Contacts of the helix formed by residues 274 - 285 (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 ASP 274 (chain Z).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250Z  ARG*     3.1    34.7    +      -       -      -
    269Z  ALA      4.2     2.0    +      -       -      -
    272Z  LEU*     3.4    18.8    -      -       -      +
    273Z  ASN*     1.3    78.0    -      -       -      +
    275Z  MET*     1.3    55.5    +      -       -      +
    276Z  GLU*     4.4     8.4    -      -       +      +
    277Z  LEU*     2.8    36.2    +      -       +      +
    278Z  VAL*     2.7    35.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 275 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273Z  ASN*     3.8    12.8    +      -       -      +
    274Z  ASP*     1.3    72.0    -      -       -      +
    276Z  GLU*     1.3    57.0    +      -       -      +
    278Z  VAL*     3.3    16.9    +      -       +      -
    279Z  GLU*     3.0    26.9    +      -       -      +
    314Z  TYR*     5.6     5.2    -      -       +      +
    317Z  LEU*     3.8    37.5    -      -       +      -
    318Z  THR*     4.7     3.8    -      -       -      +
    321Z  MET*     4.0    30.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 276 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274Z  ASP*     4.6    11.3    -      -       +      +
    275Z  MET*     1.3    77.0    -      -       -      +
    277Z  LEU*     1.3    69.4    +      -       +      +
    279Z  GLU*     4.0    11.9    -      -       -      +
    280Z  ASP*     2.8    19.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 277 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250Z  ARG*     3.9    18.6    -      -       +      -
    253Z  LEU*     4.2    16.2    -      -       +      -
    257Z  ARG*     3.6     3.2    +      -       -      +
    269Z  ALA*     3.3    25.4    -      -       +      +
    272Z  LEU*     3.6    24.7    -      -       +      -
    274Z  ASP*     2.8    36.5    +      -       +      +
    276Z  GLU*     1.3    87.3    -      -       +      +
    278Z  VAL*     1.3    62.6    +      -       -      +
    279Z  GLU      3.2     1.1    -      -       -      -
    280Z  ASP*     3.2    37.3    +      -       -      +
    281Z  ILE*     5.5     0.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 278 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269Z  ALA*     3.7    22.2    -      -       -      +
    270Z  LEU*     5.1    11.0    -      -       +      -
    273Z  ASN*     4.9     6.5    -      -       -      +
    274Z  ASP      2.7    25.8    +      -       -      +
    275Z  MET*     3.3    21.5    +      -       +      +
    277Z  LEU*     1.3    71.7    -      -       -      +
    279Z  GLU*     1.3    61.5    +      -       -      +
    280Z  ASP      3.0     2.6    +      -       -      -
    281Z  ILE*     3.8    17.4    +      -       -      +
    282Z  PHE*     4.2     2.9    +      -       -      +
    306Z  GLU*     5.4     7.2    -      -       +      -
    318Z  THR*     3.4    29.1    -      -       +      +
    321Z  MET*     3.8    11.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 279 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275Z  MET      3.0    17.0    +      -       -      +
    276Z  GLU*     4.1    11.7    -      -       -      +
    277Z  LEU      3.2     0.4    -      -       -      -
    278Z  VAL*     1.3    76.7    -      -       -      +
    280Z  ASP*     1.3    60.4    +      -       -      +
    281Z  ILE      3.5     0.4    -      -       -      -
    282Z  PHE*     3.5    23.6    +      -       -      +
    283Z  THR*     3.0    26.1    +      -       -      +
    321Z  MET*     3.2    39.9    -      -       +      +
    325Z  GLN*     5.2    10.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 280 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253Z  LEU*     4.4     3.8    -      -       -      +
    257Z  ARG*     3.4    31.6    +      -       -      +
    276Z  GLU      2.8    22.7    -      -       -      +
    277Z  LEU*     3.2    33.9    -      -       -      +
    278Z  VAL      3.0     2.0    -      -       -      -
    279Z  GLU*     1.3    79.7    -      -       -      +
    281Z  ILE*     1.3    58.8    +      -       -      +
    283Z  THR*     3.0    23.4    +      -       -      -
    284Z  SER*     3.2    15.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 281 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257Z  ARG*     3.6    20.9    -      -       -      +
    262Z  PHE*     3.9    23.8    -      -       +      +
    266Z  LEU*     3.7    33.4    -      -       +      -
    277Z  LEU      5.5     0.4    -      -       -      +
    278Z  VAL*     3.8    11.9    +      -       -      +
    280Z  ASP*     1.3    80.3    -      -       -      +
    282Z  PHE*     1.3    62.4    +      -       +      +
    284Z  SER*     3.3    21.2    +      -       -      +
    285Z  CYS*     3.4    15.6    +      -       +      +
    298Z  LEU*     3.6    29.6    -      -       +      +
    299Z  GLY*     4.7     2.6    -      -       -      -
    302Z  GLY*     4.7    11.0    -      -       -      -
    303Z  VAL*     6.1     2.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 282 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    278Z  VAL      4.2     3.8    +      -       -      +
    279Z  GLU*     3.5    27.5    +      -       -      +
    280Z  ASP      3.3     0.6    -      -       -      -
    281Z  ILE*     1.3    81.3    -      -       +      +
    283Z  THR*     1.3    58.2    +      -       -      +
    284Z  SER      3.4     0.2    -      -       -      -
    285Z  CYS*     3.9    16.2    -      -       -      -
    286Z  LYS*     3.6    42.0    -      -       +      +
    299Z  GLY*     6.0     1.1    -      -       -      -
    303Z  VAL*     5.0     7.6    -      -       +      -
    318Z  THR*     5.8     2.0    -      -       +      -
    321Z  MET*     5.4     3.4    -      -       +      -
    322Z  SER*     3.4    46.2    -      -       -      +
    325Z  GLN*     3.9    21.5    -      -       +      -
    326Z  LEU*     4.4    13.0    -      -       +      -
    336Z  GLU*     3.8    31.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 283 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279Z  GLU*     3.0    25.5    +      -       -      +
    280Z  ASP*     3.0    16.7    +      -       -      -
    282Z  PHE*     1.3    78.3    -      -       -      +
    284Z  SER*     1.3    57.4    +      -       -      +
    285Z  CYS      3.5     0.4    -      -       -      -
    286Z  LYS*     5.2     1.1    -      -       -      -
    287Z  ASP*     3.1    48.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 284 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257Z  ARG*     4.1     2.4    +      -       -      -
    262Z  PHE*     3.7    25.3    -      -       -      -
    280Z  ASP      3.2    12.7    +      -       -      -
    281Z  ILE*     3.3    22.8    +      -       -      -
    283Z  THR*     1.3    77.5    -      -       -      +
    285Z  CYS*     1.3    57.1    +      -       -      +
    286Z  LYS      3.5     1.1    -      -       -      -
    288Z  VAL*     3.1    39.6    -      -       -      +
    295Z  ALA*     3.4     9.4    -      -       -      +
    298Z  LEU*     6.1     2.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 285 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281Z  ILE*     3.4    14.6    +      -       +      +
    282Z  PHE*     3.9    27.6    -      -       -      -
    284Z  SER*     1.3    77.0    -      -       -      +
    286Z  LYS*     1.3    64.7    +      -       -      +
    289Z  VAL*     3.0    22.8    -      -       -      +
    295Z  ALA      2.9    25.1    -      -       -      +
    296Z  PHE*     4.3     5.6    -      -       +      -
    299Z  GLY*     3.8    24.5    -      -       -      +
    331Z  LEU*     3.3    17.9    -      -       +      +
    336Z  GLU*     4.6     6.7    -      -       -      -
----------------------------------------------------------
 Back to top of page


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