Contacts of the strand formed by residues 205 - 210 (chain A) in PDB entry 1W3U


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 THR 205 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  LEU      3.6     0.3    -      -       -      +
     72A  PHE*     3.5     4.5    -      -       -      -
     73A  ILE*     2.7    49.0    +      -       -      +
     74A  GLN      5.0     0.7    -      -       -      -
     76A  GLY*     3.0    48.3    +      -       -      +
     77A  ALA*     3.8     1.5    +      -       -      +
     80A  GLN*     3.9    20.9    -      -       +      -
    193A  ALA      3.4    23.8    -      -       -      +
    194A  GLY*     4.2     1.4    -      -       -      -
    204A  VAL*     1.3    76.1    +      -       -      +
    206A  VAL*     1.3    68.4    +      -       -      +
    207A  VAL*     3.7     3.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  LEU*     3.7    25.8    -      -       +      -
     70A  VAL*     4.4     4.0    -      -       +      -
     71A  LEU      3.6     7.2    -      -       -      +
     72A  PHE*     4.2    19.3    -      -       +      -
    178A  ILE*     4.8     6.7    -      -       +      -
    192A  TYR*     3.1     5.4    -      -       -      +
    193A  ALA*     2.8    42.2    +      -       +      +
    195A  ALA*     5.0     4.3    -      -       +      -
    199A  LEU*     3.7    26.5    -      -       +      -
    204A  VAL*     4.1     5.1    -      -       +      -
    205A  THR*     1.3    71.6    -      -       -      +
    207A  VAL*     1.3    64.2    +      -       -      +
    208A  ILE*     3.9    20.2    -      -       +      -
    248A  VAL*     4.9     6.3    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     69A  LYS      3.6     1.4    -      -       -      +
     70A  VAL*     3.7     0.3    -      -       -      -
     71A  LEU*     2.7    50.9    +      -       +      +
     73A  ILE*     3.7    22.0    -      -       +      -
     80A  GLN*     3.6    33.2    -      -       +      +
    190A  LEU*     3.9    33.9    -      -       +      -
    191A  VAL      3.4     4.3    -      -       -      +
    192A  TYR*     4.1     2.7    -      -       +      -
    205A  THR*     4.2     5.4    -      -       +      +
    206A  VAL*     1.3    78.8    -      -       -      +
    208A  ILE*     1.3    63.0    +      -       -      +
    209A  VAL*     4.6     0.9    -      -       +      -
    227A  TYR*     4.0    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  LEU*     3.5    29.6    -      -       +      -
     59A  LEU*     4.4     2.0    -      -       +      -
     62A  LEU*     4.0    13.9    -      -       +      -
     68A  TYR*     4.2    11.7    -      -       +      -
     69A  LYS      3.4     9.2    -      -       -      +
     70A  VAL*     4.3    16.4    -      -       +      -
    178A  ILE*     4.4     7.6    -      -       +      -
    185A  LEU*     3.6    28.1    -      -       +      +
    189A  GLY      4.6     0.2    -      -       -      -
    190A  LEU*     3.2     3.6    -      -       -      +
    191A  VAL*     2.8    58.1    +      -       +      +
    206A  VAL*     3.9    16.4    -      -       +      -
    207A  VAL*     1.3    75.8    -      -       -      +
    209A  VAL*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  TYR*     3.4     5.6    -      -       -      -
     69A  LYS*     2.9    43.0    +      -       +      +
     71A  LEU*     3.8    23.8    -      -       +      -
     88A  PHE*     4.6     2.7    -      -       +      -
    189A  GLY      3.5    10.3    -      -       -      +
    190A  LEU*     4.0    21.8    -      -       +      -
    207A  VAL*     4.6     3.1    -      -       +      -
    208A  ILE*     1.3    76.1    -      -       -      +
    210A  ARG*     1.3    76.3    -      -       -      +
    211A  GLU*     3.3     1.1    +      -       -      +
    213A  LEU*     4.9     1.1    -      -       +      -
    214A  VAL*     3.7    37.0    -      -       +      -
    227A  TYR*     5.3     0.9    -      -       +      -
    231A  VAL*     4.4     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  GLY*     3.6     9.2    -      -       -      +
     68A  TYR*     2.9    40.5    +      -       +      -
    169A  PRO*     6.0     2.0    -      -       -      +
    186A  ASN*     3.2    27.1    +      -       -      +
    187A  GLN      4.2     2.8    +      -       -      -
    188A  PHE      3.1    23.8    +      -       -      +
    189A  GLY*     2.8    24.3    +      -       -      +
    209A  VAL*     1.3    74.8    -      -       -      +
    211A  GLU*     1.3    61.6    +      -       -      +
    212A  ASP*     2.8    35.4    -      -       -      +
    213A  LEU*     2.9    38.2    +      -       +      +
    214A  VAL      3.8     1.0    +      -       -      -
----------------------------------------------------------
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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