Contacts of the strand formed by residues 163 - 174 (chain A) in PDB entry 6K0X


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 163 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  GLU*     3.2    13.7    -      -       -      +
    116A  VAL*     3.4    12.8    -      -       +      +
    119A  LEU*     3.8    21.5    -      -       +      +
    159A  VAL*     3.1    36.9    +      -       +      +
    161A  ASP      3.7     0.2    -      -       -      -
    162A  LEU*     1.3    76.6    -      -       -      +
    164A  SER*     1.3    67.9    +      -       -      +
    167A  GLY      3.7    15.0    -      -       -      +
    168A  LEU      3.6    27.1    -      -       -      +
    169A  PHE*     4.0    10.5    -      -       +      +
    191A  LEU*     4.2    17.9    -      -       +      -
    211A  PHE      4.1     7.2    -      -       -      +
    213A  LYS*     3.4    26.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  GLU*     3.2    20.4    +      -       -      +
    115A  LYS*     4.2     4.7    -      -       -      -
    116A  VAL      2.9    14.8    +      -       -      -
    117A  ASP*     2.7    27.2    +      -       -      -
    162A  LEU      3.4     1.8    +      -       -      -
    163A  LEU*     1.3    80.9    -      -       -      +
    165A  PRO*     1.3    69.6    -      -       -      +
    166A  ARG*     3.4     5.5    -      -       -      +
    167A  GLY*     2.8    29.5    +      -       -      -
    213A  LYS*     3.9     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  GLU*     4.3    16.4    -      -       +      +
    163A  LEU      4.8     0.2    -      -       -      +
    164A  SER*     1.3    89.3    -      -       -      +
    166A  ARG*     1.3    59.4    +      -       +      +
    167A  GLY      3.4     0.5    +      -       -      -
    212A  THR*     5.0     1.2    -      -       -      +
    213A  LYS*     3.7    25.1    +      -       +      +
    214A  SER*     4.7     9.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  GLU      3.9    16.9    +      -       -      -
     45A  GLY*     3.1    44.1    +      -       -      +
     46A  VAL*     3.3     8.1    -      -       -      +
     47A  GLU*     6.1     1.3    -      -       -      -
    117A  ASP*     3.1    43.0    +      -       -      +
    164A  SER*     3.4    13.0    -      -       -      +
    165A  PRO*     1.3    78.2    -      -       +      +
    167A  GLY*     1.3    63.5    +      -       -      +
    168A  LEU*     3.7    14.3    +      -       -      +
    212A  THR*     4.6     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  VAL      3.9     7.6    -      -       -      -
    117A  ASP      3.2    12.1    -      -       -      -
    163A  LEU*     3.7    12.4    -      -       -      +
    164A  SER*     2.8    26.9    +      -       -      +
    165A  PRO      3.2     0.8    -      -       -      -
    166A  ARG*     1.3    79.2    -      -       -      +
    168A  LEU*     1.3    59.0    +      -       -      -
    212A  THR*     3.4    25.6    -      -       -      +
    213A  LYS      3.9     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  GLU*     3.8    34.8    -      -       +      +
     43A  LEU*     3.6    28.0    -      -       +      -
    117A  ASP      2.9    11.4    +      -       -      +
    118A  LEU*     3.5     5.5    -      -       +      +
    119A  LEU      2.8    26.3    +      -       -      +
    163A  LEU*     3.6     5.1    -      -       -      +
    166A  ARG*     3.9     9.9    -      -       -      +
    167A  GLY*     1.3    76.5    -      -       -      +
    169A  PHE*     1.3    59.6    +      -       -      +
    170A  TYR*     3.7    28.0    -      -       +      +
    210A  LYS*     4.2     6.1    -      -       +      -
    211A  PHE      3.4     3.4    -      -       -      +
    212A  THR*     3.6    33.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  LEU*     3.3    24.9    -      -       +      -
    121A  PHE*     3.9    10.5    -      -       +      -
    155A  PHE*     3.6    31.2    -      +       -      -
    156A  PHE*     4.6     7.4    -      +       -      -
    159A  VAL*     3.7    37.2    -      -       +      -
    163A  LEU*     4.0     5.6    -      -       +      +
    168A  LEU*     1.3    72.5    -      -       -      +
    170A  TYR*     1.3    75.7    +      -       -      +
    171A  LEU*     3.8    25.8    -      -       +      -
    186A  MET*     3.9    10.3    -      -       +      -
    209A  LEU      3.6     1.2    -      -       -      +
    210A  LYS*     3.3     4.3    -      -       -      -
    211A  PHE*     2.7    70.7    +      +       +      +
----------------------------------------------------------
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Residues in contact with TYR 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  LEU*     4.1    17.2    -      -       +      +
     35A  ALA*     4.7    11.7    -      -       +      -
     36A  LEU*     3.7    23.6    -      -       +      -
     39A  ALA*     3.2    27.9    -      -       +      +
     43A  LEU*     4.5     2.0    -      -       +      -
    118A  LEU*     3.7    24.7    -      -       +      -
    119A  LEU      2.9     9.3    +      -       -      +
    120A  VAL*     3.5     7.4    -      -       +      +
    121A  PHE      3.0    26.0    +      -       -      +
    168A  LEU*     3.7    20.9    -      -       +      +
    169A  PHE*     1.3    79.0    -      -       -      +
    171A  LEU*     1.3    60.7    +      -       -      +
    196A  ALA*     4.3     9.4    -      -       +      -
    208A  VAL*     3.9    19.1    -      -       +      -
    209A  LEU      3.3     2.7    -      -       -      -
    210A  LYS*     3.6    42.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  PHE*     3.3    22.9    -      -       +      +
    123A  PRO*     3.9    19.7    -      -       +      -
    152A  MET*     4.5     5.4    -      -       +      -
    156A  PHE*     3.8    32.8    -      -       +      -
    169A  PHE*     3.8    23.8    -      -       +      -
    170A  TYR*     1.3    74.3    -      -       -      +
    172A  VAL*     1.3    69.2    +      -       -      +
    173A  THR*     3.6    20.4    +      -       +      -
    182A  ILE*     4.1    11.4    -      -       +      -
    207A  SER      3.6     0.3    -      -       -      +
    208A  VAL*     3.3     4.7    -      -       -      +
    209A  LEU*     2.8    40.3    +      -       +      +
    211A  PHE*     4.4    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  ASP*     4.1    12.1    -      -       +      +
     31A  LEU*     5.2     0.7    -      -       +      -
     32A  LEU*     3.8    41.3    -      -       +      -
    121A  PHE      3.1     6.3    +      -       -      -
    122A  ASN*     3.3    31.4    -      -       +      +
    123A  PRO*     3.2    22.9    -      -       -      +
    125A  TYR*     4.3     6.2    -      -       +      -
    152A  MET*     4.6     0.3    -      -       -      +
    171A  LEU*     1.3    74.6    -      -       -      +
    173A  THR*     1.3    68.8    +      -       -      +
    206A  LEU*     4.1    26.7    -      -       +      -
    207A  SER      3.6     4.7    -      -       -      +
    208A  VAL*     4.4    10.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  TYR*     5.0     1.8    -      -       -      -
    152A  MET*     4.5     2.2    -      -       -      -
    171A  LEU*     3.6    26.5    -      -       +      -
    172A  VAL*     1.3    82.7    -      -       -      +
    174A  ILE*     1.3    68.3    -      -       -      +
    177A  ASN*     3.5    13.9    -      -       -      +
    179A  PRO*     3.9    14.4    -      -       -      +
    182A  ILE*     3.9    17.3    -      -       +      -
    206A  LEU*     3.2     9.4    -      -       -      +
    207A  SER*     2.8    48.4    +      -       -      -
    209A  LEU*     4.0    12.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  TYR*     3.5    48.7    -      -       +      +
    126A  VAL*     4.6     6.7    -      -       +      -
    127A  VAL*     4.9     3.6    -      -       +      +
    173A  THR*     1.3    74.4    -      -       -      +
    175A  LYS*     1.3    62.9    +      -       -      +
    176A  GLU*     3.4    32.3    -      -       +      +
    177A  ASN*     2.8    46.7    +      -       -      +
    179A  PRO*     3.9     7.4    -      -       -      +
    204A  GLU*     4.0    20.2    -      -       +      +
    205A  THR      3.3     8.7    -      -       -      +
    206A  LEU*     3.5    20.2    -      -       +      -
    207A  SER      5.5     0.4    -      -       -      -
----------------------------------------------------------
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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