Contacts of the strand formed by residues 779 - 788 (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 THR 779 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238A  LEU      2.7    25.2    +      -       -      -
    239A  TYR      4.4     0.9    -      -       -      -
    577A  ASP*     3.7     0.7    -      -       -      +
    578A  LYS*     3.1    53.7    +      -       +      +
    778B  THR*     1.3    81.9    +      -       -      +
    780B  TRP*     1.3    67.9    +      -       -      +
    800B  GLU*     3.8    17.7    -      -       +      +
    801B  VAL      3.2    10.8    -      -       -      +
    802B  THR*     3.2    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 780 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    575A  ALA*     4.8    10.1    -      -       +      -
    576A  VAL*     3.7     7.9    -      -       -      -
    577A  ASP*     3.5    36.8    -      -       +      -
    578A  LYS*     4.6     0.2    -      -       -      -
    746B  PRO      3.4    25.8    -      -       -      -
    747B  GLU      4.4     1.6    -      -       -      -
    749B  TRP*     3.2    43.0    -      +       +      -
    773B  LEU*     4.6    13.4    -      -       +      +
    774B  LYS*     4.0    18.9    +      -       +      +
    776B  SER*     3.4    39.1    +      -       -      -
    778B  THR*     4.3     8.4    +      -       +      -
    779B  THR*     1.3    73.9    -      -       -      +
    781B  GLU*     1.3    60.6    +      -       -      +
    782B  ILE*     4.1     4.7    -      -       +      -
    799B  PHE      3.7     0.4    -      -       -      +
    800B  GLU*     3.1     7.1    -      -       -      +
    801B  VAL*     2.8    39.2    +      -       +      +
    803B  VAL*     3.8    29.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 781 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    574A  VAL      3.6     3.6    -      -       -      +
    576A  VAL*     2.9    36.6    +      -       -      +
    578A  LYS*     4.3    10.7    -      -       +      +
    581A  PHE*     3.1    36.5    -      -       +      -
    588A  LYS*     3.3    16.0    +      -       -      -
    780B  TRP*     1.3    73.8    -      -       -      +
    782B  ILE*     1.3    62.9    +      -       -      +
    783B  LEU*     3.7     3.9    +      -       +      +
    798B  PRO*     3.7    32.6    -      -       +      +
    799B  PHE      3.6     2.0    -      -       -      +
    800B  GLU*     3.9    23.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 782 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    543A  VAL*     4.7    14.1    -      -       +      +
    561A  LEU*     3.8    34.1    -      -       +      -
    573A  LEU*     4.7     8.5    -      -       +      -
    574A  VAL      3.4    12.1    -      -       -      +
    575A  ALA*     4.0    15.7    -      -       +      -
    749B  TRP*     6.1     1.3    -      -       +      -
    750B  LEU*     4.2    18.6    -      -       +      -
    771B  ILE*     4.6     7.9    -      -       +      -
    780B  TRP*     5.1     3.8    -      -       +      -
    781B  GLU*     1.3    74.8    -      -       -      +
    783B  LEU*     1.3    67.5    +      -       -      +
    784B  ALA*     4.1     1.5    +      -       +      +
    797B  ASP      4.6     0.7    -      -       -      +
    798B  PRO*     3.5     5.2    -      -       -      +
    799B  PHE*     2.8    52.6    +      -       +      +
    801B  VAL*     4.5    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 783 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  GLN*     3.8    23.6    +      -       +      +
    572A  VAL      3.8     1.2    -      -       -      +
    573A  LEU*     3.7     4.9    -      -       -      +
    574A  VAL*     3.0    42.3    +      -       +      +
    588A  LYS*     5.4    11.2    -      -       -      +
    589A  LEU*     4.2    25.4    -      -       +      +
    781B  GLU*     3.7     4.2    +      -       +      +
    782B  ILE*     1.3    73.9    -      -       -      +
    784B  ALA*     1.3    65.5    -      -       -      +
    785B  VAL*     4.8     2.7    -      -       +      -
    795B  VAL*     3.9    15.0    -      -       +      -
    796B  ALA      3.6    24.2    -      -       -      +
    798B  PRO*     4.4    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 784 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541A  LEU*     3.8    13.9    -      -       +      -
    543A  VAL*     3.6    30.7    -      -       +      -
    571A  VAL*     4.1     2.9    -      -       +      -
    572A  VAL      3.7     3.4    -      -       -      -
    573A  LEU*     3.7    15.9    -      -       +      -
    782B  ILE*     4.1     2.5    +      -       +      +
    783B  LEU*     1.3    77.0    -      -       -      +
    785B  VAL*     1.3    69.3    +      -       -      +
    795B  VAL*     3.7     1.4    -      -       -      +
    796B  ALA*     2.9    32.3    +      -       +      +
    797B  ASP      5.8     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 785 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  GLN*     4.5    19.3    -      -       -      +
    128A  PHE*     3.7    30.9    -      -       +      -
    541A  LEU*     3.8     1.6    -      -       -      -
    570A  ARG      3.6     1.7    -      -       -      +
    571A  VAL*     3.4     3.4    -      -       -      +
    572A  VAL*     3.1    42.5    +      -       +      +
    589A  LEU*     4.7     5.6    -      -       +      -
    783B  LEU*     4.8     3.8    -      -       +      -
    784B  ALA*     1.3    79.6    -      -       -      +
    786B  SER*     1.3    62.5    +      -       -      +
    787B  MET*     4.0     1.2    +      -       +      +
    793B  ILE*     4.0    24.5    -      -       +      -
    794B  CYS      3.5     5.2    -      -       -      +
    795B  VAL*     4.0    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 786 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    540A  SER      4.9     2.5    +      -       -      -
    541A  LEU*     3.3    24.3    -      -       -      +
    565A  GLY*     5.9     0.2    -      -       -      -
    566A  ASP*     5.4     6.4    +      -       -      -
    569A  ALA*     4.5    12.1    -      -       -      -
    570A  ARG      3.4     5.2    -      -       -      -
    571A  VAL*     4.0    13.0    -      -       -      -
    785B  VAL*     1.3    73.7    -      -       -      +
    787B  MET*     1.3    61.2    +      -       -      +
    788B  SER*     3.9     1.5    -      -       -      -
    792B  GLY      3.6     1.6    +      -       -      +
    793B  ILE*     3.3     6.9    -      -       -      +
    794B  CYS*     3.0    47.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 787 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  PHE*     3.6    35.0    -      -       +      -
    130A  VAL*     3.8    22.7    -      -       +      -
    136A  PRO*     4.0    21.1    -      -       +      -
    164A  LEU*     3.2    40.4    -      -       +      +
    165A  GLY      3.8     8.5    -      -       -      +
    166A  VAL*     4.2    10.5    -      -       +      -
    568A  GLY      5.1     0.3    -      -       -      +
    569A  ALA*     4.2     0.4    -      -       -      -
    570A  ARG*     2.9    30.9    +      -       +      +
    785B  VAL      5.3     0.7    -      -       -      +
    786B  SER*     1.3    72.7    -      -       -      +
    788B  SER*     1.3    58.0    +      -       -      +
    789B  ASP      4.1     0.3    +      -       -      -
    792B  GLY      4.0     0.2    -      -       -      -
    793B  ILE*     3.6    33.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 788 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  PRO*     3.4     8.1    -      -       -      +
    566A  ASP*     4.6     6.0    -      -       -      +
    567A  HIS      4.3     9.0    +      -       -      -
    568A  GLY      5.0     1.6    -      -       -      -
    569A  ALA*     3.5    26.5    +      -       -      +
    786B  SER*     3.9     1.1    -      -       -      -
    787B  MET*     1.3    75.6    -      -       -      +
    789B  ASP*     1.3    63.0    +      -       -      +
    790B  LYS*     3.1    15.8    +      -       -      +
    791B  LYS*     3.5    21.0    +      -       -      +
    792B  GLY*     2.9    37.2    +      -       -      -
----------------------------------------------------------
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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