Contacts of the strand formed by residues 395 - 403 (chain A) in PDB entry 1BU8


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 395 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  TYR*     3.9    18.8    -      -       +      -
    359A  LEU*     4.7     5.2    -      -       +      -
    360A  TYR      3.6    16.8    -      -       -      +
    361A  GLY*     4.1     1.1    -      -       -      -
    392A  VAL*     3.6    21.1    -      -       +      -
    393A  GLY      3.1     4.9    +      -       -      +
    394A  GLU*     1.3    72.7    -      -       -      +
    396A  GLN*     1.3    61.1    +      -       -      +
    397A  LYS      3.7     9.2    -      -       -      +
    398A  VAL*     4.1     6.7    -      -       +      -
    422A  VAL*     3.5    31.2    -      -       +      -
    430A  TYR*     3.6    39.3    -      -       +      -
    432A  PHE*     3.5    36.1    -      -       +      -
    448A  PRO*     5.5     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 396 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  TYR      2.8     8.2    +      -       -      +
    361A  GLY*     3.6     5.2    +      -       -      +
    362A  ASN*     3.5    33.7    +      -       -      +
    394A  GLU*     3.2    34.2    +      -       -      +
    395A  ILE*     1.3    73.4    -      -       -      +
    397A  LYS*     1.3    66.3    +      -       +      +
    432A  PHE*     3.4     5.2    -      -       -      -
    447A  TYR*     5.0     0.7    -      -       -      -
    448A  PRO*     3.3    28.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 397 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  TYR*     2.9    62.0    +      -       +      +
    395A  ILE*     3.7     1.4    -      -       -      +
    396A  GLN*     1.3    82.2    -      -       +      +
    398A  VAL*     1.3    69.0    +      -       -      +
    399A  LYS*     4.3    19.0    -      -       -      +
    432A  PHE*     3.4    10.1    -      -       -      -
    445A  SER*     5.0     5.5    +      -       -      +
    446A  LEU      3.4    12.6    -      -       -      +
    447A  TYR*     4.0    34.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 398 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357A  VAL*     4.3     6.3    -      -       +      -
    358A  ALA      3.3     9.2    -      -       -      +
    359A  LEU*     4.1    12.8    -      -       +      -
    360A  TYR*     4.6     0.7    -      -       -      +
    395A  ILE*     4.1     2.5    -      -       +      -
    397A  LYS*     1.3    81.4    -      -       -      +
    399A  LYS*     1.3    68.7    +      -       -      +
    420A  ILE*     4.0    22.9    -      -       +      -
    422A  VAL*     3.9    18.6    -      -       +      -
    432A  PHE*     3.6    33.8    -      -       +      -
    445A  SER*     3.6     1.6    -      -       -      -
    446A  LEU*     2.9    48.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 399 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  LEU      3.9     0.2    -      -       -      +
    357A  VAL*     3.2    10.9    -      -       -      +
    358A  ALA*     2.9    33.1    +      -       +      +
    360A  TYR*     3.4    49.1    +      -       +      +
    397A  LYS*     4.3    18.2    -      -       -      +
    398A  VAL*     1.3    79.5    -      -       -      +
    400A  PHE*     1.3    59.6    +      -       -      +
    443A  LEU*     3.9    39.4    -      -       +      +
    444A  GLN      3.1     7.6    -      -       -      +
    445A  SER*     3.6    24.0    -      -       -      +
    446A  LEU*     4.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 400 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344A  VAL*     4.0    12.3    -      -       +      -
    346A  LEU*     3.7    22.4    -      -       +      -
    355A  ILE*     3.6    39.0    -      -       +      -
    356A  LEU      3.5     8.5    -      -       -      -
    357A  VAL*     4.7     2.7    -      -       +      +
    399A  LYS*     1.3    74.1    -      -       -      +
    401A  LEU*     1.3    68.6    +      -       -      +
    402A  TRP*     4.1    15.5    -      +       +      -
    415A  LEU*     4.0    10.5    -      -       +      -
    416A  GLY*     3.6    21.8    -      -       -      -
    417A  ALA*     3.8    10.8    -      -       +      -
    420A  ILE*     4.1     8.3    -      -       +      -
    438A  VAL*     4.8     1.8    -      -       +      -
    442A  VAL      3.6     1.4    -      -       -      +
    443A  LEU*     3.5     2.7    -      -       -      -
    444A  GLN*     2.8    61.2    +      -       +      +
    446A  LEU*     3.9    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 401 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  ILE*     3.5     2.4    -      -       -      +
    356A  LEU*     2.8    47.2    +      -       +      +
    368A  GLN*     3.4    25.8    -      -       +      +
    399A  LYS      5.6     0.2    -      -       -      +
    400A  PHE*     1.3    82.0    -      -       -      +
    402A  TRP*     1.3    69.6    +      -       -      +
    403A  ASN*     3.6    26.7    -      -       -      +
    441A  ASP*     3.4    12.6    -      -       -      +
    442A  VAL      3.3    41.5    -      -       -      +
    443A  LEU*     3.9    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 402 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  LEU*     3.4    33.0    -      -       +      -
    352A  SER      4.5     9.2    -      -       -      -
    354A  TYR      3.1    11.7    -      -       -      +
    355A  ILE*     4.1     5.6    -      -       +      -
    376A  LEU*     4.1    11.9    -      -       +      -
    400A  PHE*     4.1     7.9    -      +       +      -
    401A  LEU*     1.3    79.3    -      -       -      +
    403A  ASN*     1.3    86.6    +      -       -      +
    404A  ASN*     5.4     3.1    -      -       +      -
    413A  PRO*     3.5    40.4    -      -       +      -
    414A  THR*     4.2     0.9    -      -       -      -
    415A  LEU*     3.5    40.2    -      -       +      +
    438A  VAL*     3.0    24.5    +      -       +      -
    439A  ARG      3.4    10.0    +      -       -      -
    440A  GLU*     3.5    23.5    -      -       +      -
    441A  ASP      2.8    26.0    +      -       -      +
    442A  VAL      4.8     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 403 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  GLY*     3.0     5.9    -      -       -      -
    354A  TYR*     2.7    57.6    +      -       -      +
    356A  LEU*     3.9    10.2    -      -       -      +
    401A  LEU*     3.6    17.2    -      -       -      +
    402A  TRP*     1.3    85.7    -      -       -      +
    404A  ASN*     1.3    60.6    +      -       -      +
    440A  GLU*     4.5     5.8    -      -       +      -
    441A  ASP*     3.3    27.3    +      -       -      +
----------------------------------------------------------
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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