Contacts of the helix formed by residues 165 - 180 (chain B) in PDB entry 3C51


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 SER 165 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  LEU*     3.7    13.3    -      -       -      +
    173A  GLN*     5.6     0.4    -      -       -      +
     75B  PHE*     4.2    11.3    -      -       -      -
    161B  GLU      3.8     6.5    -      -       -      -
    162B  PHE*     3.1    21.0    +      -       -      -
    163B  LEU      3.3     3.5    +      -       -      +
    164B  ASP*     1.3    77.8    -      -       -      +
    166B  LEU*     1.3    64.5    +      -       -      +
    167B  TYR*     2.9    21.7    +      -       -      +
    168B  PHE*     3.4    12.5    +      -       -      +
    169B  LEU*     3.5    14.0    +      -       -      +
    566B   BR      4.0    15.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 166 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  LEU*     4.0    15.3    -      -       +      -
    166A  LEU*     3.8    23.3    -      -       +      +
    169A  LEU*     3.6    30.1    -      -       +      -
    170A  ARG*     3.1    44.6    -      -       +      +
    173A  GLN*     3.2    15.9    -      -       -      +
    531A  TRP*     3.6    21.5    -      -       +      -
    165B  SER*     1.3    72.0    +      -       -      +
    167B  TYR*     1.3    61.8    +      -       -      +
    169B  LEU*     3.0     7.3    +      -       -      +
    170B  ARG*     2.9    28.4    +      -       -      +
    531B  TRP*     4.5     4.7    -      -       +      -
    566B   BR      3.6     9.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  ARG*     4.8     1.4    +      -       -      -
    530A  VAL      3.0    20.8    +      -       -      -
    531A  TRP*     3.0    72.2    +      +       -      -
     71B  LEU*     3.5    19.6    -      -       +      +
     74B  GLN*     4.0    19.1    -      -       +      -
     75B  PHE*     3.7    18.4    -      +       +      -
     78B  THR*     3.1    25.7    +      -       +      +
     79B  HIS*     4.9     1.1    -      +       -      -
    162B  PHE*     3.8    17.9    -      -       +      -
    165B  SER*     2.9    13.1    +      -       -      +
    166B  LEU*     1.3    77.1    -      -       -      +
    168B  PHE*     1.3    57.4    +      -       -      +
    170B  ARG*     3.2     1.9    +      -       -      +
    171B  PHE*     2.8    24.6    +      -       -      +
    566B   BR      4.1    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  ARG*     4.2    26.2    -      -       +      -
     61B  MET*     3.6    35.9    -      -       +      -
    162B  PHE*     3.2    33.9    -      +       +      +
    163B  LEU*     3.0    46.0    -      -       +      +
    165B  SER*     3.4     5.8    +      -       -      +
    166B  LEU      3.3     0.4    -      -       -      -
    167B  TYR*     1.3    80.1    -      -       -      +
    169B  LEU*     1.3    65.9    +      -       +      +
    171B  PHE*     3.0    30.8    +      +       -      +
    172B  LEU*     3.1    35.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  LEU*     3.5    17.3    -      -       +      -
    166A  LEU*     3.5    15.3    -      -       +      -
    169A  LEU*     3.2    34.8    -      -       +      -
     44B  LEU*     3.9    14.1    -      -       +      +
     47B  CYS*     5.0     0.7    -      -       -      -
     51B  ARG*     4.1    31.9    -      -       -      +
    163B  LEU      5.5     0.4    -      -       -      +
    165B  SER      3.5    10.7    +      -       -      +
    166B  LEU*     3.0     8.6    +      -       +      +
    168B  PHE*     1.3    81.3    -      -       +      +
    170B  ARG*     1.3    60.7    +      -       -      +
    172B  LEU*     3.3    11.9    +      -       +      +
    173B  GLN*     3.0    31.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  LEU*     3.0    26.2    -      -       +      +
    167A  TYR*     5.4     1.8    +      -       -      -
    531A  TRP*     3.8    24.8    -      -       +      -
     41B  LEU*     3.7    16.5    -      -       -      +
     71B  LEU*     3.7    10.8    -      -       +      -
    166B  LEU      2.9    12.3    +      -       -      +
    167B  TYR      3.5     7.9    -      -       -      +
    169B  LEU*     1.3    73.1    -      -       -      +
    171B  PHE*     1.3    66.5    +      -       -      +
    173B  GLN*     3.0    26.9    +      -       -      +
    174B  TRP*     3.0    44.2    +      -       +      +
    528B  LEU      4.3     0.4    +      -       -      -
    529B  ASN*     3.4    43.9    +      -       -      +
    530B  VAL      4.2    12.1    +      -       -      -
    531B  TRP*     5.0     5.9    -      -       -      -
    565B   BR      3.5    17.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  LEU*     3.4    24.5    -      -       +      -
     61B  MET*     3.1    44.6    -      -       +      -
     65B  GLN*     4.1     9.6    -      -       -      -
     67B  ILE*     4.4     3.1    -      -       +      -
     68B  GLY*     3.3    40.2    -      -       -      -
     71B  LEU*     3.2    16.7    -      -       +      +
    162B  PHE*     4.7     4.5    -      +       +      -
    167B  TYR      2.8    13.3    +      -       -      +
    168B  PHE*     3.0    23.8    +      +       +      +
    170B  ARG*     1.3    76.4    -      -       -      +
    172B  LEU*     1.3    62.1    +      -       +      +
    174B  TRP*     3.2     7.6    +      -       +      +
    175B  LYS*     3.0    46.9    +      -       +      +
    516B  GLN*     5.0     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  CYS*     4.2    24.0    -      -       +      +
     50B  LEU*     3.9    15.1    -      -       +      +
     51B  ARG*     4.1    32.1    -      -       +      +
     54B  LEU*     3.9    27.6    -      -       +      -
     61B  MET*     5.6     0.4    -      -       +      -
    168B  PHE*     3.1    45.6    +      -       +      +
    169B  LEU*     3.7    12.3    -      -       +      +
    170B  ARG      3.3     0.2    -      -       -      -
    171B  PHE*     1.3    78.9    -      -       +      +
    173B  GLN*     1.3    67.9    -      -       -      +
    174B  TRP      3.0     1.8    -      -       -      -
    175B  LYS*     2.8    14.8    +      -       -      +
    176B  TRP*     2.8    14.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 173 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  LEU*     3.3    20.6    -      -       -      +
     41B  LEU*     3.6    23.7    -      -       +      +
     42B  PRO*     3.3    51.4    +      -       +      +
     44B  LEU*     3.3    24.2    -      -       +      +
     47B  CYS*     4.0     9.8    -      -       -      -
    169B  LEU      3.0    15.4    +      -       -      +
    170B  ARG*     3.0    36.2    +      -       -      +
    172B  LEU*     1.3    76.4    -      -       -      +
    174B  TRP*     1.3    60.0    +      -       -      +
    176B  TRP*     3.5     0.9    -      -       -      +
    177B  LEU*     3.3    14.0    +      -       -      +
    565B   BR      3.8     9.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  LEU*     3.6    11.2    -      -       +      +
     67B  ILE*     3.5    40.8    -      -       +      -
     71B  LEU*     4.4     0.4    -      -       +      -
    170B  ARG*     3.0    47.0    +      -       +      +
    171B  PHE*     3.5     8.1    -      -       +      +
    172B  LEU      3.0     0.6    -      -       -      -
    173B  GLN*     1.3    74.3    -      -       -      +
    175B  LYS*     1.3    61.3    +      -       +      +
    176B  TRP      3.1     1.8    -      -       -      -
    177B  LEU*     3.3    24.3    +      -       +      +
    178B  GLU*     3.0    28.6    +      -       -      +
    515B  TRP*     3.6    27.2    -      +       +      -
    516B  GLN*     6.4     0.4    -      -       +      -
    519B  MET*     4.0    10.1    -      -       +      -
    524B  VAL*     4.1     2.2    -      -       +      -
    525B  PHE*     3.4    48.2    -      +       -      -
    528B  LEU*     3.7    36.1    -      -       +      -
    529B  ASN*     4.2     4.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 175 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  LEU*     3.7     8.3    -      -       +      +
     54B  LEU*     3.6    24.6    -      -       +      +
     56B  LEU*     3.8    11.9    -      -       +      +
     65B  GLN*     3.1    35.0    +      -       -      +
    171B  PHE*     3.0    43.6    +      -       +      +
    172B  LEU*     2.8    11.8    +      -       -      +
    174B  TRP*     1.3    74.2    -      -       +      +
    176B  TRP*     1.3    58.0    +      -       -      +
    178B  GLU*     2.9    42.6    +      -       -      +
    179B  ALA*     3.1    25.8    +      -       -      +
    512B  PRO*     4.0    10.1    -      -       -      +
    516B  GLN*     3.7     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 176 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  LYS      4.4    11.4    -      -       -      -
     42B  PRO*     3.5    33.7    -      -       +      -
     46B  LYS*     2.9    55.5    +      -       +      +
     47B  CYS*     4.6     2.2    -      -       -      -
     50B  LEU*     3.3    24.4    -      -       +      +
    172B  LEU      2.8     7.2    +      -       -      +
    173B  GLN*     3.5     9.2    -      -       -      +
    175B  LYS*     1.3    74.6    -      -       -      +
    177B  LEU*     1.3    86.4    +      -       +      +
    178B  GLU      3.1     1.3    -      -       -      -
    179B  ALA*     2.9    20.2    +      -       +      +
    180B  GLN*     2.9    63.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 177 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  ARG      4.3     3.4    -      -       -      +
     39B  LEU*     3.3    37.9    -      -       +      -
     40B  LYS      3.0    46.0    -      -       -      +
     41B  LEU*     4.2     3.4    -      -       +      +
    173B  GLN      3.3    10.2    +      -       -      +
    174B  TRP*     3.7    24.5    -      -       +      +
    176B  TRP*     1.3    92.3    -      -       +      +
    178B  GLU*     1.3    61.6    +      -       -      +
    180B  GLN*     3.5    19.0    +      -       +      +
    182B  MET*     4.7     6.8    -      -       -      +
    515B  TRP*     3.5    19.7    -      -       +      -
    528B  LEU*     4.6     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 178 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174B  TRP      3.0    12.4    +      -       -      +
    175B  LYS*     2.9    48.2    +      -       -      +
    177B  LEU*     1.3    78.3    -      -       -      +
    179B  ALA*     1.3    60.9    +      -       -      +
    180B  GLN      3.2     4.5    +      -       -      +
    182B  MET*     3.9     2.1    -      -       -      +
    510B  THR*     3.0    33.8    -      -       +      +
    512B  PRO*     3.5    28.3    -      -       +      +
    515B  TRP*     3.5    39.6    -      -       +      -
    516B  GLN*     3.5    14.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 179 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  LEU*     5.0    12.3    -      -       +      -
    175B  LYS      3.1    10.7    +      -       -      +
    176B  TRP*     2.9    12.7    +      -       +      +
    178B  GLU*     1.3    79.3    -      -       +      +
    180B  GLN*     1.3    69.5    +      -       -      +
    181B  PRO*     3.8     1.2    -      -       -      +
    510B  THR*     5.0     3.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 180 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176B  TRP*     2.9    78.1    +      -       +      +
    177B  LEU*     3.5    14.6    -      -       +      +
    178B  GLU      3.2    10.4    -      -       -      +
    179B  ALA*     1.3    84.5    -      -       -      +
    181B  PRO*     1.3    82.0    -      -       +      +
    182B  MET*     3.4    10.3    +      -       +      +
    186B  TRP*     6.3     1.8    -      -       +      -
    510B  THR*     4.3     4.3    -      -       -      +
----------------------------------------------------------
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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