Contacts of the strand formed by residues 131 - 141 (chain E) in PDB entry 6D6Q


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 HIS 131 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66E  MET*     4.5    19.3    -      -       +      -
     67E  GLY      3.8     9.0    -      -       -      -
     69E  PRO*     4.2     4.3    -      -       -      +
    125E  CYS*     4.5     1.6    -      -       -      -
    126E  ILE*     3.9    11.6    +      -       +      -
    127E  SER*     3.0    34.0    +      -       -      +
    130E  GLU*     1.3   100.5    +      -       +      +
    132E  CYS*     1.3    66.1    +      -       -      +
    170E  VAL*     3.6    33.5    -      -       +      +
    178E  LYS*     3.6    38.1    +      -       +      +
    180E  ILE*     5.8     3.2    -      -       +      +
     14K  GLY      5.4     6.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 132 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66E  MET*     3.4     7.1    -      -       -      +
     67E  GLY      2.9    37.0    +      -       -      +
     69E  PRO*     3.8    19.7    -      -       +      -
     76E  GLU*     3.7     7.0    -      -       -      -
     77E  GLY*     3.1    37.2    -      -       -      -
     78E  TYR*     6.0     0.2    -      -       +      -
    124E  LEU      3.1    18.8    -      -       -      -
    125E  CYS*     4.0     6.1    -      -       -      -
    126E  ILE*     4.6    10.5    -      -       -      +
    131E  HIS*     1.3    79.8    -      -       -      +
    133E  TRP*     1.3    73.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 133 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64E  ALA*     4.0    21.1    -      -       +      -
     65E  GLU      3.3    20.2    -      -       -      -
     66E  MET*     3.6    20.6    -      -       +      -
     77E  GLY*     3.7    11.8    -      -       -      -
     78E  TYR*     3.8     1.3    +      -       -      -
    123E  THR      4.8     3.0    +      -       -      -
    124E  LEU*     3.0    60.4    +      -       +      +
    125E  CYS      5.2     0.2    -      -       -      -
    126E  ILE*     4.0    17.7    -      -       +      +
    132E  CYS*     1.3    87.7    -      -       -      +
    134E  VAL*     1.3    72.6    +      -       -      +
    135E  LEU*     5.8     0.9    -      -       +      -
    165E  ILE*     3.4    24.7    -      -       +      +
    166E  PRO*     3.0    40.6    +      -       +      -
    168E  VAL*     3.8    25.4    -      -       +      -
    190E  ILE*     5.1     4.8    -      -       +      +
     16K  VAL*     4.1     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 134 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63E  LYS      3.3     4.0    -      -       -      +
     64E  ALA*     3.4     2.1    -      -       -      -
     65E  GLU*     2.9    42.9    +      -       +      +
     66E  MET      4.2     1.6    -      -       -      +
     67E  GLY*     4.1    19.5    -      -       -      +
     78E  TYR*     3.2    50.0    -      -       +      +
     80E  GLU*     6.0     0.2    -      -       +      -
    132E  CYS      4.5     0.4    -      -       -      +
    133E  TRP*     1.3    82.6    -      -       -      +
    135E  LEU*     1.3    63.3    +      -       -      +
    136E  TYR*     3.2    32.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 135 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62E  VAL*     4.5    16.8    -      -       +      -
     63E  LYS      3.6     2.0    -      -       -      -
     64E  ALA*     4.0    25.6    -      -       +      -
     78E  TYR      3.0    13.8    +      -       -      +
     79E  LEU*     3.5    30.9    -      -       +      -
     80E  GLU*     2.9    29.2    +      -       -      +
    119E  VAL*     4.8     3.4    -      -       +      -
    124E  LEU*     4.3    18.2    -      -       +      -
    133E  TRP*     5.8     0.7    -      -       +      -
    134E  VAL*     1.3    70.8    -      -       -      +
    136E  TYR*     1.3    61.2    +      -       -      +
    137E  VAL*     3.4     8.9    +      -       +      +
    160E  LEU*     5.3     8.1    -      -       +      -
    163E  THR*     4.7     4.5    -      -       +      -
    165E  ILE*     4.0    17.0    -      -       +      -
    192E  LEU*     4.1    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 136 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  ARG*     3.3    46.9    -      -       -      +
     61E  GLY      3.9     0.5    -      -       -      +
     62E  VAL*     3.5     2.1    -      -       -      -
     63E  LYS*     2.9    39.8    +      -       +      +
     65E  GLU*     2.9    39.6    +      -       +      -
     67E  GLY*     6.0     0.7    -      -       -      -
     78E  TYR*     4.1    11.6    +      +       -      -
     80E  GLU*     3.8    32.1    -      -       +      -
    134E  VAL*     3.2    29.9    +      -       +      +
    135E  LEU*     1.3    69.4    -      -       -      +
    137E  VAL*     1.3    62.3    +      -       -      +
    138E  ASP*     4.3     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 137 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  ARG*     4.9     0.5    +      -       -      -
     60E  VAL*     4.3    16.2    -      -       +      -
     61E  GLY      3.5     8.5    -      -       -      +
     62E  VAL*     4.1    19.1    -      -       +      -
     79E  LEU*     5.1     3.4    -      -       +      -
     80E  GLU      2.9     9.4    +      -       -      +
     81E  PHE*     3.3    42.6    -      -       +      -
     82E  PHE      2.9    22.3    +      -       -      -
    135E  LEU*     4.1    10.8    -      -       +      +
    136E  TYR*     1.3    72.7    -      -       -      +
    138E  ASP*     1.3    74.0    +      -       -      +
    139E  VAL*     4.1     9.6    -      -       +      -
    156E  VAL*     4.7     6.7    -      -       +      -
    160E  LEU*     4.8    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 138 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  THR*     2.4    33.5    +      -       +      +
     80B  PHE*     3.7    30.9    +      -       +      +
     85B  ARG*     3.4    31.7    +      -       -      -
     60E  VAL*     3.5     2.3    -      -       -      -
     61E  GLY      2.9    35.6    +      -       -      +
     63E  LYS*     4.7     2.6    -      -       -      +
     82E  PHE*     3.5    10.4    -      -       +      +
    136E  TYR      4.4     5.9    -      -       -      +
    137E  VAL*     1.3    91.3    -      -       -      +
    139E  VAL*     1.3    66.2    +      -       -      +
    140E  LEU      4.0     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 139 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  PHE*     5.8     0.4    -      -       -      -
     58E  ILE*     4.2    12.1    -      -       +      -
     59E  LEU      3.7     8.3    -      -       -      +
     60E  VAL*     4.3    11.2    -      -       +      -
     81E  PHE*     5.3     0.2    -      -       +      -
     82E  PHE*     2.9    15.3    +      -       -      +
     83E  VAL*     3.6    19.5    -      -       +      -
     84E  ASP*     2.9    27.1    +      -       -      +
    109E  LEU*     4.3    17.3    -      -       +      -
    137E  VAL*     4.4    10.5    -      -       +      -
    138E  ASP*     1.3    76.9    -      -       -      +
    140E  LEU*     1.3    66.9    +      -       -      +
    141E  LEU*     4.2     5.2    -      -       +      -
    152E  ILE*     4.1    33.4    -      -       +      -
    156E  VAL*     4.7     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 140 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  ALA*     4.7     2.5    -      -       +      -
     80B  PHE*     4.1    17.7    -      -       +      -
    125B  GLN*     4.1    22.0    -      -       +      +
    127B  LEU*     3.2    35.2    -      -       +      -
     58E  ILE*     3.7     4.0    -      -       -      +
     59E  LEU*     2.9    47.6    +      -       +      +
     84E  ASP*     3.5    37.7    -      -       +      +
     86E  SER*     4.4     2.9    -      -       -      -
    139E  VAL*     1.3    76.5    -      -       -      +
    141E  LEU*     1.3    70.9    +      -       -      +
    142E  LEU*     4.2     9.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 141 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57E  ASP      4.4     0.9    -      -       -      -
     58E  ILE*     4.1    17.3    -      -       +      -
     83E  VAL*     4.6    10.5    -      -       +      -
     84E  ASP      3.0    13.8    +      -       -      +
     85E  CYS*     3.7    37.2    -      -       +      -
     86E  SER*     3.4    21.8    -      -       -      +
     89E  ALA*     5.0     6.1    -      -       +      -
    101E  LEU*     4.8     3.1    -      -       +      -
    102E  GLY*     6.2     0.2    -      -       -      -
    105E  ILE*     4.5    18.6    -      -       +      -
    139E  VAL*     4.8     4.0    -      -       +      -
    140E  LEU*     1.3    74.4    -      -       -      +
    142E  LEU*     1.3    71.4    +      -       -      +
    143E  GLU      4.7     6.7    -      -       -      +
    148E  LEU*     3.6    33.4    -      -       +      -
    152E  ILE*     4.4    10.1    -      -       +      -
----------------------------------------------------------
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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