    30.0    -      -       -      +
    302Q  TYR      3.3     0.2    -      -       -      -
    303Q  ASN*     1.3    79.3    -      -       -      +
    305Q  PHE*     1.3    61.0    +      -       -      +
    307Q  LEU*     3.6     6.3    +      -       -      +
    308Q  TRP*     3.2    22.0    +      -       -      +
    319Q  PRO*     3.3    30.0    -      -       +      +
    320Q  PHE*     3.9    27.1    -      -       +      +
    323Q  LYS*     2.9    28.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 305 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301Q  LEU      2.9    16.4    +      -       -      +
    302Q  TYR*     3.8     3.1    -      +       -      +
    304Q  GLU*     1.3    71.6    -      -       -      +
    306Q  ARG*     1.3    62.8    +      -       +      +
    307Q  LEU      3.1     2.2    -      -       -      -
    308Q  TRP*     3.0    19.2    +      +       -      +
    309Q  LYS*     2.7    44.3    +      -       +      +
    320Q  PHE*     3.4    40.8    -      +       +      -
    424Q  ILE*     4.4     8.3    -      -       +      -
    434Q  VAL*     3.9    17.7    -      -       +      -
    437Q  MET*     3.8    26.7    -      -       +      -
    438Q  PHE*     3.5    43.5    -      +       +      -
    441Q  VAL*     3.7    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 306 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302Q  TYR*     2.7    54.6    +      -       +      +
    303Q  ASN*     3.7     9.4    -      -       -      +
    305Q  PHE*     1.3    78.6    -      -       -      +
    307Q  LEU*     1.3    60.9    +      -       +      +
    309Q  LYS*     3.8    12.7    -      -       -      +
    310Q  ASP*     3.8    29.8    +      -       -      +
    434Q  VAL*     3.1    44.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 307 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303Q  ASN*     2.9    20.7    +      -       +      +
    304Q  GLU*     3.8     5.8    -      -       -      +
    306Q  ARG*     1.3    76.4    -      -       +      +
    308Q  TRP*     1.3    63.4    +      -       -      +
    310Q  ASP*     3.3    21.4    +      -       +      +
    311Q  GLU*     4.0     3.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 308 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304Q  GLU      3.2    14.4    +      -       -      +
    305Q  PHE*     3.0    17.4    +      +       -      +
    307Q  LEU*     1.3    76.9    -      -       -      +
    309Q  LYS*     1.3    69.2    +      -       -      +
    311Q  GLU      3.2     6.9    -      -       -      +
    312Q  PRO*     3.1    33.3    -      -       +      -
    313Q  THR*     3.3    51.4    +      -       +      +
    318Q  CYS*     3.9    16.7    -      -       +      -
    319Q  PRO*     6.2     0.4    -      -       +      -
    320Q  PHE*     3.5    46.6    -      +       +      -
    321Q  LEU*     4.5     2.2    -      -       +      +
    421Q  ILE*     3.8    42.2    -      -       +      -
    424Q  ILE*     4.3    19.7    -      -       +      -
    425Q  GLN*     5.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 309 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305Q  PHE*     2.7    36.6    +      -       +      +
    306Q  ARG*     3.8     9.4    -      -       -      +
    307Q  LEU      3.2     0.2    -      -       -      -
    308Q  TRP*     1.3    85.0    -      -       +      +
    310Q  ASP*     1.3    78.4    +      -       -      +
    311Q  GLU      3.4     0.5    +      -       -      -
    312Q  PRO*     3.4    14.2    -      -       -      +
    424Q  ILE*     4.7     6.2    -      -       +      +
    429Q  VAL*     5.4     5.7    +      -       -      +
    434Q  VAL*     4.3    29.4    -      -       +      -
    437Q  MET*     4.2    29.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 310 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    306Q  ARG*     3.8    25.8    +      -       -      +
    307Q  LEU*     3.3    13.5    +      -       +      +
    308Q  TRP      3.2     1.2    -      -       -      -
    309Q  LYS*     1.3    96.9    +      -       -      +
    311Q  GLU*     1.3    69.7    +      -       +      +
    312Q  PRO*     3.7     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 311 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307Q  LEU      4.0     3.1    +      -       -      +
    308Q  TRP*     3.2    11.2    +      -       -      +
    310Q  ASP*     1.3    88.1    -      -       +      +
    312Q  PRO*     1.3    71.2    -      -       -      +
    313Q  THR*     3.6     8.5    +      -       -      +
----------------------------------------------------------
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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