Contacts of the helix formed by residues 46 - 57 (chain O) in PDB entry 6CNC


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 LEU 46 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  SER*     4.8     4.0    -      -       -      -
    248A  VAL*     4.3     8.5    -      -       +      -
    252A  ARG*     4.0    19.3    -      -       -      +
     43O  ASN*     6.0     0.7    -      -       -      +
     44O  PRO      2.7     4.7    +      -       -      +
     45O  ASP*     1.3    80.3    -      -       +      +
     47O  PHE*     1.3    65.6    +      -       -      +
     49O  TYR*     2.9    26.0    +      -       +      +
     50O  LYS*     3.5    26.9    +      -       +      +
     66O  GLY*     3.4    32.3    -      -       -      +
     69O  VAL*     3.4    34.8    -      -       +      -
     70O  ALA*     3.6    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 47 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39O  GLN*     4.5     8.3    -      -       -      -
     43O  ASN*     3.3    41.7    -      -       +      +
     44O  PRO      2.9     5.7    +      -       -      -
     45O  ASP      2.9     1.6    +      -       -      -
     46O  LEU*     1.3    80.6    -      -       -      +
     48O  LEU*     1.3    73.1    +      -       +      +
     49O  TYR      3.1     0.7    +      -       -      -
     50O  LYS*     3.3    24.9    +      -       +      +
     51O  GLU*     3.3    21.7    +      -       +      -
    582O  GLU*     3.1    21.8    -      -       -      +
    585O  MET      4.8     0.2    -      -       -      -
    586O  ALA*     3.3    37.0    -      -       +      -
    590O  PHE*     3.1    39.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 48 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45O  ASP      3.4    10.1    +      -       -      +
     46O  LEU      3.0     0.8    +      -       -      -
     47O  PHE*     1.3    88.9    -      -       +      +
     49O  TYR*     1.3    76.7    +      -       +      +
     51O  GLU*     3.3     2.8    +      -       -      +
     52O  LEU*     2.9    41.2    +      -       +      +
    131O  LEU*     3.5    26.2    -      -       +      -
    581O  LEU*     3.4    34.3    -      -       +      +
    582O  GLU*     4.0     2.8    +      -       -      +
    585O  MET*     3.6    39.5    -      -       +      +
    586O  ALA      4.7     0.2    -      -       -      +
    589O  LEU*     5.1     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 49 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45O  ASP*     3.9    23.1    -      -       -      -
     46O  LEU*     2.9    20.0    +      -       +      +
     48O  LEU*     1.3    86.7    -      -       +      +
     50O  LYS*     1.3    59.0    +      -       -      +
     52O  LEU*     2.7    28.5    +      -       +      +
     53O  VAL*     3.0    16.4    +      -       -      +
     65O  ILE*     4.5    16.4    -      -       +      -
     69O  VAL*     4.7    12.8    -      -       +      -
    122O  TYR*     4.4    30.8    -      +       +      -
    123O  ASN      5.7     0.2    -      -       -      -
    124O  GLU      4.9     0.2    +      -       -      -
    125O  GLU*     3.9    29.7    +      -       -      +
    127O  ILE*     3.9    26.9    -      -       +      +
    128O  HIS      5.1     1.3    -      -       -      -
    581O  LEU*     5.5     5.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 50 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  VAL*     4.8    17.2    -      -       -      +
     43O  ASN*     4.7    14.0    -      -       -      +
     46O  LEU*     3.5    30.6    +      -       +      +
     47O  PHE*     3.3    24.6    +      -       +      +
     49O  TYR*     1.3    78.1    -      -       -      +
     51O  GLU*     1.3    58.4    +      -       -      +
     53O  VAL*     3.7    12.5    -      -       +      +
     54O  LYS*     3.0    35.3    +      -       -      +
     62O  ALA*     4.3     6.7    -      -       +      +
     63O  SER*     5.5     4.9    -      -       -      -
     65O  ILE*     5.6     0.2    -      -       -      -
     66O  GLY*     3.9    34.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 51 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47O  PHE*     3.3    21.0    +      -       +      +
     48O  LEU*     3.3     7.4    +      -       +      +
     49O  TYR      2.9     1.0    +      -       -      -
     50O  LYS*     1.3    79.1    -      -       -      +
     52O  LEU*     1.3    55.9    +      -       -      +
     53O  VAL      3.4     0.2    -      -       -      -
     54O  LYS*     2.9    10.8    +      -       +      +
     55O  ALA*     2.3    41.0    +      -       +      +
    585O  MET      4.7     0.6    -      -       -      +
    586O  ALA*     3.2    19.2    -      -       -      +
    589O  LEU*     3.0    22.2    -      -       +      +
    590O  PHE*     2.7    61.5    +      -       +      -
    593O  GLU*     4.0     6.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 52 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48O  LEU*     2.9    48.5    +      -       +      +
     49O  TYR*     2.7    14.9    +      -       +      +
     51O  GLU*     1.3    71.1    -      -       -      +
     53O  VAL*     1.3    52.3    +      -       -      +
     55O  ALA*     2.9     2.3    +      -       -      +
     56O  HIS*     2.6    41.3    +      -       +      +
    127O  ILE*     3.7    28.5    -      -       +      +
    128O  HIS      5.1     0.2    -      -       -      +
    130O  LEU*     5.7     2.7    -      -       +      -
    131O  LEU*     3.7    34.5    -      -       +      +
    589O  LEU*     3.6    24.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 53 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49O  TYR      3.0    15.0    +      -       -      +
     50O  LYS*     3.7    11.4    -      -       -      -
     52O  LEU*     1.3    75.4    -      -       -      +
     54O  LYS*     1.3    56.4    +      -       -      +
     56O  HIS*     4.1     3.6    -      -       -      -
     57O  LEU*     2.5    43.8    +      -       +      +
     58O  GLY      2.4    27.6    +      -       -      -
     61O  ALA      3.8     7.6    -      -       -      +
     62O  ALA*     3.6    33.0    -      -       +      +
     65O  ILE*     4.5    21.3    -      -       +      -
    127O  ILE*     4.3    13.5    -      -       +      +
    130O  LEU*     5.3     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 54 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50O  LYS*     3.0    32.1    +      -       -      +
     51O  GLU*     2.9    12.6    +      -       +      +
     53O  VAL*     1.3    82.4    -      -       -      +
     55O  ALA*     1.3    62.2    +      -       -      +
     56O  HIS      3.1     1.4    +      -       -      -
     57O  LEU      4.2     0.3    -      -       -      -
     58O  GLY*     3.2    28.7    +      -       -      -
     59O  GLU      5.2     1.3    -      -       -      +
     62O  ALA*     3.6     9.2    -      -       +      -
    590O  PHE*     6.0     5.4    -      -       +      -
    593O  GLU*     5.1     2.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 55 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51O  GLU*     2.3    31.2    +      -       +      +
     52O  LEU      3.2     3.8    -      -       -      +
     54O  LYS*     1.3    68.5    -      -       -      +
     56O  HIS*     1.3    58.6    +      -       -      +
    589O  LEU*     3.9    24.5    -      -       +      -
    592O  LYS*     4.6     7.2    +      -       -      -
    593O  GLU*     3.2    46.3    -      -       +      +
     66Q  LYS*     5.9     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 56 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52O  LEU*     2.6    20.0    +      -       +      +
     53O  VAL*     2.9     2.9    +      -       -      +
     54O  LYS      4.3     0.2    -      -       -      -
     55O  ALA*     1.3    77.5    -      -       -      +
     57O  LEU*     1.3    69.8    +      -       +      +
    101O  LEU*     5.0     2.9    -      -       +      -
    130O  LEU*     3.3    45.2    -      -       +      +
     61Q  PHE*     3.7    23.9    -      +       -      -
     62Q  GLY*     4.4    15.0    -      -       -      +
     65Q  VAL*     3.3    41.1    -      -       +      +
     66Q  LYS*     4.3    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 57 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53O  VAL*     2.5    22.9    +      -       +      +
     54O  LYS      4.2     0.2    -      -       -      -
     56O  HIS*     1.3    84.8    -      -       +      +
     58O  GLY*     1.3    62.5    +      -       -      +
     59O  GLU*     4.2     9.9    -      -       -      +
     61O  ALA*     4.0    15.7    -      -       +      -
     97O  SER*     5.0     6.1    -      -       -      +
     98O  LEU*     3.7    30.7    -      -       +      -
    101O  LEU*     4.0    22.2    -      -       +      -
    103O  CYS*     4.6     2.2    -      -       -      -
    130O  LEU*     5.3     2.2    -      -       +      -
     65Q  VAL*     3.6    30.5    -      -       +      +
     66Q  LYS*     5.9     1.8    -      -       -      +
     70Q  PHE*     4.1    27.7    -      -       +      +
----------------------------------------------------------
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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