Contacts of the strand formed by residues 198 - 208 (chain F) 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 F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188F  SER      5.2     1.6    -      -       -      +
    190F  LEU      5.3     1.6    -      -       -      +
    192F  SER*     3.5    18.1    +      -       -      +
    194F  ARG*     2.9    63.9    +      -       +      +
    195F  GLY*     3.6     5.5    -      -       -      +
    196F  SER      3.0     9.3    +      -       -      +
    197F  ASP*     1.3   111.0    -      -       -      +
    199F  LEU*     1.3    65.9    +      -       -      +
    200F  MET      4.0     0.5    +      -       -      -
    222F  GLU*     4.4    16.8    -      -       +      -
    223F  MET      3.1    21.8    -      -       -      +
    224F  HIS*     3.3    31.8    -      +       +      -
    225F  LYS*     3.9     5.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 199 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187F  SER*     4.1    17.5    -      -       -      +
    188F  SER      4.1    17.7    -      -       -      +
    192F  SER*     4.4     0.9    -      -       -      -
    198F  TYR*     1.3    74.6    -      -       -      +
    200F  MET*     1.3    58.5    +      -       -      +
    221F  MET      3.5     0.7    -      -       -      +
    222F  GLU*     3.4     1.4    -      -       -      -
    223F  MET*     2.6    66.2    +      -       +      +
    225F  LYS*     4.1    28.3    -      -       +      +
   5402F  ADP      3.7    45.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 200 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165F  GLN*     4.0     5.6    -      -       -      +
    187F  SER*     2.9    23.6    -      -       -      -
    188F  SER*     3.1    23.1    +      -       -      +
    190F  LEU*     3.9    35.2    -      -       +      +
    191F  LEU      4.9     1.8    -      -       -      +
    192F  SER*     3.7    19.7    -      -       -      +
    193F  PRO*     3.6    21.3    -      -       +      -
    198F  TYR      4.0     1.6    +      -       -      -
    199F  LEU*     1.3    74.1    -      -       -      +
    201F  ALA*     1.3    64.6    +      -       -      +
    202F  LEU*     4.4     7.6    -      -       +      -
    220F  ARG*     3.0    53.4    -      -       +      +
    221F  MET      3.0    13.9    -      -       -      +
    222F  GLU*     4.5     1.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 201 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184F  VAL*     5.4     2.5    -      -       +      -
    185F  ILE      3.3    15.7    -      -       -      +
    186F  THR*     3.4    17.7    -      -       -      +
    200F  MET*     1.3    75.6    -      -       -      +
    202F  LEU*     1.3    63.9    +      -       -      +
    220F  ARG*     3.4     2.6    -      -       -      -
    221F  MET*     2.7    55.9    +      -       +      +
    223F  MET*     4.0    15.3    -      -       +      -
    237F  PHE*     6.2     1.6    -      -       +      -
    260F  VAL*     5.8     2.0    -      -       +      -
   5402F  ADP      5.2     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 202 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165F  GLN*     4.3    10.8    -      -       +      +
    168F  ALA*     3.4    33.2    -      -       +      -
    169F  LEU*     4.7     3.6    -      -       +      +
    172F  MET*     3.2    24.9    -      -       +      +
    184F  VAL*     3.4     4.0    -      -       -      +
    185F  ILE*     2.7    43.4    +      -       +      +
    188F  SER*     5.8     0.9    -      -       -      +
    190F  LEU*     4.1    15.5    -      -       +      -
    200F  MET*     4.4     7.4    -      -       -      -
    201F  ALA*     1.3    74.8    -      -       -      +
    203F  GLY*     1.3    59.0    +      -       -      +
    219F  ILE      3.3     2.9    -      -       -      +
    220F  ARG*     3.2    42.6    -      -       +      +
    221F  MET*     5.2     1.3    -      -       -      -
    312F  LEU*     4.2    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 203 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172F  MET*     4.3     1.1    -      -       -      -
    183F  VAL      3.4     6.3    -      -       -      -
    184F  VAL*     4.1     9.6    -      -       -      -
    202F  LEU*     1.3    75.4    -      -       -      +
    204F  SER*     1.3    59.2    +      -       -      -
    218F  ARG*     3.6     1.9    -      -       -      -
    219F  ILE*     2.7    47.6    +      -       -      +
    221F  MET*     4.9     1.4    -      -       -      +
    252F  LEU*     3.1    21.5    -      -       -      +
    256F  CYS*     5.1     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 204 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172F  MET*     3.8    23.4    -      -       -      -
    173F  ASP*     4.7     0.3    +      -       -      -
    176F  HIS*     2.8    28.6    +      -       -      -
    182F  THR*     3.4     1.9    -      -       -      -
    183F  VAL*     2.7    40.1    +      -       -      +
    203F  GLY*     1.3    74.5    -      -       -      -
    205F  GLN*     1.3    64.1    +      -       -      +
    216F  THR*     5.0     2.8    -      -       -      +
    217F  GLN      3.4     4.9    +      -       -      -
    218F  ARG*     3.5    28.4    +      -       -      +
    252F  LEU*     3.5     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 205 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176F  HIS*     4.1     2.2    -      -       -      -
    181F  ASP      3.3     9.0    -      -       -      +
    182F  THR*     3.7    21.4    +      -       +      +
    204F  SER*     1.3    76.9    +      -       -      +
    206F  ARG*     1.3    69.1    +      -       -      +
    207F  THR*     4.6    10.1    +      -       -      +
    215F  VAL      4.1     0.6    -      -       -      +
    216F  THR*     3.5     5.2    -      -       -      +
    217F  GLN*     2.6    69.4    +      -       +      +
    245F  THR*     6.2     1.8    -      -       -      +
    249F  PRO      2.8    27.0    +      -       -      +
    251F  ASN      4.2     0.2    +      -       -      -
    252F  LEU*     3.4    29.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 206 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173F  ASP*     5.8     4.9    +      -       -      +
    176F  HIS*     4.1    29.5    -      -       +      +
    181F  ASP*     2.8    49.5    +      -       -      +
    205F  GLN*     1.3    76.8    -      -       -      +
    207F  THR*     1.3    68.9    +      -       -      +
    208F  ARG*     6.1     4.0    -      -       +      +
    214F  VAL*     3.5    36.2    -      -       +      +
    215F  VAL      3.7     4.5    -      -       -      -
    216F  THR*     3.9    16.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 207 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205F  GLN*     4.4    13.5    +      -       -      +
    206F  ARG*     1.3    77.7    +      -       -      +
    208F  ARG*     1.3    73.2    +      -       -      +
    209F  ALA*     4.4     2.2    -      -       -      +
    214F  VAL*     3.0     7.5    -      -       -      -
    215F  VAL*     2.7    61.5    +      -       +      +
    217F  GLN*     5.3     2.0    +      -       -      -
    250F  ASN*     4.0    19.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 208 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206F  ARG*     5.4     4.4    -      -       +      +
    207F  THR*     1.3    78.4    -      -       -      +
    209F  ALA*     1.3    69.5    +      -       -      +
    210F  PRO*     4.5     1.0    -      -       -      +
    212F  GLY*     3.3    30.4    +      -       -      -
    213F  SER      3.5     1.6    -      -       -      -
    214F  VAL*     3.5    24.1    -      -       +      +
----------------------------------------------------------
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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