Contacts of the strand formed by residues 900 - 910 (chain B) in PDB entry 2WIN


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 SER 900 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    734B  ILE*     4.5     9.9    -      -       -      +
    738B  ASN      5.1     1.2    +      -       -      -
    739B  ILE*     3.7    31.4    -      -       -      +
    805B  GLN*     4.4     9.2    +      -       -      -
    807B  PHE*     4.4     6.9    -      -       -      +
    892B  ALA      3.4    15.0    -      -       -      -
    893B  ALA*     3.9     5.4    -      -       -      +
    899B  ILE*     1.3    86.7    -      -       -      +
    901B  ASP*     1.3    66.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 901 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    739B  ILE*     4.1     5.9    -      -       -      +
    740B  VAL      5.3     0.8    -      -       -      +
    742B  ARG*     2.8    49.9    +      -       -      +
    777B  ILE*     4.1     0.3    -      -       -      +
    805B  GLN*     4.2     7.1    -      -       -      +
    807B  PHE*     4.3     7.5    -      -       +      +
    808B  PHE*     3.0    34.4    -      -       -      +
    809B  ILE*     3.2    27.3    +      -       -      +
    892B  ALA      3.2    12.7    +      -       -      +
    900B  SER*     1.3    79.9    -      -       -      +
    902B  GLY*     1.3    71.1    +      -       -      +
    903B  VAL*     4.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 902 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    739B  ILE*     3.7     8.8    -      -       -      +
    740B  VAL      4.6     1.6    +      -       -      -
    741B  SER*     3.6    21.5    -      -       -      +
    742B  ARG*     2.7    26.5    +      -       -      +
    890B  VAL      3.3    10.5    -      -       -      -
    891B  LYS*     4.0     8.7    -      -       -      -
    901B  ASP*     1.3    83.4    +      -       -      +
    903B  VAL*     1.3    60.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 903 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    741B  SER*     3.9     2.0    -      -       -      -
    742B  ARG*     3.4    20.0    -      -       -      +
    745B  PHE*     4.0    10.1    -      -       +      -
    809B  ILE*     3.3    42.2    -      -       +      +
    811B  LEU*     3.6    28.3    -      -       +      +
    888B  VAL      3.7     1.9    -      -       -      +
    889B  GLU*     3.3     4.3    -      -       -      -
    890B  VAL*     2.8    35.6    +      -       +      -
    901B  ASP*     4.7     0.4    -      -       -      +
    902B  GLY*     1.3    75.0    -      -       -      -
    904B  ARG*     1.3    63.0    +      -       -      +
    905B  LYS*     3.7    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 904 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    741B  SER*     3.7    28.8    +      -       -      +
    742B  ARG      2.9    13.8    +      -       -      +
    743B  SER*     3.1    51.3    +      -       -      +
    887B  GLU*     3.0    46.2    +      -       +      +
    888B  VAL      3.7     2.7    -      -       -      -
    889B  GLU*     3.4    23.5    +      -       +      +
    903B  VAL*     1.3    72.3    -      -       -      +
    905B  LYS*     1.3    62.9    +      -       -      +
    906B  SER*     4.6     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 905 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    745B  PHE*     3.7    37.2    -      -       +      -
    810B  ASP*     4.0    13.9    +      -       -      +
    811B  LEU*     3.0    34.1    +      -       +      +
    812B  ARG*     5.1     4.9    -      -       -      +
    813B  LEU*     4.6    18.2    -      -       +      +
    887B  GLU*     3.8     1.4    -      -       -      +
    888B  VAL*     3.0    30.9    +      -       -      +
    903B  VAL*     3.7    23.6    -      -       +      +
    904B  ARG*     1.3    77.7    -      -       -      +
    906B  SER*     1.3    64.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 906 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    813B  LEU*     4.5     4.0    -      -       -      +
    885B  LEU*     3.6    26.9    -      -       -      +
    886B  GLN      3.1    19.6    +      -       -      -
    887B  GLU*     4.1    12.6    +      -       -      +
    904B  ARG      4.6     3.1    +      -       -      -
    905B  LYS*     1.3    79.4    +      -       -      +
    907B  LEU*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 907 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    813B  LEU*     3.6    36.3    -      -       +      -
    814B  PRO*     3.9    19.3    -      -       +      +
    815B  TYR      4.8     0.9    -      -       -      -
    817B  VAL*     3.6    40.8    -      -       +      -
    825B  ILE*     5.4     1.3    -      -       +      -
    850B  PHE*     3.6    30.3    -      -       +      -
    878B  ILE*     5.2     6.3    -      -       +      -
    885B  LEU*     3.8     4.0    -      -       -      -
    886B  GLN      3.2    27.6    +      -       -      +
    888B  VAL*     3.7     9.2    -      -       +      +
    906B  SER*     1.3    75.0    -      -       -      +
    908B  LYS*     1.3    61.2    +      -       -      +
    909B  VAL*     3.6     2.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 908 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  THR*     5.0     4.9    +      -       -      -
    119A  PRO      3.2    25.7    +      -       -      -
    120A  GLY*     4.7     3.4    -      -       -      -
    121A  SER      5.6     0.2    -      -       -      +
    175A  GLU*     3.3    17.0    +      -       -      +
    815B  TYR*     3.4    45.6    +      -       +      +
    816B  SER*     3.3    10.1    -      -       -      -
    817B  VAL*     3.1    25.8    +      -       -      +
    884B  GLY      4.3     4.0    -      -       -      -
    885B  LEU*     4.2    18.2    -      -       +      +
    907B  LEU*     1.3    73.8    -      -       -      +
    909B  VAL*     1.3    59.3    +      -       -      +
    910B  VAL*     3.9     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 909 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    817B  VAL*     3.5    24.7    -      -       +      +
    819B  ARG*     4.2    13.0    -      -       +      -
    850B  PHE*     4.7     2.2    -      -       +      -
    880B  PRO*     3.7    26.7    -      -       +      -
    882B  LYS      3.6    17.9    -      -       -      +
    883B  THR*     3.4    12.5    -      -       -      -
    884B  GLY*     3.1    31.7    +      -       -      +
    886B  GLN*     3.5    27.8    -      -       +      -
    907B  LEU*     3.9     8.3    -      -       +      +
    908B  LYS*     1.3    74.3    -      -       -      +
    910B  VAL*     1.3    59.4    +      -       -      +
    911B  PRO*     4.0     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 910 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    815B  TYR*     6.2     0.9    -      -       +      -
    816B  SER*     4.3    20.9    -      -       -      -
    817B  VAL      3.2     6.5    +      -       -      +
    818B  VAL*     3.3     7.4    -      -       -      +
    819B  ARG      3.3    17.8    +      -       -      -
    883B  THR*     4.7     1.1    -      -       -      -
    908B  LYS*     3.8     8.9    +      -       +      -
    909B  VAL*     1.3    78.3    -      -       -      +
    911B  PRO*     1.3    92.1    -      -       +      +
    913B  GLY*     5.6     4.3    -      -       -      +
   1327B  HIS*     5.3    14.8    -      -       +      +
----------------------------------------------------------
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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