Contacts of the strand formed by residues 198 - 208 (chain H) in PDB entry 1RFU


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 198 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188H  SER      5.1     1.6    -      -       -      +
    190H  LEU      5.3     1.2    -      -       -      +
    192H  SER*     3.4    20.7    +      -       -      +
    194H  ARG*     2.8    69.7    +      -       +      +
    195H  GLY*     3.8     4.1    -      -       -      +
    196H  SER      3.1     8.6    +      -       -      +
    197H  ASP*     1.3   107.2    -      -       -      +
    199H  LEU*     1.3    64.8    +      -       -      +
    200H  MET      3.9     0.3    +      -       -      -
    222H  GLU*     4.3    16.8    -      -       +      -
    223H  MET      3.1    21.5    -      -       -      +
    224H  HIS*     3.4    30.8    +      +       +      -
    225H  LYS*     3.9     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 199 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187H  SER*     4.2    15.9    -      -       -      +
    188H  SER      4.1    17.5    -      -       -      +
    192H  SER*     4.4     1.6    -      -       -      -
    198H  TYR*     1.3    74.1    -      -       -      +
    200H  MET*     1.3    60.0    +      -       -      +
    222H  GLU*     3.4     1.2    -      -       -      -
    223H  MET*     2.5    67.6    +      -       +      +
    225H  LYS*     4.1    29.7    -      -       +      +
   7402H  ADP      3.7    45.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 200 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165H  GLN*     4.2     4.5    -      -       +      +
    187H  SER*     2.9    23.5    -      -       -      -
    188H  SER*     3.1    23.6    +      -       -      +
    190H  LEU*     3.7    36.3    -      -       +      +
    191H  LEU      4.9     1.8    -      -       -      +
    192H  SER*     3.7    17.5    +      -       -      +
    193H  PRO*     3.5    22.4    -      -       +      -
    198H  TYR      3.9     1.4    +      -       -      -
    199H  LEU*     1.3    74.6    -      -       -      +
    201H  ALA*     1.3    64.2    +      -       -      +
    202H  LEU*     4.5     7.4    -      -       +      -
    220H  ARG*     3.0    52.5    -      -       +      +
    221H  MET      3.1    13.9    -      -       -      +
    222H  GLU*     4.6     1.6    -      -       +      +
    223H  MET*     4.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 201 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184H  VAL*     5.4     2.7    -      -       +      -
    185H  ILE*     3.2    17.0    -      -       -      +
    186H  THR*     3.4    17.9    -      -       -      +
    187H  SER      5.1     0.2    -      -       -      -
    200H  MET*     1.3    75.8    -      -       -      +
    202H  LEU*     1.3    62.7    +      -       -      +
    220H  ARG*     3.4     2.1    -      -       -      -
    221H  MET*     2.7    49.7    +      -       +      +
    223H  MET*     3.9    14.6    -      -       +      -
    237H  PHE*     6.3     1.3    -      -       +      -
    260H  VAL*     5.9     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 202 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165H  GLN*     4.2    11.7    -      -       +      +
    168H  ALA*     3.4    33.0    -      -       +      -
    169H  LEU*     4.6     2.9    -      -       +      +
    172H  MET*     3.2    25.2    -      -       +      +
    184H  VAL*     3.4     4.6    -      -       -      +
    185H  ILE*     2.7    43.3    +      -       +      +
    188H  SER*     5.7     1.3    -      -       -      +
    190H  LEU*     4.1    15.5    -      -       +      -
    200H  MET*     4.5     6.7    -      -       +      -
    201H  ALA*     1.3    75.3    -      -       -      +
    203H  GLY*     1.3    58.7    +      -       -      +
    219H  ILE      3.4     2.7    -      -       -      +
    220H  ARG*     3.2    42.4    -      -       +      -
    221H  MET*     5.1     0.9    -      -       -      -
    312H  LEU*     4.1    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 203 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172H  MET*     4.2     1.8    -      -       -      -
    183H  VAL      3.3     7.4    -      -       -      -
    184H  VAL*     4.0     9.4    -      -       -      -
    201H  ALA      4.3     0.2    -      -       -      -
    202H  LEU*     1.3    75.4    -      -       -      +
    204H  SER*     1.3    57.4    +      -       -      -
    218H  ARG*     3.7     1.9    -      -       -      -
    219H  ILE*     2.8    46.8    +      -       -      +
    221H  MET*     4.8     1.2    -      -       -      +
    252H  LEU*     3.2    21.6    -      -       -      +
    256H  CYS*     5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 204 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172H  MET*     3.8    25.8    -      -       -      -
    173H  ASP*     4.8     0.5    +      -       -      -
    176H  HIS*     2.7    30.2    +      -       -      -
    182H  THR*     3.4     1.7    -      -       -      -
    183H  VAL*     2.7    39.8    +      -       -      +
    203H  GLY*     1.3    74.8    -      -       -      -
    205H  GLN*     1.3    63.4    +      -       -      +
    216H  THR*     5.0     2.9    -      -       -      +
    217H  GLN      3.3     4.5    +      -       -      -
    218H  ARG*     3.7    25.5    +      -       -      +
    252H  LEU*     3.5     3.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 205 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176H  HIS*     4.1     1.8    -      -       -      -
    181H  ASP*     3.2     5.4    -      -       +      +
    182H  THR*     3.5    25.8    +      -       +      +
    204H  SER*     1.3    76.9    +      -       -      +
    206H  ARG*     1.3    67.9    +      -       -      +
    207H  THR*     4.6     9.4    +      -       -      +
    215H  VAL      4.0     0.6    -      -       -      +
    216H  THR*     3.4     4.5    -      -       -      +
    217H  GLN*     2.7    72.0    +      -       +      +
    245H  THR*     6.2     3.2    -      -       -      +
    249H  PRO      2.9    26.2    +      -       -      +
    250H  ASN*     4.8     0.4    -      -       -      -
    251H  ASN      4.2     0.2    +      -       -      -
    252H  LEU*     3.3    30.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 206 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173H  ASP*     5.9     4.0    +      -       -      +
    176H  HIS*     4.1    31.6    -      -       +      +
    181H  ASP*     2.8    42.3    +      -       -      +
    205H  GLN*     1.3    76.2    -      -       -      +
    207H  THR*     1.3    69.4    +      -       -      +
    208H  ARG*     6.1     4.5    -      -       +      +
    214H  VAL*     3.5    35.6    -      -       +      +
    215H  VAL      3.6     4.0    -      -       -      -
    216H  THR*     4.0    17.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 207 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205H  GLN*     4.6    12.7    +      -       -      +
    206H  ARG*     1.3    77.8    +      -       -      +
    208H  ARG*     1.3    73.3    +      -       -      +
    209H  ALA*     4.3     2.5    -      -       -      +
    214H  VAL*     3.0     6.9    -      -       -      -
    215H  VAL*     2.7    61.9    +      -       +      +
    217H  GLN*     5.3     1.8    +      -       -      -
    250H  ASN*     4.0    18.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 208 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206H  ARG*     6.1     4.8    -      -       +      +
    207H  THR*     1.3    78.8    -      -       -      +
    209H  ALA*     1.3    70.2    +      -       -      +
    210H  PRO*     4.4     1.0    -      -       -      +
    212H  GLY*     3.3    29.6    +      -       -      -
    213H  SER      3.5     1.6    -      -       -      -
    214H  VAL*     3.6    21.3    -      -       +      +
----------------------------------------------------------
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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