Contacts of the strand formed by residues 189 - 201 (chain B) in PDB entry 4G7Z


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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  GLU*     4.8    11.3    +      -       -      -
    185B  ARG*     3.3     1.9    -      -       -      -
    186B  LEU*     2.5    65.6    +      -       -      +
    188B  GLN*     1.3    90.9    -      -       +      +
    190B  THR*     1.3    57.8    +      -       -      +
    191B  ASP      3.6     1.1    -      -       -      -
    192B  LEU*     3.5    36.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183B  ASP*     3.7    10.1    -      -       -      +
    184B  THR      3.4    13.7    +      -       -      +
    185B  ARG*     3.0    47.8    +      -       -      +
    188B  GLN      3.5     6.0    +      -       -      -
    189B  ARG*     1.3    71.2    -      -       -      +
    191B  ASP*     1.3    60.1    +      -       -      +
    192B  LEU      3.5     1.6    -      -       -      -
    720D  LEU      5.1     0.7    -      -       -      +
    721D  VAL*     5.3     1.3    -      -       +      -
    722D  GLU*     3.4    46.8    +      -       +      +
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Residues in contact with ASP 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  ARG*     3.2    42.6    +      -       +      +
    183B  ASP*     3.3    17.4    -      -       -      +
    189B  ARG*     3.6     1.6    -      -       -      +
    190B  THR*     1.3    78.8    -      -       -      +
    192B  LEU*     1.3    72.8    +      -       +      +
    193B  ASP*     3.7     8.0    +      -       -      +
    851C  LYS*     5.8     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 192 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  PRO*     4.3    20.0    -      -       +      -
     28B  LEU      3.6    11.0    -      -       -      +
     29B  GLU*     3.9    21.3    -      -       -      +
     30B  ARG*     4.9     3.4    -      -       +      +
    183B  ASP*     3.6     4.2    -      -       -      -
    184B  THR*     2.8    38.1    +      -       +      +
    186B  LEU*     3.5    22.0    -      -       +      +
    189B  ARG*     3.5    56.5    -      -       +      +
    191B  ASP*     1.3    89.0    -      -       +      +
    193B  ASP*     1.3    60.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 193 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  GLU*     4.1     1.2    -      -       -      +
     27B  PRO*     3.6     6.8    -      -       -      +
     28B  LEU*     2.8    56.0    +      -       +      +
     29B  GLU      3.8     0.7    -      -       -      +
     30B  ARG*     3.1    12.6    -      -       -      +
     31B  GLY*     2.8    31.8    +      -       -      -
     33B  GLY*     3.2    20.8    +      -       -      +
     34B  VAL*     4.1     4.0    -      -       -      +
    181B  VAL*     3.1    25.1    -      -       +      +
    182B  GLU      3.8     3.6    -      -       -      -
    184B  THR*     4.7     1.6    -      -       -      -
    191B  ASP      4.0     3.2    -      -       -      +
    192B  LEU*     1.3    73.7    -      -       -      +
    194B  LYS*     1.3    58.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  VAL*     3.8    19.0    -      -       +      +
     26B  GLU*     3.4    38.7    +      -       +      +
    180B  GLN      3.8     1.6    -      -       -      +
    181B  VAL*     3.5     7.1    -      -       -      -
    182B  GLU*     3.0    62.7    +      -       +      +
    184B  THR*     3.5    21.8    -      -       -      +
    193B  ASP*     1.3    73.0    -      -       -      +
    195B  LEU*     1.3    64.0    +      -       -      +
    196B  THR*     4.0    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  PHE*     5.5     5.2    -      -       +      -
     23B  PHE      3.2     2.1    -      -       -      +
     24B  VAL*     3.2     8.6    -      -       -      -
     25B  LEU*     3.1    47.9    +      -       +      +
     28B  LEU*     4.1    19.5    -      -       +      -
     33B  GLY*     3.6    25.1    -      -       -      +
     36B  LEU*     4.1    15.5    -      -       +      +
     37B  GLY*     4.4     5.6    -      -       -      +
     40B  LEU*     6.1     1.3    -      -       +      -
    179B  PHE*     3.6    31.2    -      -       +      -
    180B  GLN      4.3     0.4    -      -       -      +
    181B  VAL*     3.7     9.0    -      -       +      +
    194B  LYS*     1.3    75.8    -      -       -      +
    196B  THR*     1.3    66.7    +      -       -      +
    197B  LEU*     5.2     6.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  ARG*     5.4     0.4    -      -       -      +
     22B  GLU*     3.9    22.4    -      -       +      +
     23B  PHE      3.4     6.3    -      -       -      +
     24B  VAL*     3.7    15.1    -      -       +      +
    179B  PHE*     3.3     5.9    -      -       -      +
    180B  GLN*     3.0    47.3    +      -       +      +
    182B  GLU*     4.4     8.3    +      -       -      -
    194B  LYS*     3.9    13.9    +      -       -      -
    195B  LEU*     1.3    75.4    -      -       -      +
    197B  LEU*     1.3    66.8    +      -       -      +
    198B  ARG*     4.7     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  PHE*     6.5     0.4    -      -       +      -
     22B  GLU*     3.2     6.6    -      -       -      +
     23B  PHE*     2.9    43.9    +      -       +      +
     37B  GLY      6.0     2.5    -      -       -      +
     40B  LEU*     5.5     8.1    -      -       +      -
     44B  LEU*     4.6     4.5    -      -       +      -
    177B  VAL*     3.5    25.1    -      -       +      -
    178B  ALA      3.3    15.3    -      -       -      +
    179B  PHE*     3.6    13.0    -      -       +      -
    195B  LEU*     5.2     7.0    -      -       +      +
    196B  THR*     1.3    77.6    -      -       -      +
    198B  ARG*     1.3    74.5    +      -       -      +
    199B  ILE*     4.1    14.8    -      -       +      -
    211B  LEU*     4.0    32.1    -      -       +      -
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Residues in contact with ARG 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  TYR*     3.5    25.3    +      -       +      +
     21B  GLY      3.3     4.7    -      -       -      -
     22B  GLU*     3.9    16.6    -      -       +      +
    176B  ARG*     4.0    17.4    -      -       -      +
    177B  VAL*     3.6     3.1    -      -       -      -
    178B  ALA*     3.0    41.2    +      -       -      +
    180B  GLN*     5.2     7.7    +      -       -      -
    196B  THR*     4.7     8.3    -      -       +      +
    197B  LEU*     1.3    78.2    -      -       -      +
    199B  ILE*     1.3    65.4    +      -       -      +
    200B  TRP*     3.6    32.1    -      -       +      -
    888D  GLU*     4.1    17.6    +      -       -      -
    937D  TYR*     4.6    11.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  TYR*     3.3     4.8    -      -       -      -
     21B  GLY      3.1    29.3    +      -       -      -
     23B  PHE*     4.0    17.0    -      -       +      -
     44B  LEU*     3.5    31.9    -      -       +      -
    174B  VAL*     4.0    22.9    -      -       +      -
    176B  ARG      3.5    10.1    -      -       -      +
    177B  VAL*     4.7     2.5    -      -       +      -
    197B  LEU*     4.1    10.5    -      -       +      -
    198B  ARG*     1.3    79.9    -      -       -      +
    200B  TRP*     1.3    68.5    +      -       -      +
    201B  THR*     4.9     1.3    -      -       -      +
    207B  PRO*     3.6    35.4    -      -       +      +
    210B  ALA*     5.1     1.6    -      -       +      -
    211B  LEU*     4.1    13.2    -      -       +      -
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Residues in contact with TRP 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  GLU      3.2    10.3    -      -       -      +
     20B  TYR*     3.2    36.5    -      +       +      -
    174B  VAL*     3.5     6.4    -      -       -      -
    175B  ARG*     2.8    32.2    +      -       +      -
    176B  ARG*     3.1    81.9    +      -       +      +
    178B  ALA      4.3     2.9    -      -       -      -
    198B  ARG*     3.6    49.6    -      -       +      -
    199B  ILE*     1.3    77.3    -      -       -      +
    201B  THR*     1.3    61.5    +      -       -      +
    847D  ASP*     5.5     2.0    -      -       -      +
    888D  GLU*     5.0     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  ARG      3.2    15.7    -      -       -      -
     19B  GLU*     2.7    29.3    +      -       -      +
    173B  PRO*     2.9    25.1    -      -       +      +
    174B  VAL*     5.1     1.1    -      -       +      +
    175B  ARG*     4.1     9.6    -      -       -      +
    199B  ILE*     4.9     1.7    -      -       -      +
    200B  TRP*     1.3    76.5    +      -       -      +
    202B  ASP*     1.3    67.8    +      -       -      +
    203B  GLY      3.0     5.6    -      -       -      +
    205B  VAL*     2.9    31.0    -      -       +      +
    206B  THR      3.8     0.6    -      -       -      -
    207B  PRO*     3.2    30.0    -      -       -      +
    210B  ALA*     5.5     3.6    -      -       +      +
----------------------------------------------------------
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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