Contacts of the strand formed by residues 189 - 199 (chain B) in PDB entry 6G4O


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 GLY 189 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108B  SER*     4.8     2.0    +      -       -      -
    109B  THR*     3.5     5.6    -      -       -      -
    111B  VAL*     3.5    18.4    -      -       -      -
    142B  VAL*     4.6     3.1    -      -       -      -
    184B  ILE*     2.8    20.7    +      -       -      +
    185B  GLN*     3.2    16.7    -      -       -      +
    187B  PHE      3.4     1.4    -      -       -      -
    188B  GLY*     1.3    77.8    -      -       -      +
    190B  ASP*     1.3    60.6    +      -       -      -
    191B  PRO*     3.1    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108B  SER*     3.7    29.1    +      -       -      +
    109B  THR      2.7    22.5    +      -       -      +
    111B  VAL*     3.6     2.4    -      -       -      +
    184B  ILE*     4.1     1.6    -      -       -      -
    189B  GLY*     1.3    69.3    -      -       -      -
    191B  PRO*     1.3    64.3    -      -       -      +
    192B  LYS*     2.7    45.7    +      -       -      +
    193B  THR*     3.1    40.3    +      -       -      +
    194B  VAL*     3.6     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108B  SER*     5.5     0.7    -      -       -      +
    181B  HIS*     3.5    48.4    +      -       +      +
    184B  ILE*     4.0    11.7    -      -       +      -
    185B  GLN*     4.0    22.0    -      -       +      +
    189B  GLY      3.1    11.8    -      -       -      +
    190B  ASP*     1.3    90.7    -      -       -      +
    192B  LYS*     1.3    60.5    +      -       +      -
    193B  THR      3.4     0.4    -      -       -      -
    194B  VAL*     3.9    17.7    +      -       +      +
    218B  LEU      5.6     2.9    -      -       -      +
    219B  PHE*     5.9     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 192 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190B  ASP*     2.7    27.5    +      -       -      +
    191B  PRO*     1.3    78.2    -      -       +      +
    193B  THR*     1.3    59.0    +      -       -      +
    194B  VAL      3.8     1.8    -      -       -      -
    220B  ARG*     3.1    30.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 193 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110B  THR*     3.6    32.7    -      -       +      +
    111B  VAL      3.0    22.3    +      -       -      +
    190B  ASP*     3.1    27.2    +      -       -      +
    192B  LYS*     1.3    82.1    +      -       -      +
    194B  VAL*     1.3    57.3    +      -       -      +
    220B  ARG*     3.5    22.9    +      -       -      +
    221B  ARG*     5.1     2.2    -      -       -      +
    477B  ALA      3.7    13.0    -      -       -      +
    478B  LYS      4.0    11.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  VAL*     3.2    19.1    -      -       +      +
    113B  VAL*     3.8    29.4    -      -       +      -
    177B  LEU*     4.9     1.8    -      -       +      -
    180B  VAL*     4.5    11.9    -      -       +      +
    181B  HIS*     5.9     1.8    -      -       -      +
    190B  ASP      3.6    16.2    -      -       -      +
    191B  PRO*     3.9    19.1    -      -       +      +
    192B  LYS      3.8     2.2    -      -       -      -
    193B  THR*     1.3    74.6    -      -       -      +
    195B  THR*     1.3    66.3    +      -       -      +
    196B  ILE*     4.6     2.2    -      -       +      -
    218B  LEU      4.5     8.1    -      -       -      +
    219B  PHE*     3.5    20.5    -      -       +      +
    220B  ARG*     2.7    33.0    +      -       -      +
    221B  ARG      3.5     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110B  THR*     4.6     0.5    -      -       -      +
    111B  VAL      2.6    10.8    +      -       -      -
    112B  MET*     3.1     8.4    -      -       +      +
    113B  VAL*     2.7    26.3    +      -       -      +
    193B  THR      4.0     0.2    +      -       -      -
    194B  VAL*     1.3    73.0    -      -       -      +
    196B  ILE*     1.3    74.8    +      -       -      +
    197B  PHE*     4.2     1.5    -      -       +      -
    221B  ARG*     3.4    19.8    -      -       -      +
    223B  ILE*     3.7    26.9    -      -       +      -
    476B  PHE*     4.5     2.5    -      -       +      -
    477B  ALA*     3.1    45.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  VAL*     3.4    10.5    -      -       +      +
    115B  ILE*     4.2     7.4    -      -       +      -
    177B  LEU*     3.5    34.5    -      -       +      -
    194B  VAL*     4.0     1.5    +      -       +      -
    195B  THR*     1.3    79.0    -      -       -      +
    197B  PHE*     1.3    63.6    +      -       -      +
    206B  VAL*     4.0    29.2    -      -       +      +
    209B  HIS*     4.0    15.3    -      -       +      -
    219B  PHE*     3.7    53.4    -      -       +      -
    221B  ARG      3.2     5.8    +      -       -      +
    222B  ALA*     3.5     6.1    -      -       -      -
    223B  ILE      2.9    22.9    +      -       -      -
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Residues in contact with PHE 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112B  MET*     3.7    29.4    -      -       +      -
    113B  VAL      3.0    41.7    +      -       -      +
    114B  TRP*     3.3    37.3    -      +       +      -
    115B  ILE*     2.8    24.6    +      -       -      +
    135B  LEU*     4.6     2.9    -      -       +      -
    143B  LEU*     3.8    22.2    -      -       +      -
    195B  THR*     4.2     2.7    -      -       +      -
    196B  ILE*     1.3    80.9    -      -       -      +
    198B  GLY*     1.3    58.4    +      -       -      +
    206B  VAL*     3.5     7.8    -      -       -      +
    223B  ILE*     3.2    32.3    -      -       +      +
    225B  GLN*     4.1     8.3    -      -       -      +
    447B  VAL*     4.2    15.5    -      -       +      -
    448B  PHE*     4.6     3.4    -      +       -      -
    473B  TRP*     4.4     6.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  TRP*     3.4    12.6    -      -       -      -
    115B  ILE*     3.1    16.6    -      -       -      -
    197B  PHE*     1.3    78.3    -      -       -      +
    199B  GLU*     1.3    59.4    +      -       -      -
    202B  GLY      3.7     7.2    -      -       -      -
    203B  GLY*     3.1    14.4    +      -       -      -
    206B  VAL*     3.8     1.4    -      -       -      +
    223B  ILE      3.5     4.0    +      -       -      -
    224B  LEU      4.0     0.5    -      -       -      -
    225B  GLN*     3.1    25.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  TRP*     3.4    20.9    -      -       +      -
    115B  ILE      3.5     3.6    +      -       -      -
    117B  GLY*     3.1    15.3    +      -       -      +
    130B  TYR*     4.8     0.7    +      -       -      -
    198B  GLY*     1.3    73.6    -      -       -      -
    200B  SER*     1.3    68.1    +      -       -      +
    202B  GLY      2.6    22.0    +      -       -      -
    203B  GLY      3.3     3.1    -      -       -      +
    225B  GLN*     3.4     8.7    -      -       +      +
    226B  SER*     4.4     1.9    -      -       -      -
    440B  HIS*     3.0    32.6    +      -       -      -
    441B  GLY*     3.5     8.3    +      -       -      -
    443B  GLU*     3.0    27.2    -      -       -      +
    444B  ILE*     3.5    23.9    -      -       +      +
    609B  P6G      2.9    21.9    +      -       -      -
----------------------------------------------------------
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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