Contacts of the strand formed by residues 209 - 221 (chain B) in PDB entry 6D6U


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 GLU 209 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  THR*     3.4     7.3    -      -       -      -
    164B  ARG*     2.6    75.9    +      -       +      +
    202B  ILE*     4.7    10.1    -      -       +      -
    203B  VAL      4.1     4.9    -      -       -      -
    204B  GLN*     4.4    26.0    +      -       +      +
    208B  GLY*     1.3    70.7    -      -       -      -
    210B  TYR*     1.3    60.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 210 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  PHE*     5.6     0.9    -      +       -      -
    102B  HIS*     5.1    12.6    -      +       +      -
    159B  SER*     4.5    14.4    -      -       -      +
    160B  TYR*     4.8    13.2    -      +       -      -
    161B  ALA*     4.0    20.6    +      -       -      -
    162B  TYR      3.5    30.7    -      -       -      +
    163B  THR*     4.0     9.0    -      -       +      -
    164B  ARG*     4.5     5.9    -      -       -      +
    202B  ILE*     3.4    19.1    -      -       -      +
    203B  VAL*     3.1    26.2    +      -       +      +
    205B  SER*     3.9    17.3    -      -       -      -
    207B  THR*     2.6    34.8    +      -       +      +
    208B  GLY      3.4     5.3    +      -       -      -
    209B  GLU*     1.3    80.7    -      -       -      +
    211B  VAL*     1.3    66.5    +      -       -      +
    212B  VAL*     5.2     4.9    -      -       +      -
    115C  MET*     4.1     9.2    -      -       -      +
    117C  ARG*     4.5     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 211 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158B  GLY*     3.5    18.7    -      -       -      -
    159B  SER*     3.7    12.4    +      -       -      +
    162B  TYR      5.4     1.3    +      -       -      +
    163B  THR      5.8     0.4    -      -       -      +
    164B  ARG*     5.0    13.2    -      -       +      +
    167B  VAL      3.8    22.2    -      -       -      +
    168B  VAL*     4.5     5.8    -      -       +      -
    169B  TYR*     4.1    30.0    -      -       +      +
    201B  GLY      3.9    11.0    -      -       -      +
    202B  ILE*     4.8     3.6    -      -       +      +
    210B  TYR*     1.3    77.3    -      -       -      +
    212B  VAL*     1.3    65.0    +      -       -      +
    213B  MET*     3.7    22.8    +      -       +      -
    102J  ARG*     4.5    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 212 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  HIS*     3.5    29.2    -      -       +      +
    156B  LYS*     4.1    20.4    -      -       +      -
    157B  PHE      4.5     1.8    -      -       -      -
    158B  GLY*     4.5     0.4    -      -       -      -
    201B  GLY*     3.1    34.3    +      -       -      +
    203B  VAL*     3.6    38.4    -      -       +      +
    210B  TYR*     5.1     2.9    -      -       +      -
    211B  VAL*     1.3    82.0    -      -       -      +
    213B  MET*     1.3    74.3    +      -       -      +
    214B  THR*     3.6    19.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 213 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  THR*     5.5     1.6    -      -       -      +
    155B  LEU      3.7     1.2    -      -       -      +
    156B  LYS*     3.2     5.9    -      -       -      -
    157B  PHE*     3.1    69.9    +      -       +      +
    169B  TYR*     3.8    38.1    -      -       +      +
    170B  GLU*     4.9     1.6    -      -       -      -
    171B  TRP*     3.9    22.0    -      -       +      -
    199B  ASP      4.3     0.9    -      -       -      -
    200B  SER*     3.0    33.9    -      -       -      +
    211B  VAL*     3.7    22.9    +      -       +      -
    212B  VAL*     1.3    93.0    -      -       -      +
    214B  THR*     1.3    60.0    +      -       -      +
    102J  ARG*     5.1     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 214 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154B  PRO*     4.7     3.1    -      -       +      -
    155B  LEU      3.7     2.5    -      -       -      -
    156B  LYS*     3.5    29.9    -      -       +      +
    171B  TRP*     4.3     2.8    -      -       -      -
    198B  VAL*     3.6     2.8    -      -       -      +
    199B  ASP*     2.9    45.0    +      -       -      -
    201B  GLY      5.3     1.6    +      -       -      -
    212B  VAL*     3.6    11.3    +      -       -      +
    213B  MET*     1.3    75.5    -      -       -      +
    215B  THR*     1.3    69.8    +      -       -      +
    216B  HIS*     3.4    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 215 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  ILE*     4.9     2.8    -      -       +      +
    154B  PRO*     3.2     3.6    -      -       -      +
    155B  LEU*     2.8    50.7    +      -       +      +
    157B  PHE*     4.5     4.6    -      -       -      -
    171B  TRP*     3.7    22.5    -      -       -      -
    179B  VAL*     4.0    23.5    -      -       +      +
    196B  GLN*     5.2     0.7    -      -       +      -
    197B  THR      3.3    12.6    -      -       -      +
    198B  VAL*     4.2     2.2    -      -       +      +
    214B  THR*     1.3    77.3    +      -       -      +
    216B  HIS*     1.3    67.8    +      -       -      +
    217B  PHE*     4.0    24.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 216 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152B  ALA*     4.7    19.3    -      -       +      -
    153B  CYS      4.2     2.9    -      -       -      -
    154B  PRO*     4.0    19.0    -      -       +      +
    195B  GLY      4.0     0.2    -      -       -      +
    196B  GLN*     3.8     3.1    -      -       -      -
    197B  THR*     2.8    55.9    +      -       +      +
    199B  ASP*     5.0    13.1    -      -       +      +
    214B  THR*     3.4    29.5    +      -       +      +
    215B  THR*     1.3    71.6    -      -       -      +
    217B  PHE*     1.3    62.4    +      -       -      +
    218B  HIS*     3.7    14.5    +      +       +      +
     28I  TYR*     5.6     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 217 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  ILE*     5.9     0.9    -      -       +      -
     47B  VAL*     3.8    20.4    -      -       +      -
     50B  PHE*     3.9    32.3    -      +       +      -
     60B  TYR*     4.6     7.0    -      -       -      -
     62B  ILE*     3.6    30.5    -      -       +      -
    152B  ALA*     3.8     3.1    -      -       -      -
    153B  CYS*     3.3    38.8    +      -       +      +
    155B  LEU*     4.7    11.0    -      -       +      -
    179B  VAL*     4.2    11.9    -      -       +      -
    181B  VAL*     5.7     0.7    -      -       +      -
    193B  LEU*     4.2    19.1    -      -       +      -
    195B  GLY      4.0     1.3    -      -       -      -
    196B  GLN*     3.6    33.9    -      -       +      -
    215B  THR*     4.1    16.4    -      -       +      -
    216B  HIS*     1.3    72.7    -      -       -      +
    218B  HIS*     1.3    63.8    +      -       -      +
    219B  LEU*     3.8     4.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 218 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  HIS      4.0    10.4    +      -       -      +
    152B  ALA*     4.5    13.6    -      -       +      +
    193B  LEU*     3.5    12.6    -      -       -      +
    194B  LEU*     3.6    22.2    +      -       +      -
    195B  GLY*     3.2    31.7    +      -       -      +
    197B  THR*     3.0    31.7    +      -       +      +
    216B  HIS*     4.3    10.3    +      -       +      -
    217B  PHE*     1.3    73.8    -      -       -      +
    219B  LEU*     1.3    71.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  PHE*     3.9    37.0    -      -       +      -
     53B  VAL*     4.1     6.1    -      -       +      -
    150B  ALA*     3.4    10.2    -      -       -      +
    151B  HIS*     3.2    38.3    +      -       +      +
    153B  CYS*     4.6    18.8    -      -       +      -
    188B  LEU*     4.1     9.9    -      -       +      -
    191B  TYR*     3.7    32.8    -      -       +      -
    192B  ASP      4.3     3.6    -      -       -      -
    193B  LEU*     4.0    21.5    -      -       +      +
    194B  LEU*     5.1     5.1    -      -       -      +
    217B  PHE      4.1     6.3    -      -       -      +
    218B  HIS*     1.3    85.5    -      -       -      +
    220B  LYS*     1.3    60.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 220 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148B  MET*     5.7     4.9    -      -       -      +
    149B  ASP      4.1    11.7    -      -       -      +
    150B  ALA*     4.5     7.6    -      -       +      +
    151B  HIS*     6.0     0.9    -      -       -      -
    191B  TYR*     3.4     7.3    -      -       -      -
    192B  ASP*     3.2    36.8    +      -       +      +
    194B  LEU*     5.3    15.5    -      -       +      -
    219B  LEU*     1.3    76.6    -      -       -      +
    221B  ARG*     1.3    74.5    +      -       -      +
    222B  LYS*     3.8     0.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 221 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  ASP*     3.4    17.4    +      -       -      -
    143B  LEU*     4.5     5.5    -      -       -      +
    146B  PHE*     3.4    28.7    -      -       -      -
    147B  PRO*     3.2    41.8    -      -       -      +
    148B  MET*     5.5     2.4    -      -       -      -
    149B  ASP*     3.6    22.1    +      -       -      +
    151B  HIS*     4.4     5.9    +      -       -      -
    190B  GLN*     2.8    36.0    +      -       +      +
    191B  TYR*     2.8    42.3    +      -       +      -
    220B  LYS*     1.3    87.6    -      -       -      +
    222B  LYS*     1.3    71.7    +      -       -      +
    223B  ILE*     3.6     3.6    +      -       -      +
    226B  PHE*     3.9    14.0    -      -       +      -
    277B  LEU*     5.3     0.8    -      -       -      +
----------------------------------------------------------
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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