Contacts of the helix formed by residues 211 - 225 (chain C) in PDB entry 3OEE


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 LYS 211 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210C  GLN*     1.3    74.3    -      -       -      +
    212C  ARG*     1.3    67.3    +      -       -      +
    213C  SER*     3.0    26.2    -      -       -      +
    214C  THR*     2.8    40.3    +      -       -      +
    215C  VAL*     3.4     6.1    +      -       -      +
    238C  ALA*     4.5     8.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 212 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117C  ILE*     6.2     3.7    -      -       +      +
    210C  GLN      3.8     2.4    +      -       -      -
    211C  LYS*     1.3    69.1    -      -       -      +
    213C  SER*     1.3    63.8    +      -       -      +
    215C  VAL*     3.0     7.9    +      -       -      +
    216C  ALA*     2.9    22.7    +      -       -      +
    237C  THR*     3.3    28.9    +      -       +      +
    239C  SER*     3.9    19.2    +      -       -      -
    240C  GLU*     3.8    30.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 213 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211C  LYS*     3.0    32.9    -      -       -      +
    212C  ARG*     1.3    76.5    -      -       -      +
    214C  THR*     1.3    60.8    +      -       -      +
    216C  ALA*     3.2     8.8    +      -       -      +
    217C  GLN*     3.0    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 214 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210C  GLN*     3.6    21.8    -      -       +      +
    211C  LYS*     2.8    45.0    +      -       -      +
    213C  SER*     1.3    72.1    +      -       -      +
    215C  VAL*     1.3    57.3    +      -       -      +
    217C  GLN*     3.4    10.4    -      -       +      +
    218C  LEU*     3.1    26.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 215 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  VAL*     5.3     3.8    -      -       +      -
    205C  TYR*     5.4     3.6    -      -       +      -
    207C  ALA*     3.9    13.9    -      -       +      -
    210C  GLN*     3.9    17.3    -      -       +      +
    211C  LYS      3.6    13.5    -      -       -      +
    212C  ARG*     3.0     5.3    +      -       -      +
    214C  THR*     1.3    73.8    -      -       -      +
    216C  ALA*     1.3    60.1    +      -       -      +
    217C  GLN      3.1     0.2    -      -       -      -
    218C  LEU*     3.0     8.2    +      -       +      +
    219C  VAL*     2.9    34.2    +      -       +      +
    233C  ILE*     4.1    26.0    -      -       +      -
    235C  ALA*     4.5     7.9    -      -       +      -
    237C  THR*     3.8    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 216 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212C  ARG      2.9    12.0    +      -       -      +
    213C  SER*     3.6    11.7    -      -       -      +
    215C  VAL*     1.3    74.6    -      -       -      +
    217C  GLN*     1.3    53.3    +      -       -      +
    219C  VAL*     3.5    11.8    +      -       -      +
    220C  GLN*     2.8    35.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 217 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213C  SER      3.0    15.7    +      -       -      +
    214C  THR*     3.4    10.5    -      -       +      +
    216C  ALA*     1.3    78.4    -      -       -      +
    218C  LEU*     1.3    57.2    +      -       -      +
    220C  GLN*     3.6    21.4    +      -       -      +
    221C  THR*     3.1    38.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 218 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178C  THR*     3.9    24.2    -      -       +      -
    182C  LEU*     3.8    32.9    -      -       +      +
    185C  ILE*     6.2     0.2    -      -       +      -
    205C  TYR*     3.8    38.8    -      -       +      +
    210C  GLN*     5.8     1.8    -      -       -      +
    214C  THR*     3.1    14.8    +      -       +      +
    215C  VAL*     3.0    12.1    +      -       +      +
    217C  GLN*     1.3    74.6    -      -       -      +
    219C  VAL*     1.3    62.9    +      -       +      +
    220C  GLN      3.1     1.3    -      -       -      -
    221C  THR*     3.1     6.8    +      -       -      -
    222C  LEU*     3.0    45.3    +      -       +      +
    233C  ILE*     4.8     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 219 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  VAL*     4.1    14.1    -      -       +      -
    215C  VAL*     2.9    24.5    +      -       +      +
    216C  ALA*     3.6    14.8    -      -       -      +
    218C  LEU*     1.3    74.5    -      -       +      +
    220C  GLN*     1.3    65.1    +      -       -      +
    221C  THR      3.3     0.2    -      -       -      -
    222C  LEU*     4.1     0.4    -      -       -      -
    223C  GLU*     3.1    37.7    +      -       -      +
    228C  MET*     3.3    19.9    -      -       +      +
    233C  ILE*     3.8    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 220 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216C  ALA      2.8    19.7    +      -       -      +
    217C  GLN*     3.7    24.2    -      -       -      +
    218C  LEU      3.1     0.2    -      -       -      -
    219C  VAL*     1.3    78.9    -      -       -      +
    221C  THR*     1.3    60.0    +      -       -      +
    223C  GLU*     3.4    10.5    -      -       +      +
    224C  GLN*     3.1    60.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 221 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182C  LEU*     4.6    21.1    -      -       +      -
    186C  LEU*     4.9     6.1    -      -       +      -
    217C  GLN*     3.1    25.6    +      -       -      -
    218C  LEU*     3.1     9.9    +      -       -      -
    220C  GLN*     1.3    76.8    +      -       -      +
    222C  LEU*     1.3    65.1    +      -       -      +
    223C  GLU      3.2     0.7    -      -       -      -
    224C  GLN*     3.2    12.1    +      -       -      +
    225C  HIS*     3.1    48.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 222 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182C  LEU*     4.0    15.0    -      -       +      -
    185C  ILE*     3.8    24.0    -      -       +      -
    186C  LEU*     3.5    24.7    -      -       +      -
    205C  TYR*     5.8     0.9    -      -       +      -
    218C  LEU*     3.0    29.0    +      -       +      +
    221C  THR*     1.3    76.3    -      -       -      +
    223C  GLU*     1.3    61.0    +      -       -      +
    225C  HIS      3.2     2.1    +      -       -      -
    226C  ASP      3.0     4.2    +      -       -      -
    227C  ALA*     2.8    31.9    +      -       +      -
    228C  MET*     3.4    35.0    -      -       +      +
    231C  SER*     4.3    15.3    -      -       -      +
    233C  ILE*     3.9    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 223 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120C  LYS*     6.3     0.9    -      -       -      -
    219C  VAL*     3.1    34.2    +      -       -      +
    220C  GLN*     3.4    11.3    -      -       +      +
    222C  LEU*     1.3    78.8    -      -       -      +
    224C  GLN*     1.3    58.8    +      -       +      +
    226C  ASP*     2.8    23.4    +      -       -      +
    228C  MET*     3.2    35.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 224 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220C  GLN*     3.1    40.3    +      -       -      +
    221C  THR*     3.2    17.1    +      -       -      +
    223C  GLU*     1.3    78.1    -      -       +      +
    225C  HIS*     1.3    67.7    +      -       +      +
    226C  ASP*     3.3     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 225 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186C  LEU*     3.6    43.0    -      -       +      +
    189C  LYS*     2.5    34.0    +      -       +      +
    221C  THR*     3.1    39.9    +      -       +      +
    222C  LEU      3.2     1.1    +      -       -      +
    223C  GLU      3.1     0.6    -      -       -      -
    224C  GLN*     1.3    85.8    +      -       +      +
    226C  ASP*     1.3    61.1    +      -       -      +
    227C  ALA*     3.3     1.8    +      -       -      +
----------------------------------------------------------
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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