Contacts of the strand formed by residues 46 - 55 (chain A) in PDB entry 6BCH


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 46 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  VAL*     3.6    23.1    -      -       +      -
     37A  SER      3.4     7.6    -      -       -      -
     38A  LYS*     3.2    42.4    -      -       +      -
     39A  ASP*     3.7     1.3    +      -       -      +
     42A  ARG*     3.2    17.3    -      -       -      +
     44A  THR*     3.2    25.1    +      -       -      -
     45A  GLY*     1.3    90.2    +      -       -      +
     47A  SER*     1.3    60.5    +      -       -      +
     48A  VAL*     4.2     1.8    +      -       -      +
    127A  HIS*     5.6     1.4    -      -       -      +
    128A  LEU*     6.0     1.6    -      -       -      +
    133A  LEU*     3.9    19.2    -      -       +      +
    150A  GLU      5.5     0.7    -      -       -      -
    151A  LEU*     3.6    26.2    -      -       +      -
    154A  ALA*     3.7    18.2    -      -       +      -
    155A  PHE*     3.1    38.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  THR*     3.3     2.1    -      -       -      +
     36A  VAL*     3.2     5.9    -      -       -      +
     37A  SER*     2.8    50.4    +      -       -      -
     39A  ASP*     4.0     9.5    +      -       -      +
     42A  ARG*     3.8    31.0    -      -       -      +
     46A  TRP*     1.3    74.6    -      -       -      +
     48A  VAL*     1.3    61.2    +      -       -      +
     49A  ARG*     6.0     2.0    -      -       -      -
      5C    T      5.9     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LEU*     5.1     3.1    -      -       +      -
     35A  THR      3.2     4.0    -      -       -      +
     36A  VAL*     3.6    20.6    -      -       +      -
     46A  TRP      4.2     2.6    +      -       -      +
     47A  SER*     1.3    78.5    -      -       -      +
     49A  ARG*     1.3    67.7    +      -       -      +
     50A  PRO*     4.6     1.2    -      -       -      +
    122A  ILE*     3.8    20.0    -      -       +      +
    127A  HIS*     4.3    25.7    +      -       +      +
    133A  LEU*     3.5    31.6    -      -       +      -
    136A  ILE*     3.7    35.7    -      -       +      -
      4C    A      5.4     1.2    +      -       -      -
      5C    T      5.5     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LEU*     3.4     8.5    -      -       -      -
     35A  THR*     2.9    51.2    +      -       -      +
     47A  SER*     6.0     1.8    -      -       -      -
     48A  VAL*     1.3    78.1    -      -       -      +
     50A  PRO*     1.3    72.0    +      -       +      +
     51A  ARG*     3.5    28.0    -      -       -      +
     87A  GLU*     3.1    34.7    +      -       -      +
      5C    T      4.1    40.4    -      -       +      +
      6C    G      2.8    39.8    +      -       -      -
      7C    C      3.6     0.8    -      -       -      +
     21X    G      3.3    16.7    +      -       -      -
     22X    C      4.1     5.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  MET      3.5     5.6    -      -       -      +
     34A  LEU*     3.8    11.4    -      -       +      -
     48A  VAL      4.6     0.2    -      -       -      +
     49A  ARG*     1.3    92.5    +      -       +      +
     51A  ARG*     1.3    64.3    +      -       -      +
     87A  GLU*     3.9    14.8    -      -       -      +
     89A  LEU*     5.0     4.9    -      -       +      -
     92A  LEU*     3.5    25.1    -      -       +      +
    115A  PHE*     3.5    22.7    -      -       +      -
    119A  PHE*     4.5    15.0    -      -       +      -
    122A  ILE*     3.8    27.6    -      -       +      -
      5C    T      5.7     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  SER      4.5     0.2    -      -       -      -
     32A  PHE*     3.6     1.0    -      -       -      -
     33A  MET*     2.9    66.4    +      -       +      +
     35A  THR*     2.8    28.8    +      -       -      +
     49A  ARG*     3.5    27.7    -      -       -      +
     50A  PRO*     1.3    81.6    -      -       +      +
     52A  PHE*     1.3    61.3    +      -       -      +
     53A  ARG*     4.7     6.7    -      -       +      +
     86A  PHE      3.6     7.6    -      -       -      +
     87A  GLU*     3.1    32.5    +      -       +      +
    115A  PHE*     3.2    12.5    -      -       -      -
      7C    C      3.4     5.1    -      -       -      +
      8C    T      4.6     0.2    +      -       -      -
     20X    A      3.6    19.0    +      -       -      +
     21X    G      2.9    45.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  ALA*     4.4     1.3    -      -       +      -
     30A  SER*     3.6    31.4    -      -       -      -
     31A  SER      3.5     6.5    -      -       -      -
     32A  PHE*     3.3    45.3    -      +       +      -
     51A  ARG*     1.3    75.1    -      -       -      +
     53A  ARG*     1.3    67.7    +      -       -      +
     54A  ILE*     4.2    18.2    -      -       +      -
     85A  ARG*     3.5     1.6    -      -       -      +
     86A  PHE*     2.9    68.2    +      +       +      +
     92A  LEU*     3.8    17.7    -      -       +      +
     95A  VAL*     3.8    17.7    -      -       +      -
     99A  PHE*     3.8    18.8    -      +       -      -
    115A  PHE*     4.7     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  SER*     3.4     5.0    -      -       -      -
     31A  SER*     2.9    36.0    +      -       -      +
     33A  MET*     3.6    31.0    -      -       +      +
     51A  ARG*     4.7     7.9    -      -       +      +
     52A  PHE*     1.3    79.8    -      -       -      +
     54A  ILE*     1.3    74.2    +      -       -      +
     55A  GLY*     5.0     0.4    -      -       -      +
     83A  ARG*     2.9    39.4    -      -       +      +
     84A  ILE      3.4    12.6    -      -       -      +
     85A  ARG*     4.3    17.3    -      -       +      +
     87A  GLU*     5.3     3.6    +      -       -      -
      8C    T      4.9     3.0    +      -       -      -
     18X    G      2.8    35.4    +      -       -      -
     19X    G      2.8    31.9    +      -       -      -
     20X    A      4.4     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ILE*     5.8     2.2    -      -       +      +
     25A  PHE*     4.4     8.1    -      -       +      +
     26A  ALA*     4.5    12.3    -      -       +      +
     29A  ASP*     5.2     4.5    -      -       +      +
     30A  SER*     3.6    21.1    -      -       -      +
     52A  PHE*     4.2    21.1    -      -       +      -
     53A  ARG*     1.3    83.5    -      -       -      +
     55A  GLY*     1.3    60.8    +      -       -      +
     56A  LEU*     3.6    30.7    -      -       +      -
     64A  LEU*     3.8    10.8    -      -       +      +
     67A  ILE*     4.1    25.8    -      -       +      -
     82A  ALA      3.7     0.3    -      -       -      +
     83A  ARG*     3.1     6.1    -      -       -      +
     84A  ILE*     2.9    50.4    +      -       +      -
     86A  PHE*     5.7     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  ASP*     4.2     5.9    +      -       -      +
     53A  ARG*     4.4     0.8    -      -       -      +
     54A  ILE*     1.3    73.2    -      -       -      +
     56A  LEU*     1.3    76.3    +      -       -      +
     81A  ASP*     5.1     4.5    -      -       -      -
     82A  ALA      3.2    10.5    -      -       -      -
     83A  ARG*     4.2    10.1    -      -       -      -
     16X    T      2.4    27.8    -      -       -      -
     17X    A      6.4     1.3    -      -       -      -
----------------------------------------------------------
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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