Contacts of the strand formed by residues 189 - 201 (chain L) in PDB entry 5D4E


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 ARG 189 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  LEU*     4.5    22.9    -      -       +      +
     29L  GLU*     3.5    32.1    +      -       -      -
    185L  ARG*     3.1     8.3    -      -       -      +
    186L  LEU*     3.0    37.0    +      -       +      +
    188L  GLN*     1.3    76.9    -      -       -      +
    190L  THR*     1.3    60.1    +      -       -      +
    191L  ASP*     3.6     7.0    -      -       -      +
    192L  LEU*     4.0    31.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 190 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183L  ASP*     4.9     6.8    -      -       -      +
    184L  THR      3.5    13.7    +      -       -      +
    185L  ARG*     4.0    19.7    -      -       +      +
    187L  GLY      5.7     0.4    -      -       -      +
    188L  GLN*     3.3    14.0    +      -       -      +
    189L  ARG*     1.3    75.3    -      -       -      +
    191L  ASP*     1.3    63.7    +      -       -      +
    192L  LEU      3.5     2.2    -      -       -      -
    646N  LYS*     5.8     0.4    -      -       +      -
    722N  GLU*     3.3    44.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 191 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29L  GLU*     4.5     4.8    -      -       -      +
     30L  ARG*     3.9    41.9    +      -       -      +
    183L  ASP*     4.6    10.1    -      -       -      +
    189L  ARG*     4.6     7.1    -      -       -      +
    190L  THR*     1.3    80.2    +      -       -      +
    192L  LEU*     1.3    84.2    +      -       -      +
    193L  ASP*     3.4    10.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 192 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  LEU*     4.8     8.7    -      -       +      -
     27L  PRO*     3.7    17.9    -      -       +      -
     28L  LEU      3.4    13.5    -      -       -      +
     29L  GLU*     3.9    20.2    -      -       -      +
     30L  ARG      4.7     1.3    -      -       -      +
    183L  ASP*     3.7     5.0    -      -       -      -
    184L  THR*     2.9    44.0    +      -       +      +
    186L  LEU*     3.6    38.4    -      -       +      +
    189L  ARG*     4.0    28.5    -      -       +      +
    191L  ASP*     1.3    96.1    -      -       -      +
    193L  ASP*     1.3    61.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 193 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25L  LEU      4.2     0.2    -      -       -      +
     27L  PRO*     3.5     7.8    -      -       -      +
     28L  LEU*     2.7    53.2    +      -       +      +
     29L  GLU      3.8     2.0    -      -       -      -
     30L  ARG*     3.8     1.7    -      -       -      +
     31L  GLY*     3.0    31.9    +      -       -      -
     33L  GLY*     3.1    23.6    +      -       -      +
     34L  VAL*     4.7     0.3    +      -       -      +
    181L  VAL*     3.7    17.4    -      -       +      +
    182L  GLU      3.7     3.0    -      -       -      +
    183L  ASP*     5.3     2.3    -      -       -      +
    184L  THR*     3.6     2.6    -      -       -      +
    191L  ASP      3.4     9.7    -      -       -      +
    192L  LEU*     1.3    80.3    -      -       -      +
    194L  LYS*     1.3    59.2    +      -       -      +
    195L  LEU      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 194 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24L  VAL*     3.7    26.9    -      -       +      +
     25L  LEU      3.8     3.1    -      -       -      -
     26L  GLU*     3.3    35.3    +      -       +      +
    180L  GLN      3.6     1.7    -      -       -      +
    181L  VAL*     3.4     6.8    -      -       -      -
    182L  GLU*     2.9    61.6    +      -       +      +
    184L  THR*     4.1    11.7    -      -       +      -
    193L  ASP*     1.3    75.3    -      -       -      +
    195L  LEU*     1.3    61.4    +      -       -      +
    196L  THR*     3.8    13.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 195 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225K  PHE*     4.8    14.1    -      -       +      -
     23L  PHE      3.2     6.1    -      -       -      +
     24L  VAL*     3.2     2.4    -      -       -      -
     25L  LEU*     2.9    47.8    +      -       +      +
     28L  LEU*     4.1    15.7    -      -       +      -
     33L  GLY*     3.5    28.5    -      -       -      +
     36L  LEU*     4.0    13.7    -      -       +      -
     37L  GLY*     4.0    14.6    -      -       -      +
     40L  LEU*     5.6     2.9    -      -       +      -
    179L  PHE*     3.8    27.4    -      -       +      -
    180L  GLN      3.9     4.7    -      -       -      +
    181L  VAL*     4.0     4.0    -      -       +      +
    193L  ASP      4.2     0.6    -      -       -      -
    194L  LYS*     1.3    72.9    -      -       -      +
    196L  THR*     1.3    68.4    +      -       -      +
    197L  LEU*     5.0     8.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 196 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22L  GLU*     5.1     9.0    -      -       +      +
     23L  PHE      3.6     4.7    -      -       -      +
     24L  VAL*     3.9    19.7    -      -       +      +
    178L  ALA      4.0     0.5    -      -       -      +
    179L  PHE*     3.2     5.4    -      -       -      +
    180L  GLN*     2.9    50.9    +      -       +      +
    182L  GLU*     5.2     7.4    +      -       -      -
    194L  LYS*     3.8    16.0    +      -       -      +
    195L  LEU*     1.3    74.2    -      -       -      +
    197L  LEU*     1.3    62.2    +      -       -      +
    198L  ARG*     4.4    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 197 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225K  PHE*     5.6     3.8    -      -       +      -
     22L  GLU*     3.4     2.9    -      -       -      -
     23L  PHE*     2.9    51.5    +      -       +      +
     37L  GLY*     5.6     3.8    -      -       -      +
     40L  LEU*     4.2    17.0    -      -       +      -
     41L  ARG*     5.6     1.8    -      -       +      +
     44L  LEU*     4.5     8.1    -      -       +      -
    177L  VAL*     3.6    27.4    -      -       +      -
    178L  ALA      3.9     0.4    -      -       -      +
    179L  PHE*     3.6    22.4    -      -       +      -
    195L  LEU*     5.1    10.3    -      -       +      -
    196L  THR*     1.3    75.5    -      -       -      +
    198L  ARG*     1.3    66.1    +      -       -      +
    199L  ILE*     4.3    10.3    -      -       +      -
    211L  LEU*     3.8    32.1    -      -       +      -
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Residues in contact with ARG 198 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20L  TYR*     3.2    24.8    +      -       -      +
     21L  GLY      3.4     3.6    -      -       -      -
     22L  GLU*     4.4     8.0    -      -       +      -
    176L  ARG*     5.6     0.8    -      -       -      +
    177L  VAL*     3.4     5.2    -      -       -      +
    178L  ALA*     2.9    53.2    +      -       -      +
    180L  GLN*     6.5     0.9    -      -       -      -
    196L  THR*     4.4    18.2    -      -       +      -
    197L  LEU*     1.3    75.0    -      -       -      +
    199L  ILE*     1.3    64.2    +      -       -      +
    200L  TRP*     3.4    39.6    -      -       +      -
    888N  GLU*     4.0    17.4    +      -       -      -
    937N  TYR*     5.5     5.1    +      -       -      -
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Residues in contact with ILE 199 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20L  TYR*     3.2     6.3    -      -       -      -
     21L  GLY      2.9    36.4    +      -       -      +
     23L  PHE*     4.0    15.9    -      -       +      -
     44L  LEU*     3.6    31.0    -      -       +      -
    174L  VAL*     4.0    14.8    -      -       +      -
    176L  ARG      3.5     7.4    -      -       -      +
    177L  VAL*     4.6     3.1    -      -       +      -
    197L  LEU*     4.3    13.7    -      -       +      -
    198L  ARG*     1.3    79.4    -      -       -      +
    200L  TRP*     1.3    65.0    +      -       -      +
    201L  THR*     3.9    22.2    -      -       +      -
    207L  PRO*     3.6    32.4    -      -       +      +
    210L  ALA*     5.0     0.9    -      -       +      -
    211L  LEU*     4.1    10.3    -      -       +      -
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Residues in contact with TRP 200 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19L  GLU*     3.3     6.5    -      -       +      -
     20L  TYR*     3.4    34.9    -      +       +      -
    174L  VAL*     3.4     4.2    -      -       -      +
    175L  ARG*     2.6    35.9    +      -       +      -
    176L  ARG*     2.9    81.9    +      -       +      +
    178L  ALA*     4.0     8.3    -      -       +      -
    198L  ARG*     3.4    60.6    -      -       +      -
    199L  ILE*     1.3    73.7    -      -       -      +
    201L  THR*     1.3    57.3    +      -       -      +
    888N  GLU*     5.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 201 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18L  ARG      3.0    21.0    +      -       -      -
     19L  GLU*     2.7    28.5    +      -       -      +
    173L  PRO      3.2    13.7    -      -       -      +
    174L  VAL*     4.2    11.9    -      -       +      -
    175L  ARG*     3.8    13.1    -      -       -      +
    199L  ILE*     3.9    19.1    -      -       +      -
    200L  TRP*     1.3    79.9    -      -       -      +
    202L  ASP*     1.3    61.1    +      -       -      +
    203L  GLY      3.4     1.8    +      -       -      -
    205L  VAL*     2.9    29.9    +      -       +      +
    206L  THR      4.3     0.7    -      -       -      +
    207L  PRO*     3.9    13.9    -      -       +      -
    210L  ALA*     4.7     2.2    -      -       +      -
----------------------------------------------------------
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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