Contacts of the strand formed by residues 162 - 173 (chain C) in PDB entry 5IXG


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 LYS 162 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ASP*     3.0    18.0    +      -       -      +
    101B  VAL*     6.3     3.1    -      -       +      -
    119B  LYS*     4.4    19.3    -      -       +      +
     21C  GLU      4.2     4.2    -      -       -      +
     22C  ALA*     4.6     6.8    -      -       -      -
     23C  ASP*     4.6     3.3    +      -       -      +
    143C  GLU*     3.1    36.6    +      -       +      +
    144C  PHE      3.6     7.9    -      -       -      +
    145C  SER*     4.5     4.2    +      -       -      +
    160C  LYS*     3.4    13.3    -      -       +      +
    161C  MET*     1.3    75.7    -      -       -      +
    163C  THR*     1.3    64.5    +      -       -      +
    164C  LYS*     4.3     7.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 163 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20C  PHE*     4.5     4.3    -      -       +      -
     21C  GLU      3.5    11.7    -      -       -      +
     22C  ALA*     4.8     6.3    -      -       +      +
    143C  GLU*     3.3     3.6    -      -       -      -
    144C  PHE*     2.7    62.6    +      -       +      -
    146C  ARG*     3.7    20.3    +      -       -      +
    161C  MET      3.0    13.5    +      -       -      -
    162C  LYS*     1.3    76.5    +      -       -      +
    164C  LYS*     1.3    68.4    +      -       -      +
    165C  LEU*     3.9     0.8    +      -       +      -
    201C  OTP      4.1    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 164 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20C  PHE*     3.1    10.2    -      -       -      +
     21C  GLU*     2.9    62.7    +      -       +      +
    141C  VAL*     4.4    17.9    -      -       -      +
    142C  GLY      3.6    11.0    -      -       -      +
    143C  GLU*     4.4    15.7    -      -       +      +
    162C  LYS*     4.2     7.9    +      -       -      +
    163C  THR*     1.3    72.9    -      -       -      +
    165C  LEU*     1.3    63.9    +      -       -      +
    166C  LEU*     3.8    31.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 165 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18C  PRO*     5.1     1.1    -      -       +      -
     19C  SER      3.4    11.0    -      -       -      +
     20C  PHE*     4.3     7.0    -      -       +      -
    107C  LEU*     5.0     0.7    -      -       +      -
    116C  LEU*     4.0    25.4    -      -       +      -
    118C  LEU*     4.6     7.2    -      -       +      -
    141C  VAL*     3.2     7.7    -      -       -      +
    142C  GLY      2.8    41.4    +      -       -      +
    144C  PHE*     3.8    28.3    -      -       +      -
    163C  THR*     5.1     0.2    -      -       +      -
    164C  LYS*     1.3    80.0    -      -       -      +
    166C  LEU*     1.4    64.2    +      -       -      +
    167C  ILE*     4.0    16.4    -      -       +      -
    201C  OTP      4.0    48.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 166 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17C  TYR      3.9     0.7    -      -       -      +
     19C  SER*     2.8    44.7    +      -       -      +
     20C  PHE*     4.4     3.4    -      -       -      -
     21C  GLU*     3.9    27.8    -      -       +      +
    140C  ALA      3.6     4.3    -      -       -      +
    141C  VAL*     4.5     5.8    -      -       +      -
    164C  LYS*     3.8    44.6    -      -       +      +
    165C  LEU*     1.4    78.1    -      -       -      +
    167C  ILE*     1.3    61.5    +      -       -      +
    168C  THR      4.0     0.3    +      -       -      -
     21D  GLU*     4.4     8.1    -      -       -      +
     32D  ARG*     3.8    41.5    +      -       -      +
    166D  LEU*     5.9     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 167 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17C  TYR      3.8     1.8    -      -       -      +
     18C  PRO*     3.7    28.3    -      -       +      -
    118C  LEU*     4.3    21.3    -      -       +      -
    138C  VAL*     3.7     1.3    -      -       +      +
    139C  ASP*     3.0    12.6    -      -       -      +
    140C  ALA*     2.8    47.1    +      -       +      +
    165C  LEU*     4.0    23.1    -      -       +      -
    166C  LEU*     1.3    75.0    -      -       -      +
    168C  THR*     1.3    65.7    +      -       -      +
    169C  ALA*     4.4     2.0    -      -       +      +
    201C  OTP      3.6    57.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 168 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15C  HIS*     3.4    20.2    -      -       +      +
     16C  THR*     3.3     1.4    -      -       -      +
     17C  TYR*     2.9    45.4    +      -       +      +
     19C  SER*     5.2     1.6    +      -       -      -
     34C  LYS*     5.7     1.0    +      -       -      -
    138C  VAL      3.8     3.6    -      -       -      -
    139C  ASP*     4.3     2.7    -      -       -      -
    166C  LEU      4.0     0.7    +      -       -      -
    167C  ILE*     1.3    73.0    -      -       -      +
    169C  ALA*     1.3    67.1    +      -       -      +
     29D  SER*     3.7    19.5    -      -       -      +
     30D  VAL      2.7    30.1    +      -       -      +
     31D  TRP*     4.9     3.6    -      -       +      +
     32D  ARG*     3.5    17.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 169 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11C  PHE*     3.8    24.0    -      -       +      -
     15C  HIS      3.5     3.6    -      -       -      -
     16C  THR*     3.7     9.9    -      -       +      -
    137C  GLY*     3.3     2.9    -      -       -      -
    138C  VAL*     2.9    53.3    +      -       +      +
    167C  ILE*     4.4     0.7    -      -       +      -
    168C  THR*     1.3    79.6    -      -       -      +
    170C  GLU*     1.3    64.7    +      -       -      +
    201C  OTP      4.0    13.1    -      -       +      +
     29D  SER*     4.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 170 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11C  PHE*     3.5     3.0    -      -       -      -
     12C  ASP*     2.8    30.2    +      -       +      +
     15C  HIS*     3.3    26.2    +      -       +      +
     16C  THR*     3.2    11.0    +      -       -      -
    128C  HIS*     5.6     2.4    -      -       -      -
    135C  VAL*     4.2    10.6    -      -       +      +
    136C  CYS      3.3     7.6    -      -       -      +
    137C  GLY*     4.3     5.8    -      -       -      -
    169C  ALA*     1.3    78.6    -      -       -      +
    171C  ALA*     1.3    60.5    +      -       -      +
     24D  HIS*     2.6    36.6    +      -       -      -
     28D  LEU*     3.6    20.5    -      -       +      +
     29D  SER*     2.4    32.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 171 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9C  TYR*     3.5    26.0    -      -       +      -
     10C  GLN      3.4    11.4    -      -       -      +
     11C  PHE*     3.9    11.0    -      -       +      -
     12C  ASP      4.2     0.7    -      -       -      +
     42C  VAL*     3.8    17.9    -      -       +      -
    135C  VAL*     3.2     4.4    -      -       -      -
    136C  CYS*     2.8    31.9    +      -       +      +
    170C  GLU*     1.3    76.1    -      -       -      +
    172C  VAL*     1.3    64.0    +      -       -      +
    201C  OTP      4.2     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 172 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9C  TYR*     3.7     2.0    -      -       -      -
     10C  GLN      2.9    25.7    +      -       -      +
     12C  ASP*     4.4    20.4    -      -       +      +
    131C  LEU*     4.5    19.7    -      -       +      -
    133C  ARG*     3.5    45.3    -      -       +      +
    134C  GLU      3.6     9.4    -      -       -      +
    135C  VAL*     4.5    11.9    -      -       +      -
    171C  ALA*     1.3    77.1    -      -       -      +
    173C  LYS*     1.4    63.6    +      -       -      +
    174C  GLN*     2.9    20.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 173 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  SER      4.9     4.9    +      -       -      +
      7C  ALA*     3.6    31.5    -      -       +      +
      8C  THR      3.6     0.9    -      -       -      +
      9C  TYR*     3.4    16.9    +      -       +      -
    133C  ARG*     3.0    27.2    +      -       +      -
    134C  GLU*     3.0    54.4    +      -       +      +
    172C  VAL*     1.4    70.3    -      -       -      +
    174C  GLN*     1.3    71.3    +      -       -      +
----------------------------------------------------------
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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