Contacts of the strand formed by residues 186 - 194 (chain B) in PDB entry 1O0W


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 186 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184B  PRO*     3.6    27.0    -      -       -      +
    185B  PRO*     1.3    83.5    -      -       -      +
    187B  TYR*     1.3    64.5    +      -       -      +
    188B  ILE*     4.5    15.0    -      -       +      -
    204B  GLU      3.5     1.0    -      -       -      +
    205B  VAL*     3.1     5.4    -      -       -      -
    206B  ARG*     2.7    50.0    +      -       +      +
    208B  ASN      5.8     4.0    -      -       -      +
    209B  GLY      6.1     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170B  LYS*     3.9    25.0    +      -       +      +
    173B  LEU*     3.6    12.5    -      -       -      +
    185B  PRO*     4.2    19.4    -      -       +      +
    186B  GLU*     1.3    75.8    +      -       -      +
    188B  ILE*     1.3    69.3    +      -       -      +
    189B  LEU      4.2     0.7    +      -       -      -
    203B  VAL*     4.0     7.2    -      -       +      -
    204B  GLU      3.5     2.0    -      -       -      -
    205B  VAL*     3.4    29.2    -      -       +      -
    224B  GLU*     3.6    62.5    -      -       +      +
    227B  ALA*     4.7     0.2    -      -       +      -
    228B  ALA*     3.5    20.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 188 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  GLU*     4.5    12.6    -      -       +      +
    187B  TYR*     1.3    88.9    -      -       -      +
    189B  LEU*     1.3    65.5    +      -       -      +
    190B  VAL*     3.0    21.0    +      -       +      +
    203B  VAL*     4.0     3.1    -      -       -      +
    204B  GLU      2.8    37.5    +      -       -      +
    206B  ARG*     3.6    45.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 189 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187B  TYR      4.2     1.4    +      -       -      -
    188B  ILE*     1.3    75.7    -      -       -      +
    190B  VAL*     1.3    59.1    +      -       -      +
    191B  ARG*     3.3    20.4    -      -       -      +
    192B  THR*     3.6    21.1    -      -       +      -
    201B  PHE*     3.6    28.9    -      -       +      -
    202B  VAL      3.2    20.2    -      -       -      +
    203B  VAL*     4.0     8.9    -      -       +      +
    220B  LYS*     2.8    34.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188B  ILE*     3.0    18.4    +      -       +      +
    189B  LEU*     1.3    74.6    -      -       -      +
    191B  ARG*     1.3    76.9    +      -       -      +
    202B  VAL*     2.9    34.5    +      -       +      +
    204B  GLU*     3.5    36.3    -      -       +      +
    206B  ARG*     3.7    15.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  LEU*     3.3     9.9    -      -       -      +
    190B  VAL*     1.3   102.0    +      -       +      +
    192B  THR*     1.3    73.2    +      -       -      +
    193B  GLU*     3.0    24.6    +      -       -      +
    202B  VAL*     2.7    57.2    +      -       +      +
    216B  LYS*     4.2    13.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 192 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  LEU*     3.6    26.0    -      -       +      -
    191B  ARG*     1.3    86.6    -      -       -      +
    193B  GLU*     1.3    66.3    +      -       -      +
    199B  ARG*     3.3    36.4    +      -       -      +
    200B  ILE      3.4     7.0    -      -       -      -
    201B  PHE*     3.7    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 193 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191B  ARG*     3.0    34.1    +      -       +      -
    192B  THR*     1.3    77.7    -      -       -      +
    194B  LYS*     1.3    58.3    +      -       -      +
    195B  ASN*     3.0    27.1    +      -       -      +
    199B  ARG*     3.1     8.8    -      -       -      +
    200B  ILE*     2.5    54.1    +      -       +      +
    202B  VAL*     3.3    14.2    -      -       -      +
    216B  LYS*     5.2     2.9    +      -       -      +
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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
----------------------------------------------------------
    193B  GLU*     1.3    71.4    -      -       -      +
    195B  ASN*     1.3    64.2    +      -       -      +
    196B  ASP*     3.7     9.2    +      -       -      +
    197B  GLY      5.4     1.1    -      -       -      +
    198B  ASP*     3.0    18.4    -      -       -      +
    199B  ARG*     4.0     5.2    -      -       +      +
----------------------------------------------------------
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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