Contacts of the strand formed by residues 210 - 219 (chain A) in PDB entry 2QDC


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 TYR 210 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  CYS*     2.8    57.3    +      -       +      +
    208A  PRO*     6.3     0.2    -      -       +      -
    209A  GLU*     1.3    92.0    -      -       +      +
    211A  THR*     1.3    62.5    +      -       -      +
    212A  VAL*     3.8     9.2    -      -       +      -
    229A  ILE*     3.7    23.8    -      -       +      -
    230A  LEU      3.2    17.3    -      -       -      +
    231A  PHE*     4.0    14.4    -      +       +      -
    232A  SER*     5.2     0.9    -      -       -      +
    245A  PRO      5.0     0.2    -      -       -      -
    248A  ARG*     3.7    28.9    +      -       +      +
    249A  LEU*     4.1    11.2    -      -       +      -
    252A  GLU*     2.7    44.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  MET*     3.9    22.9    -      -       +      -
    205A  LYS      3.5    13.2    -      -       -      +
    206A  GLU*     4.1    16.7    -      -       +      +
    207A  CYS      5.5     0.2    +      -       -      -
    210A  TYR*     1.3    74.8    +      -       -      +
    212A  VAL*     1.3    64.8    +      -       -      +
    213A  ARG*     3.7    29.2    +      -       -      +
    228A  HIS      3.5     1.9    -      -       -      +
    229A  ILE*     3.4     3.3    -      -       -      -
    230A  LEU*     2.9    39.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  ASP*     4.0     0.9    -      -       -      +
    204A  MET*     3.5     2.1    -      -       -      -
    205A  LYS*     2.8    53.1    +      -       +      +
    207A  CYS*     4.4     7.9    -      -       -      -
    210A  TYR*     3.8    30.3    -      -       +      -
    211A  THR*     1.3    72.3    -      -       -      +
    213A  ARG*     1.3    65.9    +      -       -      +
    214A  GLN*     4.4     9.6    -      -       +      +
    227A  LYS*     3.7    31.9    -      -       +      -
    228A  HIS      3.3     3.6    -      -       -      +
    229A  ILE*     4.3     8.5    -      -       +      -
    252A  GLU*     4.1    13.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  HIS*     5.6     2.4    +      -       -      -
    187A  TRP*     3.3    43.3    -      -       -      +
    201A  ILE*     3.7    21.5    -      -       +      +
    203A  ASP      3.3     4.7    -      -       -      +
    204A  MET*     3.6    35.7    -      -       +      -
    211A  THR*     3.7    20.5    +      -       +      +
    212A  VAL*     1.3    73.7    -      -       -      +
    214A  GLN*     1.3    63.3    +      -       -      +
    215A  LEU*     3.9    11.2    -      -       +      -
    226A  VAL      3.8     0.2    -      -       -      +
    227A  LYS*     3.6     4.2    -      -       -      +
    228A  HIS*     2.7    55.7    +      -       +      +
    230A  LEU*     3.9    27.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 214 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  ILE*     3.6     3.5    -      -       -      +
    202A  GLN*     2.7    40.2    +      -       +      -
    203A  ASP*     2.8    34.2    +      -       +      +
    212A  VAL*     4.2     9.5    -      -       +      +
    213A  ARG*     1.3    71.7    -      -       -      +
    215A  LEU*     1.3    58.5    +      -       -      +
    225A  SER*     5.0     6.8    -      -       -      -
    226A  VAL      3.9     4.9    +      -       -      +
    227A  LYS*     3.7    40.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  TRP*     3.8    29.6    -      -       +      -
    187A  TRP*     4.3    22.9    -      -       +      -
    188A  PRO*     4.8     4.3    -      -       +      -
    199A  ILE*     4.5     5.4    -      -       +      -
    200A  ARG      3.1    10.8    -      -       -      +
    201A  ILE*     3.8    28.3    -      -       +      +
    202A  GLN*     4.5     1.6    -      -       -      +
    213A  ARG*     4.1    15.5    -      -       +      +
    214A  GLN*     1.3    76.4    -      -       -      +
    216A  THR*     1.3    71.6    +      -       -      +
    225A  SER*     3.5     2.9    -      -       -      -
    226A  VAL*     2.8    46.1    +      -       +      +
    228A  HIS*     4.1    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  GLN      3.6     1.4    +      -       -      +
    199A  ILE*     3.3     9.6    -      -       -      +
    200A  ARG*     2.8    50.8    +      -       -      +
    202A  GLN*     3.8    19.3    -      -       +      +
    215A  LEU*     1.3    80.6    -      -       -      +
    217A  ILE*     1.3    60.5    +      -       -      +
    223A  ARG*     3.7    32.8    -      -       +      +
    224A  ARG      3.1    13.0    -      -       -      +
    225A  SER*     4.3    12.1    -      -       -      +
    226A  VAL*     4.7     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  TRP*     3.9    28.7    -      -       +      +
    162A  VAL*     4.4     8.7    -      -       +      -
    163A  TRP*     3.5    24.1    -      -       +      -
    167A  VAL      5.7     0.2    -      -       -      +
    197A  PHE*     3.8    29.6    -      -       +      -
    198A  GLN      3.4     2.9    -      -       -      -
    199A  ILE*     3.6    26.5    -      -       +      -
    216A  THR*     1.3    74.3    -      -       -      +
    218A  GLN*     1.3    63.3    +      -       -      +
    223A  ARG*     3.3     2.0    -      -       -      -
    224A  ARG*     2.8    49.6    +      -       +      +
    226A  VAL*     3.9    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  TRP*     4.3     1.6    -      -       -      -
    196A  PRO      3.9     1.2    -      -       -      +
    197A  PHE*     3.4     7.9    -      -       -      -
    198A  GLN*     2.9    57.3    +      -       +      +
    200A  ARG*     6.2     0.3    -      -       -      -
    217A  ILE*     1.3    75.7    -      -       -      +
    219A  TYR*     1.3    63.4    +      -       -      +
    220A  GLN      2.9    23.3    +      -       -      +
    221A  GLU*     3.9    12.3    +      -       -      +
    222A  GLU      3.2    11.4    -      -       -      +
    223A  ARG*     3.0    42.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  ALA      4.6     2.9    +      -       -      -
    121A  GLN*     3.7    47.6    +      -       +      -
    163A  TRP*     3.6    24.7    -      +       +      -
    196A  PRO*     3.7    38.6    -      -       +      -
    197A  PHE*     3.8    12.3    -      +       +      -
    218A  GLN*     1.3    74.0    -      -       -      +
    220A  GLN*     1.3    98.0    +      -       +      +
    221A  GLU*     4.4     0.3    -      -       -      +
    222A  GLU*     2.9    23.9    +      -       -      +
----------------------------------------------------------
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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