Contacts of the strand formed by residues 198 - 208 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188E  SER      5.2     1.4    -      -       -      +
    190E  LEU      5.4     0.9    -      -       -      +
    192E  SER*     3.4    20.9    +      -       -      +
    194E  ARG*     2.8    66.8    +      -       +      +
    195E  GLY*     3.6     6.1    -      -       -      +
    196E  SER*     3.1     9.8    +      -       -      +
    197E  ASP*     1.3   109.1    -      -       -      +
    199E  LEU*     1.3    63.6    +      -       -      +
    200E  MET      3.9     0.2    +      -       -      -
    222E  GLU*     4.4    16.2    -      -       +      -
    223E  MET      3.1    20.0    -      -       -      +
    224E  HIS*     3.3    29.5    +      +       +      -
    225E  LYS*     3.9     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 199 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187E  SER*     4.1    17.0    -      -       -      +
    188E  SER      4.2    16.4    -      -       -      +
    192E  SER*     4.3     0.7    -      -       -      -
    198E  TYR*     1.3    73.3    -      -       -      +
    200E  MET*     1.3    60.0    +      -       -      +
    221E  MET      3.5     0.5    -      -       -      +
    222E  GLU*     3.4     2.8    -      -       -      -
    223E  MET*     2.6    65.6    +      -       +      +
    225E  LYS*     4.1    30.4    -      -       +      +
   4402E  ADP      3.9    42.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 200 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165E  GLN*     4.1     5.6    -      -       +      +
    187E  SER*     2.9    23.8    -      -       -      -
    188E  SER*     3.0    24.7    +      -       -      +
    190E  LEU*     3.5    39.3    -      -       +      +
    191E  LEU      4.8     2.2    -      -       -      +
    192E  SER*     3.7    17.5    -      -       -      +
    193E  PRO*     3.5    22.7    -      -       +      -
    198E  TYR      3.9     0.8    +      -       -      -
    199E  LEU*     1.3    74.8    -      -       -      +
    201E  ALA*     1.3    63.9    +      -       -      +
    202E  LEU*     4.8     6.3    -      -       +      -
    220E  ARG*     3.0    52.7    -      -       +      +
    221E  MET      3.1    10.8    -      -       -      +
    222E  GLU*     4.6     1.3    -      -       +      +
    223E  MET*     4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 201 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184E  VAL*     5.4     2.7    -      -       +      -
    185E  ILE*     3.3    16.4    -      -       -      +
    186E  THR*     3.4    18.2    -      -       -      +
    200E  MET*     1.3    74.5    -      -       -      +
    202E  LEU*     1.3    62.4    +      -       -      +
    220E  ARG*     3.4     2.4    -      -       -      -
    221E  MET*     2.7    55.2    +      -       +      +
    223E  MET*     4.0    15.3    -      -       +      -
    237E  PHE*     6.3     0.9    -      -       +      -
    260E  VAL*     5.9     1.8    -      -       +      -
   4402E  ADP      5.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 202 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165E  GLN*     4.2    11.4    -      -       +      +
    168E  ALA*     3.5    32.5    -      -       +      -
    169E  LEU*     4.6     3.6    -      -       +      +
    172E  MET*     3.3    25.5    -      -       +      +
    184E  VAL*     3.4     4.5    -      -       -      -
    185E  ILE*     2.8    42.5    +      -       +      +
    188E  SER*     5.9     0.7    -      -       -      +
    190E  LEU*     4.2    14.8    -      -       +      -
    200E  MET*     4.8     7.0    -      -       +      -
    201E  ALA*     1.3    75.2    -      -       -      +
    203E  GLY*     1.3    59.8    +      -       -      +
    219E  ILE      3.3     2.7    -      -       -      +
    220E  ARG*     3.1    43.7    -      -       +      +
    221E  MET*     5.1     0.9    -      -       -      -
    312E  LEU*     4.2    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 203 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172E  MET*     4.2     1.3    -      -       -      -
    183E  VAL      3.3     7.0    -      -       -      -
    184E  VAL*     4.1    10.3    -      -       -      -
    202E  LEU*     1.3    75.0    -      -       -      +
    204E  SER*     1.3    59.2    +      -       -      -
    218E  ARG*     3.6     1.9    -      -       -      -
    219E  ILE*     2.7    47.0    +      -       -      +
    221E  MET*     4.8     1.4    -      -       -      +
    252E  LEU*     3.1    20.7    -      -       -      +
    256E  CYS*     5.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 204 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172E  MET*     3.6    27.2    -      -       -      +
    173E  ASP*     4.6     1.0    +      -       -      -
    176E  HIS*     2.7    30.0    +      -       -      -
    182E  THR*     3.4     1.9    -      -       -      -
    183E  VAL      2.6    40.1    +      -       -      +
    203E  GLY*     1.3    73.7    -      -       -      -
    205E  GLN*     1.3    62.8    +      -       -      +
    216E  THR*     5.2     2.4    -      -       -      +
    217E  GLN      3.4     5.3    +      -       -      -
    218E  ARG*     3.6    22.1    +      -       -      +
    252E  LEU*     3.5     3.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 205 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176E  HIS*     4.2     2.2    -      -       -      -
    181E  ASP      3.3     5.4    -      -       -      +
    182E  THR*     3.6    24.4    +      -       +      +
    204E  SER*     1.3    75.6    +      -       -      +
    206E  ARG*     1.3    66.1    +      -       -      +
    207E  THR*     4.4    13.8    +      -       -      +
    215E  VAL      4.1     0.4    -      -       -      +
    216E  THR*     3.5     5.4    -      -       -      +
    217E  GLN*     2.5    71.6    +      -       +      +
    245E  THR*     6.3     1.0    -      -       -      -
    249E  PRO      2.8    27.4    +      -       -      +
    250E  ASN*     4.8     0.4    -      -       -      -
    251E  ASN      4.2     0.2    +      -       -      -
    252E  LEU*     3.4    28.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 206 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173E  ASP*     5.6     6.1    +      -       -      +
    176E  HIS*     4.2    28.5    -      -       +      +
    181E  ASP*     2.8    46.3    +      -       -      +
    205E  GLN*     1.3    76.0    -      -       -      +
    207E  THR*     1.3    69.6    +      -       -      +
    208E  ARG*     6.0     5.1    -      -       +      +
    214E  VAL*     3.7    34.6    -      -       +      +
    215E  VAL      3.7     4.9    -      -       -      -
    216E  THR*     4.1    16.6    +      -       +      +
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Residues in contact with THR 207 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205E  GLN*     4.4    14.4    +      -       -      +
    206E  ARG*     1.3    77.7    +      -       -      +
    208E  ARG*     1.3    70.8    +      -       -      +
    209E  ALA*     4.5     2.2    -      -       -      +
    214E  VAL*     3.0     7.1    -      -       -      +
    215E  VAL*     2.7    57.0    +      -       +      +
    217E  GLN*     5.2     2.3    +      -       -      -
    250E  ASN*     4.0    19.7    +      -       -      +
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Residues in contact with ARG 208 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206E  ARG*     6.0     5.7    -      -       +      +
    207E  THR*     1.3    77.2    -      -       -      +
    209E  ALA*     1.3    69.0    +      -       -      +
    210E  PRO*     4.5     0.9    -      -       -      +
    212E  GLY*     3.3    29.6    +      -       -      -
    213E  SER      3.5     1.8    -      -       -      -
    214E  VAL*     3.5    23.5    -      -       +      +
----------------------------------------------------------
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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