Contacts of the strand formed by residues 140 - 148 (chain H) 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 LEU 140 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7E  SER*     5.0     4.4    -      -       -      +
     10E  GLU*     3.1    29.4    -      -       +      +
     85H  VAL*     4.6     4.7    -      -       +      -
     86H  GLY      3.2    17.0    -      -       -      +
     87H  ARG*     3.7    35.0    -      -       +      +
    139H  ASP*     1.3    77.0    -      -       -      +
    141H  ILE*     1.3    69.0    +      -       -      +
    165H  LYS*     3.5     8.0    -      -       -      +
    166H  LEU*     3.3    34.6    +      -       +      +
    171H  LEU*     4.0    15.5    -      -       +      -
    202H  PHE*     6.0     0.9    -      -       +      -
    204H  TRP*     3.2    29.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 141 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84H  VAL      5.1     0.2    -      -       -      +
     85H  VAL*     3.3     4.7    -      -       -      +
     86H  GLY*     2.9    50.0    +      -       -      +
     88H  ILE*     4.2     9.4    -      -       +      -
     98H  VAL*     4.6    13.0    -      -       +      -
    108H  LEU*     4.4    18.2    -      -       +      -
    113H  MET*     5.4     4.0    -      -       -      -
    135H  LEU*     3.8    30.3    -      -       +      -
    140H  LEU*     1.3    80.3    -      -       -      +
    142H  SER*     1.3    59.2    +      -       -      +
    143H  ALA*     3.7    24.9    -      -       +      +
    156H  LEU*     3.8    16.4    -      -       +      -
    164H  GLY      3.1    15.5    -      -       -      +
    166H  LEU*     3.3     4.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 142 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84H  VAL      3.5     8.3    -      -       -      -
     85H  VAL*     4.4     8.5    -      -       -      -
    141H  ILE*     1.3    71.6    -      -       -      +
    143H  ALA*     1.3    59.5    +      -       -      +
    162H  LYS      4.3     4.3    +      -       -      -
    163H  TYR*     3.1    29.1    -      -       -      +
    164H  GLY*     2.8    22.1    +      -       -      -
    165H  LYS      5.2     0.5    +      -       -      -
    166H  LEU*     3.1    22.9    -      -       -      +
    186H  PHE*     4.6    11.7    -      -       -      -
    196H  ILE*     4.5    13.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 143 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83H  ILE*     3.3     8.5    -      -       -      +
     84H  VAL*     2.9    30.1    +      -       -      +
    108H  LEU*     5.1     1.3    -      -       +      -
    141H  ILE*     3.7    11.3    -      -       +      -
    142H  SER*     1.3    75.6    -      -       -      +
    144H  GLU*     1.3    61.2    +      -       -      +
    156H  LEU*     3.4    28.5    -      -       +      -
    157H  HIS      3.1    19.1    -      -       -      +
    158H  THR*     4.4     6.7    -      -       +      -
    163H  TYR*     4.2     9.1    -      -       -      -
    186H  PHE*     5.4     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 144 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81H  GLY*     4.0    14.7    -      -       -      +
     82H  ASP      3.5    11.9    -      -       -      +
     83H  ILE*     3.8     8.7    -      -       +      +
     84H  VAL*     4.4     1.8    -      -       -      -
    143H  ALA*     1.3    75.5    -      -       -      +
    145H  VAL*     1.3    70.4    +      -       -      +
    156H  LEU*     3.5     4.3    -      -       -      +
    157H  HIS*     3.1    34.7    +      -       -      +
    159H  ARG*     2.6    47.5    +      -       -      +
    163H  TYR*     3.3    33.5    +      -       +      -
    576M  VAL*     4.9     9.7    -      -       -      +
    577M  GLU      5.0     2.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 145 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76H  TYR*     4.5    17.9    -      -       +      +
     79H  GLU      2.9    29.6    -      -       -      +
     80H  VAL*     3.2    22.0    -      -       -      +
     81H  GLY*     4.5     1.3    -      -       -      -
     82H  ASP      2.9    21.2    +      -       -      +
     84H  VAL*     4.9     9.6    -      -       +      -
    144H  GLU*     1.3    79.0    -      -       -      +
    146H  GLN*     1.3    63.2    +      -       -      +
    147H  ALA      3.5    14.6    -      -       -      +
    154H  VAL*     3.4    32.5    -      -       +      -
    156H  LEU*     3.9     8.5    -      -       +      -
    157H  HIS*     3.6     9.2    -      -       -      -
    159H  ARG*     5.8     0.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 146 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80H  VAL*     4.1    10.2    -      -       -      +
    109H  LEU*     5.3     2.8    -      -       -      +
    112H  SER*     3.8    15.7    +      -       -      -
    144H  GLU      3.5     1.0    +      -       -      -
    145H  VAL*     1.3    74.7    -      -       -      +
    147H  ALA*     1.3    63.3    +      -       +      +
    155H  SER*     2.8    38.2    +      -       -      +
    156H  LEU*     4.0     2.3    -      -       -      +
    157H  HIS*     3.0    28.1    -      -       -      +
    238M  ARG*     3.6    28.0    +      -       +      +
    239M  GLY      3.7     4.4    +      -       -      -
    240M  SER*     3.7    30.7    +      -       -      +
    241M  GLU*     4.3     4.2    -      -       -      +
    244M  ARG*     4.7     2.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 147 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80H  VAL*     5.0     5.6    -      -       -      -
    145H  VAL*     3.5     5.6    -      -       -      +
    146H  GLN*     1.3    85.5    -      -       +      +
    148H  VAL*     1.3    66.5    +      -       -      +
    149H  PHE*     4.3     2.2    -      -       +      -
    154H  VAL*     3.6     3.3    -      -       -      -
    155H  SER*     2.9    35.3    +      -       -      +
    238M  ARG*     3.6    18.8    -      -       -      +
     25O    C      3.8    21.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 148 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77H  ILE*     6.4     0.4    -      -       +      -
     78H  GLY*     3.3    36.1    -      -       -      +
     79H  GLU      3.4    19.5    -      -       -      +
     80H  VAL*     4.7     7.7    -      -       +      +
    145H  VAL*     4.6     1.3    -      -       +      -
    147H  ALA*     1.3    78.9    -      -       -      +
    149H  PHE*     1.3    72.7    +      -       -      +
    152H  GLY*     4.0    11.9    -      -       -      +
    153H  ALA      3.5    12.6    -      -       -      +
    154H  VAL*     4.7     2.0    -      -       +      -
   1012M  LYS*     6.0     1.4    -      -       -      -
     25O    C      3.4    16.1    +      -       -      +
----------------------------------------------------------
 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