Contacts of the strand formed by residues 338 - 347 (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 TRP 338 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A  ASN*     6.0     1.6    -      -       +      -
    278A  ASP*     3.0    29.0    +      -       +      +
    279A  GLY*     3.8    16.8    -      -       -      -
    281A  LEU*     5.7     5.4    -      -       +      -
    336A  THR*     3.5    32.3    -      -       +      -
    337A  ARG*     1.3    74.8    -      -       -      +
    339A  ARG*     1.3    60.3    +      -       -      +
    340A  TYR*     3.2    29.4    -      -       +      +
    387A  ASP*     4.4     1.3    -      -       -      -
    388A  VAL      2.8    30.8    +      -       -      -
    389A  ASP      3.8     6.7    -      -       -      -
    390A  ILE*     3.4    39.5    -      -       -      +
    391A  ASN*     3.6    40.4    -      -       +      +
    451A  NAG      5.3     6.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 339 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283A  TYR*     3.6    26.7    +      -       +      +
    291A  PHE*     3.2    64.5    +      -       -      -
    292A  GLN*     4.5     7.5    -      -       -      +
    294A  ASN*     4.5     3.0    +      -       -      -
    295A  ASP      5.5     0.4    +      -       -      -
    297A  PHE*     3.6    32.7    -      -       +      +
    328A  ASN*     4.1     1.2    +      -       -      -
    337A  ARG      4.2     0.6    -      -       -      -
    338A  TRP*     1.3    72.8    -      -       -      +
    340A  TYR*     1.3    67.2    +      -       -      +
    385A  ASP*     3.4    40.7    +      -       +      +
    386A  ILE      3.3     7.0    -      -       -      +
    387A  ASP*     2.8    48.9    +      -       -      +
    424A  SER*     4.5     0.2    -      -       -      -
    425A  GLY      3.6    10.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 340 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  PHE*     3.9     3.1    -      -       -      -
    338A  TRP*     3.2    41.9    -      +       +      +
    339A  ARG*     1.3    74.4    -      -       -      +
    341A  LYS*     1.3    60.5    +      -       -      +
    342A  VAL*     4.6     1.1    -      -       +      -
    359A  LEU*     4.0     8.5    -      -       +      -
    385A  ASP*     3.2     3.1    -      -       -      -
    386A  ILE*     2.8    44.1    +      -       +      +
    388A  VAL*     3.4    21.5    -      -       +      -
    390A  ILE      4.2     2.5    -      -       -      -
    391A  ASN*     3.4    24.4    +      -       -      -
    392A  VAL*     3.5    20.9    +      -       +      +
    393A  GLY      4.4     2.3    +      -       -      -
    395A  ILE*     3.9    18.4    -      -       +      -
    422A  VAL*     3.9    25.6    -      -       +      -
    423A  GLN      3.4    14.1    -      -       -      +
    424A  SER*     4.1    19.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  ASN*     2.9    27.9    +      -       -      +
    297A  PHE*     3.4    43.7    -      -       +      -
    340A  TYR*     1.3    71.6    -      -       -      +
    342A  VAL*     1.3    58.8    +      -       -      +
    343A  SER*     4.1     6.6    +      -       -      +
    383A  VAL*     3.6    21.9    -      -       +      +
    385A  ASP*     2.7    33.0    +      -       -      +
    421A  THR*     3.6     2.6    -      -       -      +
    422A  VAL*     3.4     4.2    -      -       -      -
    423A  GLN*     3.0    49.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  TYR*     4.3     1.1    -      -       +      +
    341A  LYS*     1.3    76.8    -      -       -      +
    343A  SER*     1.3    64.5    +      -       -      +
    344A  VAL*     4.0     4.0    -      -       +      -
    357A  VAL*     4.0    17.9    -      -       +      -
    359A  LEU*     4.5     5.6    -      -       +      -
    371A  ILE*     3.8    26.1    -      -       +      +
    382A  HIS      3.7     0.9    -      -       -      +
    383A  VAL*     3.2     5.1    -      -       -      +
    384A  ARG      2.9    33.4    +      -       -      +
    386A  ILE*     3.7    32.1    -      -       +      -
    420A  ILE*     4.0    21.8    -      -       +      -
    421A  THR      3.4     2.9    -      -       -      +
    422A  VAL*     4.2    19.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  LYS*     4.1     7.3    +      -       -      +
    342A  VAL*     1.3    72.5    -      -       -      +
    344A  VAL*     1.3    62.6    +      -       -      +
    381A  ARG*     3.5    25.6    +      -       -      -
    382A  HIS      3.3     4.3    -      -       -      -
    383A  VAL*     3.4    21.3    -      -       -      +
    419A  GLN      4.7     0.2    -      -       -      -
    420A  ILE*     3.1     8.5    -      -       -      +
    421A  THR*     2.9    49.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342A  VAL*     4.0     7.6    -      -       +      -
    343A  SER*     1.3    79.7    -      -       -      +
    345A  THR*     1.3    67.8    +      -       -      +
    346A  LEU*     3.9     6.9    +      -       +      -
    355A  ILE*     4.5    10.3    -      -       +      -
    357A  VAL*     3.7    28.9    -      -       +      -
    371A  ILE*     4.4    12.6    -      -       +      -
    380A  ALA      3.7     1.2    -      -       -      +
    381A  ARG*     3.1     4.2    -      -       -      +
    382A  HIS*     2.8    41.7    +      -       -      +
    400A  PHE*     4.0    17.0    -      -       +      -
    417A  ALA*     3.6    27.6    -      -       +      -
    419A  GLN      3.7     2.5    -      -       -      -
    420A  ILE*     3.8     6.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  SER      5.7     0.2    -      -       -      -
    344A  VAL*     1.3    72.2    -      -       -      +
    346A  LEU*     1.3    67.3    +      -       -      +
    379A  GLU*     4.3    13.7    -      -       -      +
    380A  ALA      3.5     9.4    -      -       -      +
    381A  ARG*     3.5    24.1    -      -       +      +
    417A  ALA*     3.2     5.0    -      -       -      +
    418A  SER*     3.0    41.0    +      -       -      +
    419A  GLN*     2.9    22.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344A  VAL*     4.3     7.0    -      -       +      -
    345A  THR*     1.3    79.5    -      -       -      +
    347A  SER*     1.3    59.1    +      -       -      +
    355A  ILE*     4.0    10.8    -      -       +      -
    376A  LEU*     4.0    18.4    -      -       +      -
    377A  LYS      3.6    37.9    -      -       -      +
    378A  PRO*     4.1     3.1    -      -       +      -
    379A  GLU*     2.7    27.1    +      -       -      +
    380A  ALA      2.9    12.6    +      -       -      +
    382A  HIS*     3.9    27.4    -      -       +      +
    400A  PHE*     3.7    27.8    -      -       +      -
    415A  LEU*     4.0     8.3    -      -       +      -
    416A  GLY      3.3    14.6    -      -       -      +
    418A  SER*     4.2     1.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346A  LEU*     1.3    76.4    -      -       -      +
    348A  GLY*     1.3    59.3    +      -       -      +
    378A  PRO*     4.0     8.5    -      -       -      -
    379A  GLU*     4.5     1.3    -      -       -      +
    415A  LEU*     3.5     8.1    -      -       -      +
    416A  GLY*     2.8    46.8    +      -       -      +
    417A  ALA      3.7     1.6    +      -       -      -
    418A  SER*     3.8    24.1    +      -       -      -
    434A  SER      5.4     0.2    +      -       -      -
    435A  SER      5.7     1.0    -      -       -      -
    436A  ASP      3.8    10.2    +      -       -      -
    437A  THR*     3.9     3.7    -      -       -      +
----------------------------------------------------------
 Back to top of page


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