Contacts of the helix formed by residues 286 - 294 (chain N) in PDB entry 3FKS


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 286 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238K  ALA*     4.2     6.1    -      -       -      +
    245K  GLN*     5.7     7.0    -      -       -      +
    275K  LYS      6.2     0.2    -      -       -      +
    278K  VAL*     4.3    25.0    -      -       +      +
    279K  ALA*     6.0     1.6    -      -       -      +
    282K  GLN*     5.0     3.3    +      -       -      +
    283N  PRO      5.0     0.4    +      -       -      -
    284N  THR      3.4     0.2    -      -       -      -
    285N  LEU*     1.3    78.7    -      -       -      +
    287N  THR*     1.3    63.2    +      -       +      +
    289N  MET*     3.3     4.7    +      -       -      +
    290N  GLY*     3.0    22.7    +      -       -      -
    324N  THR*     4.3    14.5    -      -       +      +
    328N  HIS*     5.4     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 287 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238K  ALA      4.2     7.1    -      -       -      +
    239K  SER      5.6     0.7    -      -       -      -
    240K  GLU      4.0    12.8    -      -       -      +
    241K  ALA*     4.7     1.1    -      -       -      -
    242K  ALA*     4.1    10.5    -      -       -      +
    245K  GLN*     3.9    20.6    -      -       -      +
    279K  ALA*     6.4     0.9    -      -       +      -
    282K  GLN*     3.3    39.5    +      -       -      +
    284N  THR*     3.6     4.5    -      -       -      +
    286N  ALA*     1.3    74.4    -      -       +      +
    288N  ASP*     1.3    70.2    +      -       -      +
    289N  MET      3.0     1.8    -      -       -      -
    290N  GLY*     2.9     1.4    +      -       -      -
    291N  LEU*     2.9    41.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 288 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261N  PHE*     3.8    25.4    -      -       +      -
    265N  GLY*     4.9     8.0    -      -       -      +
    274N  ARG*     5.3     2.0    +      -       -      -
    282N  GLN*     3.9    16.4    +      -       -      +
    284N  THR*     2.9    37.9    +      -       -      +
    285N  LEU      4.5     0.4    -      -       -      +
    286N  ALA      3.4     0.4    -      -       -      -
    287N  THR*     1.3    82.4    +      -       -      +
    289N  MET*     1.3    60.0    +      -       -      +
    291N  LEU*     3.9    20.6    +      -       -      +
    292N  LEU*     4.2     5.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 289 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258N  ILE*     4.9     2.9    -      -       +      -
    261N  PHE*     4.3    18.2    -      -       +      -
    262N  THR*     3.4    33.0    -      -       +      +
    285N  LEU*     3.3    19.4    +      -       +      +
    286N  ALA      3.3     5.3    +      -       -      +
    287N  THR      3.0     0.8    -      -       -      -
    288N  ASP*     1.3    77.4    -      -       -      +
    290N  GLY*     1.3    58.7    +      -       -      +
    291N  LEU      3.4     0.2    -      -       -      -
    292N  LEU*     3.8     2.1    +      -       -      +
    293N  GLN*     3.1    61.7    +      -       +      +
    321N  ALA      5.1     0.7    -      -       -      +
    324N  THR*     4.0    20.4    -      -       +      +
    325N  THR*     3.8    26.5    -      -       +      +
    328N  HIS*     4.3    13.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 290 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238K  ALA*     3.6    20.6    -      -       -      -
    239K  SER*     3.9     7.9    +      -       -      -
    121N  PRO*     4.3     0.2    -      -       -      +
    286N  ALA      3.0     6.9    +      -       -      -
    287N  THR      2.9     7.5    +      -       -      -
    289N  MET*     1.3    76.0    -      -       -      +
    291N  LEU*     1.3    55.1    +      -       -      +
    292N  LEU      3.0    10.1    +      -       -      -
    293N  GLN      4.6     0.2    -      -       -      -
    294N  GLU*     3.2    34.8    +      -       -      +
    328N  HIS*     4.5     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 291 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239K  SER*     3.5    32.5    -      -       -      +
    119N  ALA      5.1     1.2    -      -       -      +
    120N  ASP*     5.8     2.9    -      -       -      +
    121N  PRO*     4.9     8.1    -      -       +      -
    234N  LEU*     4.1    11.1    -      -       +      +
    287N  THR*     2.9    25.7    +      -       -      +
    288N  ASP*     4.2    16.8    -      -       -      +
    289N  MET      3.4     0.6    -      -       -      -
    290N  GLY*     1.3    76.1    -      -       -      +
    292N  LEU*     1.3    57.9    +      -       -      +
    295N  ARG*     3.4    24.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 292 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233N  ALA*     3.7    26.9    -      -       +      +
    234N  LEU*     3.6    21.1    -      -       +      -
    237N  LEU*     3.5    24.4    -      -       +      +
    253N  LEU*     6.2     1.1    -      -       +      -
    255N  ILE*     5.6     4.0    -      -       +      -
    258N  ILE*     4.1    11.4    -      -       +      -
    261N  PHE*     4.0    26.5    -      -       +      -
    288N  ASP      4.4     8.3    -      -       -      +
    289N  MET*     3.8     6.6    +      -       -      +
    290N  GLY      3.0     0.4    -      -       -      -
    291N  LEU*     1.3    79.8    -      -       -      +
    293N  GLN*     1.3    85.8    -      -       -      +
    294N  GLU      3.2     1.3    -      -       -      -
    295N  ARG*     3.2    17.9    +      -       -      +
    296N  ILE*     3.6    14.1    -      -       +      +
    308N  GLN*     4.8     6.1    -      -       -      +
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Residues in contact with GLN 293 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152N  LYS*     2.8    49.4    +      -       -      +
    258N  ILE*     3.9     5.3    -      -       -      +
    289N  MET*     3.1    35.7    +      -       -      +
    292N  LEU*     1.3    94.6    -      -       -      +
    294N  GLU*     1.3    58.7    +      -       -      +
    296N  ILE*     3.2    17.2    +      -       -      +
    308N  GLN*     3.6    32.1    +      -       -      +
    325N  THR*     4.5     5.5    -      -       -      +
    328N  HIS*     3.2    39.6    -      -       +      +
    329N  LEU*     5.9     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 294 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210K  GLN      3.6     5.9    -      -       -      +
    211K  LYS*     3.2    21.9    -      -       -      +
    212K  ARG*     2.7    42.9    +      -       +      +
    213K  SER*     4.7     2.6    +      -       -      -
    237K  THR*     4.0     5.4    -      -       -      -
    238K  ALA*     4.0     5.5    +      -       +      +
    239K  SER*     3.7    18.4    -      -       -      +
    121N  PRO*     3.3    26.6    -      -       +      +
    122N  PRO*     3.8     7.6    -      -       -      +
    127N  GLN*     4.8     2.4    +      -       -      -
    152N  LYS*     4.6     3.1    +      -       -      -
    290N  GLY*     3.2    23.8    +      -       -      +
    292N  LEU      3.2     0.8    -      -       -      -
    293N  GLN*     1.3    77.0    -      -       -      +
    295N  ARG*     1.3    58.1    +      -       -      +
    296N  ILE      3.1     6.0    +      -       -      -
    297N  THR*     4.1    14.0    -      -       -      +
    328N  HIS*     4.9     2.9    -      -       +      -
----------------------------------------------------------
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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