Contacts of the strand formed by residues 416 - 424 (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 GLY 416 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346A  LEU*     3.3    13.7    -      -       -      +
    347A  SER*     2.8    40.2    +      -       -      +
    400A  PHE*     3.6     8.7    -      -       -      -
    415A  LEU*     1.3    76.4    -      -       -      +
    417A  ALA*     1.3    59.5    +      -       -      -
    436A  ASP      4.0     8.5    -      -       -      -
    437A  THR*     4.0     0.8    -      -       -      +
    444A  GLN*     3.4    13.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 417 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344A  VAL*     3.6    28.9    -      -       +      -
    345A  THR      3.2     7.6    -      -       -      +
    347A  SER*     3.9     2.1    +      -       -      -
    400A  PHE*     3.8    15.7    -      -       +      -
    416A  GLY*     1.3    73.6    -      -       -      -
    418A  SER*     1.3    63.3    +      -       -      +
    419A  GLN      4.5     0.2    -      -       -      +
    420A  ILE*     3.8    18.4    -      -       +      -
    434A  SER*     3.9     3.5    -      -       -      +
    436A  ASP      4.6     0.2    -      -       -      +
    444A  GLN*     3.0    24.6    -      -       -      +
    446A  LEU*     3.6     8.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 418 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345A  THR*     3.0    25.6    +      -       -      +
    346A  LEU      4.2     2.8    +      -       -      -
    347A  SER*     3.8    18.9    +      -       -      -
    417A  ALA*     1.3    73.9    -      -       -      +
    419A  GLN*     1.3    64.6    +      -       -      +
    433A  CYS*     3.2     7.4    -      -       -      +
    434A  SER      3.0    36.9    +      -       -      +
    446A  LEU*     4.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 419 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  SER      4.0     0.3    -      -       -      +
    344A  VAL*     3.7     0.2    -      -       -      -
    345A  THR*     2.9    36.7    +      -       -      +
    417A  ALA      3.3     0.4    -      -       -      -
    418A  SER*     1.3    86.3    +      -       -      +
    420A  ILE*     1.3    74.3    +      -       -      +
    421A  THR*     3.8     5.1    +      -       -      +
    431A  ASN*     3.5    22.3    +      -       -      -
    432A  PHE      3.2    16.6    -      -       -      +
    433A  CYS*     4.0    14.5    -      -       -      -
    446A  LEU*     4.2     1.3    -      -       -      -
    449A  CYS*     4.6     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 420 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342A  VAL*     4.0    15.9    -      -       +      -
    343A  SER      3.1    10.3    -      -       -      +
    344A  VAL*     3.8    12.6    -      -       +      -
    357A  VAL*     4.0    23.8    -      -       +      -
    398A  VAL*     4.0    28.5    -      -       +      -
    400A  PHE*     4.1    12.3    -      -       +      -
    417A  ALA*     3.8    23.1    -      -       +      -
    419A  GLN*     1.3    80.4    -      -       -      +
    421A  THR*     1.3    71.3    +      -       -      +
    422A  VAL*     4.0    11.4    -      -       +      -
    431A  ASN*     3.6     1.7    -      -       -      -
    432A  PHE*     2.9    34.3    +      -       -      -
    446A  LEU*     4.0     7.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 421 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  LYS      3.6     1.6    -      -       -      +
    342A  VAL*     3.4     4.0    -      -       -      -
    343A  SER*     2.9    45.2    +      -       -      +
    419A  GLN*     3.8     8.7    +      -       -      -
    420A  ILE*     1.3    75.1    -      -       -      +
    422A  VAL*     1.3    67.6    +      -       -      +
    423A  GLN*     4.8     2.2    -      -       +      +
    429A  GLU*     3.9    32.3    -      -       +      +
    430A  TYR      3.2     7.0    -      -       -      +
    431A  ASN*     2.8    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 422 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  TYR*     3.9    22.9    -      -       +      -
    341A  LYS      3.4     2.9    -      -       -      -
    342A  VAL*     4.2     8.5    -      -       +      -
    359A  LEU*     3.8    28.9    -      -       +      -
    395A  ILE*     3.5    27.6    -      -       +      -
    398A  VAL*     3.9    18.8    -      -       +      -
    420A  ILE*     4.0    10.5    -      -       +      -
    421A  THR*     1.3    79.3    -      -       -      +
    423A  GLN*     1.3    60.9    -      -       -      +
    430A  TYR*     2.8    39.3    +      -       -      +
    432A  PHE*     4.4     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 423 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  PHE*     3.6    15.0    +      -       +      -
    298A  PRO*     3.6    21.3    -      -       -      +
    340A  TYR*     3.4     9.8    -      -       -      +
    341A  LYS*     3.0    55.7    +      -       +      +
    421A  THR*     5.2     2.5    -      -       +      -
    422A  VAL*     1.3    74.3    -      -       -      +
    424A  SER*     1.3    67.7    +      -       -      +
    427A  GLY*     3.0    36.0    -      -       -      +
    428A  LYS      3.2     4.5    -      -       -      +
    429A  GLU*     3.9    23.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 424 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  PHE*     3.9     0.7    -      -       -      -
    298A  PRO*     4.0     0.2    -      -       -      +
    340A  TYR*     4.1    23.5    -      -       -      -
    422A  VAL      4.2     0.6    +      -       -      -
    423A  GLN*     1.3    74.8    -      -       -      +
    425A  GLY*     1.3    60.4    +      -       -      +
    426A  VAL*     3.5     8.4    -      -       -      +
    427A  GLY*     3.1    48.4    +      -       -      -
    428A  LYS*     3.0    18.1    +      -       -      +
    430A  TYR*     4.0    12.4    +      -       -      -
----------------------------------------------------------
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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