Contacts of the strand formed by residues 201 - 210 (chain I) in PDB entry 2QC8


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 GLN 201 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136I  GLU*     5.0     2.2    -      -       +      -
    137I  TYR      3.4    17.7    -      -       -      +
    138I  THR*     3.7    14.5    +      -       -      +
    195I  ALA*     4.0     1.2    -      -       -      +
    196I  GLU*     2.8    50.4    +      -       +      +
    198I  MET*     3.0    40.3    +      -       +      +
    199I  PRO      3.1     0.6    -      -       -      -
    200I  ALA*     1.3    77.7    +      -       -      +
    202I  TRP*     1.3    70.8    +      -       -      +
    242I  PRO*     5.5     1.2    -      -       -      +
    248I  ASN*     3.7    15.2    +      -       -      +
    249I  GLY      2.9    33.5    +      -       -      +
    250I  ALA*     3.9    10.5    -      -       -      +
    601I  P3S      4.2     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 202 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136I  GLU*     3.3     6.9    -      -       -      +
    137I  TYR*     2.9    53.4    +      -       +      +
    139I  LEU*     4.1    15.7    -      -       +      +
    170I  ALA*     4.0    21.1    -      -       +      -
    171I  TYR      2.9    28.7    +      -       -      +
    172I  GLY      4.5     0.4    -      -       -      -
    173I  ARG*     3.9    45.5    -      -       +      -
    176I  VAL*     3.3    30.5    -      -       +      -
    194I  ASN*     3.6     7.9    -      -       -      -
    195I  ALA*     3.3    45.3    -      -       +      -
    196I  GLU*     4.0     5.3    -      -       -      +
    200I  ALA*     3.6    16.0    -      -       -      +
    201I  GLN*     1.3    78.4    +      -       -      +
    203I  GLU*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 203 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134I  GLU*     2.8    13.7    -      -       +      +
    135I  GLN      3.3    13.0    -      -       -      +
    136I  GLU*     3.4     7.2    -      -       +      +
    137I  TYR*     4.1     3.0    +      -       -      -
    176I  VAL*     5.1     1.9    -      -       -      +
    193I  THR*     3.2     9.5    -      -       -      +
    194I  ASN*     2.9    47.0    +      -       -      +
    196I  GLU*     3.0     8.3    -      -       +      +
    202I  TRP*     1.3    79.7    -      -       -      +
    204I  PHE*     1.3    70.6    +      -       -      +
    205I  GLN*     2.9    14.3    +      -       -      +
    401I   MN      2.0    34.7    +      -       -      -
    403I   MN      2.2    28.4    +      -       -      -
    501I  ADP      3.1     0.2    +      -       -      -
    601I  P3S      3.2     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 204 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133I  MET      3.7     0.5    -      -       -      +
    134I  GLU      3.6     0.5    -      -       -      -
    135I  GLN*     2.8    65.8    +      -       +      -
    137I  TYR*     3.9    15.5    -      +       -      -
    179I  HIS*     3.4    32.1    -      +       +      +
    190I  ILE*     4.0     8.5    -      -       +      -
    192I  GLY      3.4     6.3    -      -       -      +
    193I  THR*     3.7    18.2    -      -       +      +
    203I  GLU*     1.3    76.3    -      -       -      +
    205I  GLN*     1.3    60.4    +      -       -      +
    206I  ILE*     3.6    31.4    -      -       +      -
    218I  LEU*     4.2     3.8    -      -       +      -
    221I  ALA*     3.7    22.4    -      -       +      -
    222I  ARG*     4.6     4.7    -      -       -      -
    225I  LEU*     4.2    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 205 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43H  LYS*     6.2     0.8    -      -       -      +
     44H  THR      4.5     1.7    -      -       -      +
     60H  TRP*     5.2     4.9    -      -       -      -
    133I  MET      3.3     4.5    -      -       -      -
    134I  GLU*     3.8     9.6    -      -       +      -
    190I  ILE*     3.5     7.1    -      -       -      +
    191I  ALA*     2.6    38.8    +      -       +      -
    192I  GLY*     3.0    33.6    +      -       -      +
    193I  THR*     3.6     2.1    +      -       -      +
    194I  ASN*     3.1    18.0    +      -       -      -
    203I  GLU*     2.9    28.1    +      -       -      +
    204I  PHE*     1.3    73.5    -      -       -      +
    206I  ILE*     1.3    58.5    +      -       -      +
    501I  ADP      3.0    51.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 206 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132I  GLY*     3.2     2.6    -      -       -      -
    133I  MET      3.0    29.7    +      -       -      +
    183I  CYS*     5.5     0.2    -      -       -      -
    188I  VAL*     3.5    27.8    -      -       +      -
    189I  LYS      3.3     6.3    -      -       -      +
    190I  ILE*     3.9    15.9    -      -       +      -
    204I  PHE*     3.6    25.4    -      -       +      -
    205I  GLN*     1.3    76.6    -      -       -      +
    207I  GLY*     1.3    60.0    +      -       -      +
    209I  CYS*     4.1     4.3    -      -       -      -
    214I  MET*     3.6    25.7    -      -       +      +
    217I  HIS*     3.9    22.4    -      -       +      -
    218I  LEU*     4.3     9.2    -      -       +      +
    221I  ALA*     3.8    14.4    -      -       +      -
    501I  ADP      3.9     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 207 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131I  PHE      4.0     1.3    -      -       -      -
    132I  GLY*     4.3     0.2    -      -       -      -
    189I  LYS*     2.8    28.4    +      -       -      +
    191I  ALA*     3.6    14.7    -      -       -      +
    206I  ILE*     1.3    75.2    -      -       -      +
    208I  PRO*     1.3    76.1    -      -       -      +
    209I  CYS*     3.8     6.3    -      -       -      -
    501I  ADP      3.3    11.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 208 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130I  TRP*     4.1    29.6    -      -       +      -
    131I  PHE      3.3     8.7    -      -       -      +
    189I  LYS*     3.1    26.5    -      -       -      +
    207I  GLY*     1.3    81.3    -      -       -      +
    209I  CYS*     1.3    61.2    +      -       -      +
    210I  GLU      4.1     0.9    +      -       -      -
    501I  ADP      3.3    46.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 209 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130I  TRP*     3.4     3.0    -      -       -      -
    131I  PHE*     2.7    37.4    +      -       -      +
    189I  LYS*     4.3    11.2    -      -       -      -
    206I  ILE*     4.1    16.2    -      -       -      -
    207I  GLY*     4.1     6.3    -      -       -      -
    208I  PRO*     1.3    77.2    -      -       -      +
    210I  GLU*     1.3    61.3    +      -       -      +
    211I  GLY      3.5     1.2    +      -       -      -
    213I  SER*     3.4    27.4    -      -       -      +
    214I  MET*     3.5    20.6    -      -       -      +
    217I  HIS*     4.1    20.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 210 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125I  SER*     4.1     8.3    -      -       -      +
    128I  HIS*     2.7    46.2    +      -       -      +
    129I  PRO*     3.2    14.7    -      -       +      +
    130I  TRP*     3.5    22.1    +      -       +      +
    208I  PRO      4.1     1.4    +      -       -      -
    209I  CYS*     1.3    70.1    -      -       -      +
    211I  GLY*     1.3    68.9    +      -       -      +
    212I  ILE*     3.5     0.7    +      -       -      +
    213I  SER*     2.8    28.5    +      -       -      +
----------------------------------------------------------
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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