Contacts of the strand formed by residues 189 - 199 (chain X) in PDB entry 2W6C


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 X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107X  LYS      4.4     3.3    -      -       -      +
    108X  SER*     4.5     1.5    +      -       -      -
    109X  THR      3.6     3.1    -      -       -      -
    111X  VAL*     3.5    19.3    -      -       -      -
    142X  VAL*     4.0     8.3    -      -       -      +
    184X  ILE*     3.1    18.6    +      -       -      +
    185X  GLN*     3.3    22.2    -      -       -      +
    187X  PHE      3.3     4.2    +      -       -      -
    188X  GLY*     1.3    80.3    -      -       -      +
    190X  ASP*     1.3    59.8    +      -       -      -
    191X  PRO*     3.9     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 190 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108X  SER*     3.5    28.3    +      -       -      +
    109X  THR      2.9    21.1    +      -       -      +
    111X  VAL*     3.5     6.6    -      -       -      +
    189X  GLY*     1.3    69.9    -      -       -      -
    191X  PRO*     1.3    65.5    -      -       -      +
    192X  LYS*     2.6    49.9    +      -       -      +
    193X  THR*     2.9    40.6    +      -       -      -
    194X  VAL      4.1     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 191 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108X  SER*     5.5     0.7    -      -       -      +
    181X  HIS*     3.4    43.1    -      -       +      +
    184X  ILE*     3.9    18.8    -      -       +      -
    185X  GLN*     4.5    21.3    -      -       +      +
    189X  GLY      3.9     7.4    -      -       -      +
    190X  ASP*     1.3    85.8    -      -       -      +
    192X  LYS*     1.3    67.8    +      -       +      +
    193X  THR      3.2     1.6    -      -       -      -
    194X  VAL*     3.4    19.2    -      -       +      +
    218X  LEU      6.1     0.3    -      -       -      -
    219X  PHE*     5.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 192 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108X  SER*     4.8     4.6    +      -       -      -
    190X  ASP*     2.6    39.2    +      -       -      +
    191X  PRO*     1.3    85.1    -      -       +      +
    193X  THR*     1.3    52.2    +      -       -      +
    194X  VAL      3.8     1.3    -      -       -      -
    220X  ARG*     2.6    45.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 193 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110X  THR*     3.8    20.7    -      -       +      +
    111X  VAL      3.3    19.6    +      -       -      +
    190X  ASP*     2.9    32.3    +      -       -      -
    192X  LYS*     1.3    83.8    +      -       -      +
    194X  VAL*     1.3    61.3    +      -       -      +
    195X  THR      3.7     0.9    +      -       -      -
    220X  ARG*     4.0    12.9    +      -       +      +
    221X  ARG*     4.2     7.0    -      -       -      +
    477X  ALA      3.6    22.6    -      -       -      +
    478X  LYS      4.1    11.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 194 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111X  VAL*     3.3    18.8    -      -       +      +
    113X  VAL*     4.2    20.4    -      -       +      -
    177X  LEU*     5.1     2.0    -      -       +      -
    180X  VAL*     4.6    13.7    -      -       +      -
    181X  HIS*     5.7     2.5    -      -       -      -
    190X  ASP      4.2     1.1    -      -       -      +
    191X  PRO*     3.4    31.6    -      -       +      +
    192X  LYS      3.8     1.4    -      -       -      -
    193X  THR*     1.3    74.7    -      -       -      +
    195X  THR*     1.3    63.6    +      -       -      +
    196X  ILE*     4.3     3.4    -      -       +      -
    218X  LEU      4.4     6.5    -      -       -      +
    219X  PHE*     3.7    25.7    -      -       +      +
    220X  ARG*     2.7    35.0    +      -       -      +
    221X  ARG      3.4     2.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 195 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111X  VAL      2.9     9.4    +      -       -      -
    112X  MET*     3.4     7.2    -      -       +      +
    113X  VAL*     2.9    24.6    +      -       -      +
    193X  THR      3.7     0.4    +      -       -      -
    194X  VAL*     1.3    72.1    -      -       -      +
    196X  ILE*     1.3    76.9    +      -       -      +
    197X  PHE*     3.9     2.7    +      -       +      +
    221X  ARG*     3.3    23.2    +      -       +      +
    222X  ALA      4.3     0.2    -      -       -      +
    223X  ILE*     4.0    27.6    -      -       +      -
    476X  PHE*     4.6     1.3    -      -       +      -
    477X  ALA*     3.0    42.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 196 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113X  VAL*     3.5    13.0    -      -       +      +
    115X  ILE*     4.5     6.1    -      -       +      -
    177X  LEU*     3.5    31.9    -      -       +      -
    194X  VAL*     4.0     2.1    +      -       +      -
    195X  THR*     1.3    76.3    -      -       -      +
    197X  PHE*     1.3    60.8    +      -       -      +
    206X  VAL*     3.8    36.1    -      -       +      +
    209X  HIS*     4.2    13.7    -      -       +      -
    219X  PHE*     3.8    52.9    -      -       +      -
    221X  ARG      3.0     6.2    +      -       -      +
    222X  ALA*     3.3     1.4    -      -       -      +
    223X  ILE      2.9    24.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 197 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112X  MET*     3.8    32.1    -      -       +      -
    113X  VAL      3.0    21.2    +      -       -      -
    114X  TRP*     3.3    58.2    -      +       +      -
    115X  ILE*     2.8    24.3    +      -       -      +
    135X  LEU*     4.4     2.9    -      -       +      -
    143X  LEU*     4.1    14.4    -      -       +      -
    195X  THR*     4.4     1.1    -      -       +      -
    196X  ILE*     1.3    75.3    -      -       -      +
    198X  GLY*     1.3    59.5    +      -       -      +
    206X  VAL*     3.9     6.2    -      -       -      +
    223X  ILE*     3.2    30.7    -      -       +      -
    225X  GLN*     3.6    14.4    -      -       -      -
    447X  VAL*     3.9    20.6    -      -       +      -
    448X  PHE*     4.0    10.5    -      +       -      -
    473X  TRP*     4.0    12.6    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 198 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114X  TRP*     3.5    11.6    -      -       -      -
    115X  ILE      3.2    16.4    -      -       -      -
    197X  PHE*     1.3    77.6    -      -       -      +
    199X  GLU*     1.3    58.7    +      -       -      -
    202X  GLY      3.8     7.4    -      -       -      -
    203X  GLY*     3.2    12.7    -      -       -      -
    206X  VAL*     3.8     2.6    -      -       -      +
    223X  ILE      3.4     4.9    +      -       -      -
    225X  GLN*     2.9    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 199 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114X  TRP*     3.7    12.8    -      -       +      -
    115X  ILE      3.8     2.8    +      -       -      -
    117X  GLY*     3.0     7.8    -      -       -      -
    198X  GLY*     1.3    73.9    -      -       -      -
    200X  SER*     1.3   104.4    +      -       -      +
    202X  GLY      3.0     8.8    +      -       -      -
    203X  GLY      3.3     0.6    -      -       -      +
    225X  GLN*     3.1    14.4    -      -       -      +
    226X  SER*     4.3     2.6    -      -       -      -
    440X  HIS*     3.5    17.2    +      -       -      -
    441X  GLY*     3.5    18.6    +      -       -      -
    443X  GLU*     3.2    23.1    -      -       -      +
    444X  ILE*     3.7    25.6    -      -       +      +
    601X  BM4      3.5    17.3    -      -       -      +
----------------------------------------------------------
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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