Contacts of the strand formed by residues 97 - 108 (chain D) in PDB entry 1WUR


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 VAL 97 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150C  GLU*     3.7    37.7    -      -       +      +
    192C  THR*     4.3    15.7    -      -       +      -
    193C  VAL      3.6     9.2    -      -       -      +
    194C  THR*     4.4     4.9    -      -       +      -
     95D  GLU      4.3     7.2    -      -       -      +
     96D  MET*     1.3    76.7    -      -       -      +
     98D  VAL*     1.3    63.9    +      -       -      +
     99D  VAL*     4.3    11.2    -      -       +      +
    121D  ILE      3.8     0.9    -      -       -      +
    122D  GLY*     3.3     3.3    -      -       -      -
    123D  TYR*     2.8    65.0    +      -       +      +
    125D  PRO*     4.9     4.0    -      -       +      -
    129D  ILE*     5.1     2.5    -      -       +      -
    132D  LEU*     4.6     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 98 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191C  ARG      3.9     0.2    -      -       -      +
    192C  THR*     3.3     3.6    -      -       -      +
    193C  VAL*     2.7    53.2    +      -       +      +
     96D  MET*     3.8    29.2    -      -       +      +
     97D  VAL*     1.3    78.5    -      -       -      +
     99D  VAL*     1.3    63.6    +      -       -      +
    100D  LYS*     3.9    15.3    +      -       +      +
    121D  ILE      3.3     7.9    -      -       -      +
    211D  PHE*     4.1    22.4    -      -       +      -
    214D  HIS*     4.3    19.5    -      -       +      +
    215D  LEU*     4.1    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 99 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180C  MET*     5.1     4.0    -      -       +      -
    190C  SER*     3.7    20.6    -      -       -      +
    191C  ARG      3.7     2.7    -      -       -      -
    192C  THR*     4.0    12.3    -      -       +      +
     97D  VAL*     4.3     6.3    -      -       +      -
     98D  VAL*     1.3    74.1    -      -       -      +
    100D  LYS*     1.3    59.3    +      -       -      +
    102D  VAL*     3.9    13.9    -      -       +      +
    119D  VAL      4.1     2.3    -      -       -      +
    120D  HIS*     3.6     1.7    -      -       -      -
    121D  ILE*     2.7    42.4    +      -       +      +
    123D  TYR*     5.7     0.4    -      -       +      -
    132D  LEU*     3.8    33.2    -      -       +      +
    135D  PHE*     3.9    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 100 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174C  GLU*     3.0    31.2    +      -       -      -
    190C  SER*     3.0     9.4    +      -       -      -
    191C  ARG*     2.9    60.7    +      -       +      +
    193C  VAL*     3.8    18.6    -      -       -      +
     98D  VAL*     4.4     9.9    -      -       +      +
     99D  VAL*     1.3    73.9    -      -       -      +
    101D  GLY*     1.3    61.9    +      -       -      +
    102D  VAL      3.4     2.9    -      -       -      -
    120D  HIS*     3.3    18.6    -      -       +      +
    214D  HIS*     2.9    31.7    +      -       -      +
    215D  LEU*     3.9    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 101 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189C  HIS*     3.0    36.7    -      -       -      +
    190C  SER*     3.1     2.3    +      -       -      -
    191C  ARG*     6.2     1.1    -      -       -      -
    100D  LYS*     1.3    72.9    -      -       -      +
    102D  VAL*     1.3    60.5    +      -       -      +
    103D  GLU      3.1     7.4    +      -       -      -
    118D  LYS*     4.0    15.7    -      -       -      -
    119D  VAL      3.6     0.6    +      -       -      -
    120D  HIS*     3.0    25.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 102 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180C  MET*     5.2     2.2    -      -       +      -
    187C  LYS*     4.0    11.9    -      -       +      -
    190C  SER*     3.7    22.9    -      -       -      +
     99D  VAL*     3.9    21.1    -      -       +      +
    100D  LYS      4.4     0.9    -      -       -      +
    101D  GLY*     1.3    73.1    -      -       -      +
    103D  GLU*     1.3    71.7    +      -       -      +
    104D  PHE      3.6     0.2    +      -       -      -
    118D  LYS*     4.1     0.4    -      -       -      -
    119D  VAL*     2.7    46.2    +      -       +      +
    121D  ILE*     5.5     2.0    -      -       +      -
    135D  PHE*     5.4     2.2    -      -       +      -
    136D  ALA*     4.0    33.7    -      -       +      +
    139D  VAL*     4.0    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 103 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186C  GLU      4.4     0.9    -      -       -      +
    187C  LYS*     2.9    48.7    +      -       +      +
    188C  GLN*     2.7    34.4    +      -       -      +
    189C  HIS*     3.0    44.3    +      -       +      +
    190C  SER      4.2     0.2    +      -       -      -
    101D  GLY      3.1     4.6    +      -       -      +
    102D  VAL*     1.3    76.1    -      -       -      +
    104D  PHE*     1.3    59.2    +      -       -      +
    105D  TYR*     4.5    20.4    -      -       +      +
    117D  GLY      3.2    13.0    -      -       -      +
    118D  LYS*     4.2     3.1    -      -       +      +
    139D  VAL*     4.6     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 104 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187C  LYS*     4.8     2.5    -      -       -      +
    103D  GLU*     1.3    75.8    -      -       -      +
    105D  TYR*     1.3    76.5    +      -       -      +
    106D  SER*     4.2     2.2    -      -       -      -
    115D  PHE*     3.6    42.2    -      +       -      -
    116D  PHE*     3.2    12.4    -      -       -      +
    117D  GLY*     2.9    55.6    +      -       -      +
    118D  LYS      3.5    11.0    -      -       -      -
    119D  VAL*     3.6    17.0    -      -       +      -
    139D  VAL*     3.7    23.3    -      -       +      -
    140D  ASP*     5.1     1.6    -      -       -      -
    143D  ALA*     4.3     5.6    -      -       +      -
    149D  GLN*     5.0     0.2    -      -       -      -
    152D  LEU*     3.7    14.8    -      -       +      -
    173D  VAL*     3.4    28.3    -      -       +      -
    174D  GLU      3.8     2.9    -      -       -      -
    175D  GLY*     4.5     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 105 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187C  LYS*     5.8     3.1    -      -       -      -
     72D  LEU*     6.2     4.4    -      -       +      +
    103D  GLU*     4.5    22.0    -      -       +      +
    104D  PHE*     1.3    82.2    -      -       -      +
    106D  SER*     1.3    59.8    +      -       -      +
    114D  PRO*     6.1     4.3    -      -       +      -
    115D  PHE      3.8     3.6    -      -       -      -
    116D  PHE*     3.4    36.6    -      +       +      -
    140D  ASP*     5.6     1.0    +      -       -      -
    143D  ALA*     3.4    19.7    -      -       -      +
    144D  ARG*     4.4     8.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 106 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104D  PHE*     4.3     5.2    -      -       -      -
    105D  TYR*     1.3    74.0    -      -       -      +
    107D  MET*     1.3    70.8    +      -       -      +
    114D  PRO*     3.1    10.1    -      -       -      +
    115D  PHE*     2.9    52.0    +      -       -      +
    143D  ALA*     2.7    30.0    +      -       -      -
    145D  ARG      3.4     6.1    +      -       -      -
    147D  GLN*     3.5    17.5    -      -       -      +
    152D  LEU*     4.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 107 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  TRP*     3.6    28.7    -      -       +      +
     72D  LEU*     3.6    38.1    -      -       +      +
    106D  SER*     1.3    80.0    +      -       -      +
    108D  CYS*     1.3    60.6    +      -       -      +
    112D  LEU      3.6    14.4    -      -       -      +
    113D  LEU      3.6     5.6    -      -       -      -
    114D  PRO*     3.5    37.9    -      -       +      -
    115D  PHE*     3.6     4.8    -      -       -      -
    145D  ARG      3.7    10.9    +      -       -      +
    146D  LEU*     3.5    15.7    -      -       +      -
    147D  GLN      2.7    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 108 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107D  MET*     1.3    70.7    -      -       -      +
    109D  GLU*     1.3    58.6    +      -       -      +
    110D  HIS      4.2     0.2    -      -       -      +
    111D  HIS*     3.2    19.5    -      -       -      -
    112D  LEU*     2.7    36.5    +      -       -      +
    113D  LEU      2.9    23.9    +      -       -      +
    115D  PHE*     3.6    14.1    -      -       +      -
    147D  GLN      3.3     6.1    -      -       -      +
    177D  HIS*     5.1     1.1    -      -       -      +
    179D  CYS*     4.1     5.2    -      -       -      -
    824D  8DG      3.6    18.2    -      -       +      +
   1004D   ZN      2.4    36.8    -      -       -      -
----------------------------------------------------------
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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