Contacts of the strand formed by residues 200 - 207 (chain A) 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 ILE 200 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192A  THR*     2.9     7.3    -      -       -      -
    193A  GLU*     2.5    59.9    +      -       +      +
    195A  ASN*     3.6    39.3    -      -       +      +
    196A  ASP*     4.4     5.6    -      -       -      +
    198A  ASP*     3.7    12.1    -      -       +      +
    199A  ARG*     1.3    80.5    -      -       -      +
    201A  PHE*     1.3    73.8    +      -       -      +
    202A  VAL*     4.7     1.1    -      -       +      -
    216A  LYS*     4.0    20.0    -      -       +      -
    217A  GLY*     3.4    13.5    -      -       -      +
    218A  ARG*     5.3     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  LEU*     3.7    25.6    -      -       +      -
    191A  ARG      3.9     3.4    -      -       -      -
    192A  THR*     3.6    19.5    -      -       +      -
    199A  ARG*     4.0    39.9    -      -       +      -
    200A  ILE*     1.3    76.5    -      -       -      +
    202A  VAL*     1.3    60.9    +      -       -      +
    216A  LYS*     3.3     4.2    -      -       -      -
    217A  GLY      2.9    29.2    +      -       -      -
    218A  ARG      3.5    17.0    -      -       -      -
    219A  THR*     3.5    35.2    -      -       -      +
    220A  LYS*     3.7    18.4    -      -       +      -
    223A  ALA*     3.2    10.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  LEU*     3.6     3.1    -      -       -      +
    190A  VAL*     2.8    37.7    +      -       +      +
    191A  ARG*     2.9    58.5    +      -       +      +
    193A  GLU*     3.8    20.0    -      -       +      -
    200A  ILE*     4.5     1.1    -      -       +      +
    201A  PHE*     1.3    76.7    -      -       -      +
    203A  VAL*     1.3    60.2    +      -       -      +
    214A  THR*     3.4    29.6    -      -       +      -
    215A  GLY      3.5     4.0    -      -       -      +
    216A  LYS*     4.2    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187A  TYR*     4.1    10.8    -      -       +      -
    188A  ILE      3.2    17.9    -      -       -      +
    189A  LEU*     4.0    23.6    -      -       +      +
    202A  VAL*     1.3    78.1    -      -       -      +
    204A  GLU*     1.3    73.5    +      -       -      +
    214A  THR*     3.3     2.8    -      -       -      +
    215A  GLY      2.7    41.6    +      -       -      +
    220A  LYS*     4.3     5.8    -      -       +      +
    223A  ALA*     3.6    28.0    -      -       +      -
    224A  GLU*     4.0    28.9    -      -       +      -
    227A  ALA*     3.6     4.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  GLU      3.6     1.2    -      -       -      +
    187A  TYR*     3.6     1.9    -      -       -      -
    188A  ILE*     3.0    32.4    +      -       -      +
    190A  VAL*     3.4    31.6    -      -       +      +
    191A  ARG*     5.8     1.0    +      -       -      -
    203A  VAL*     1.3    76.9    -      -       -      +
    205A  VAL*     1.3    61.5    +      -       -      +
    206A  ARG*     2.8    36.7    +      -       -      +
    211A  THR*     3.1    23.4    +      -       +      +
    213A  ALA      3.2     9.2    -      -       -      +
    214A  THR*     3.7    17.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  LEU*     3.6    24.2    -      -       +      -
    185A  PRO*     3.8    11.2    -      -       +      -
    186A  GLU      3.3     7.9    -      -       -      +
    187A  TYR*     3.6    27.8    -      -       +      +
    203A  VAL      4.2     0.6    +      -       -      -
    204A  GLU*     1.3    75.0    -      -       -      +
    206A  ARG*     1.3    64.0    +      -       -      +
    207A  VAL*     5.9     0.4    -      -       +      -
    211A  THR*     3.7     0.7    -      -       -      -
    212A  ILE*     2.8    27.9    +      -       +      -
    213A  ALA      2.8    19.1    +      -       -      +
    227A  ALA*     3.8    11.9    -      -       +      +
    231A  ALA*     3.4    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  PRO*     3.5     6.4    -      -       -      +
    186A  GLU*     2.8    57.5    +      -       +      +
    188A  ILE*     3.6    31.9    -      -       +      +
    190A  VAL*     3.9    13.1    -      -       -      +
    204A  GLU*     2.8    33.2    +      -       +      +
    205A  VAL*     1.3    80.6    -      -       -      +
    207A  VAL*     1.3    64.4    +      -       -      +
    209A  GLY*     3.9    16.6    +      -       -      -
    210A  LYS      3.1    11.7    -      -       -      +
    211A  THR*     3.4    17.5    +      -       -      +
    212A  ILE      4.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  LEU*     6.5     0.2    -      -       +      -
    177A  VAL*     3.6    42.6    -      -       +      -
    181A  HIS*     3.6    29.8    -      -       +      +
    183A  VAL*     4.1     9.6    -      -       +      -
    184A  PRO      5.0     3.6    -      -       -      +
    185A  PRO*     4.8     3.8    -      -       +      -
    186A  GLU*     4.2     0.4    -      -       -      -
    205A  VAL*     5.9     0.9    -      -       +      -
    206A  ARG*     1.3    79.0    -      -       -      +
    208A  ASN*     1.3    78.5    -      -       -      +
    209A  GLY      3.2     0.2    -      -       -      -
    210A  LYS*     2.9    22.7    +      -       -      +
    212A  ILE*     3.5    26.2    -      -       +      -
    235A  LEU*     5.4     2.7    -      -       +      -
----------------------------------------------------------
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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