Contacts of the strand formed by residues 162 - 173 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  GLU      4.3     4.0    -      -       -      +
     22A  ALA*     4.5     7.6    -      -       -      -
     23A  ASP*     4.6     4.5    +      -       -      +
    143A  GLU*     3.4    27.6    -      -       +      +
    144A  PHE      3.5     8.1    -      -       -      +
    145A  SER*     4.5     3.7    +      -       -      +
    160A  LYS*     3.5    11.0    -      -       +      +
    161A  MET*     1.3    76.0    -      -       -      +
    163A  THR*     1.3    66.8    +      -       -      +
    164A  LYS*     3.2    39.8    -      -       +      +
     96D  ASP*     2.9    16.3    +      -       -      +
    101D  VAL*     6.3     5.2    -      -       +      -
    119D  LYS*     3.8    21.7    -      -       -      +
    121D  ASP*     5.2     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PHE*     4.6     3.4    -      -       +      -
     21A  GLU      3.5    12.1    -      -       -      +
     22A  ALA*     4.8     7.4    -      -       +      +
    143A  GLU*     3.3     3.7    -      -       -      -
    144A  PHE*     2.7    65.5    +      -       +      -
    146A  ARG*     3.8    19.4    +      -       -      +
    161A  MET      3.0    13.7    +      -       -      -
    162A  LYS*     1.3    74.9    +      -       -      +
    164A  LYS*     1.3    68.5    +      -       -      +
    165A  LEU*     5.1     0.2    -      -       +      -
    201A  OTP      4.0    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PHE*     3.1    10.4    -      -       -      +
     21A  GLU*     2.9    61.6    +      -       +      +
    142A  GLY      3.5     4.9    -      -       -      +
    143A  GLU*     3.6    22.1    +      -       +      +
    162A  LYS*     3.2    38.7    -      -       +      +
    163A  THR*     1.3    75.6    -      -       -      +
    165A  LEU*     1.3    62.3    +      -       -      +
    166A  LEU*     4.3     8.3    -      -       +      -
    119D  LYS*     4.4     7.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  PRO*     4.9     4.3    -      -       +      -
     19A  SER      3.4    11.7    -      -       -      +
     20A  PHE*     4.3     7.0    -      -       +      -
    116A  LEU*     4.0    25.8    -      -       +      -
    118A  LEU*     4.7     7.6    -      -       +      -
    141A  VAL*     3.2     7.7    -      -       -      +
    142A  GLY      2.8    38.3    +      -       -      +
    144A  PHE*     3.8    27.4    -      -       +      -
    163A  THR*     5.1     0.2    -      -       +      -
    164A  LYS*     1.3    78.9    -      -       -      +
    166A  LEU*     1.3    64.9    +      -       -      +
    167A  ILE*     4.1    14.4    -      -       +      -
    201A  OTP      4.0    47.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  TYR      3.9     1.0    -      -       -      +
     19A  SER*     2.8    43.6    +      -       -      +
     20A  PHE      4.4     2.9    -      -       -      -
     21A  GLU*     3.9    38.4    -      -       +      +
    140A  ALA      3.6     4.9    -      -       -      +
    141A  VAL*     4.8    10.5    -      -       +      -
    164A  LYS*     4.2    13.0    -      -       +      +
    165A  LEU*     1.3    79.2    -      -       -      +
    167A  ILE*     1.3    61.3    +      -       -      +
    168A  THR*     4.9     0.2    +      -       -      -
     21B  GLU*     4.4     7.4    -      -       -      +
     32B  ARG*     3.8    42.3    +      -       -      +
    166B  LEU*     5.7     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  TYR      3.7     2.7    -      -       -      +
     18A  PRO*     4.3    14.8    -      -       +      -
    118A  LEU*     3.7    39.3    -      -       +      -
    138A  VAL*     3.8     1.0    -      -       +      +
    139A  ASP*     3.1    12.5    -      -       -      +
    140A  ALA*     2.8    46.7    +      -       +      +
    141A  VAL      5.3     0.2    -      -       -      -
    165A  LEU*     4.3    17.7    -      -       +      -
    166A  LEU*     1.3    75.8    -      -       -      +
    168A  THR*     1.3    68.2    +      -       -      +
    169A  ALA*     4.5     2.5    -      -       +      -
    201A  OTP      3.5    50.7    -      -       +      -
     32B  ARG*     4.3     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  HIS*     3.4    23.3    -      -       +      +
     16A  THR*     3.3     1.2    -      -       -      +
     17A  TYR*     2.9    45.7    +      -       +      +
     19A  SER*     5.1     1.4    +      -       -      -
     34A  LYS*     5.7     0.9    +      -       -      -
    138A  VAL      3.9     3.4    -      -       -      -
    139A  ASP*     4.4     2.5    -      -       -      -
    166A  LEU      4.9     0.5    +      -       -      -
    167A  ILE*     1.3    75.4    -      -       -      +
    169A  ALA*     1.3    65.5    +      -       -      +
     29B  SER*     3.8    18.6    -      -       -      +
     30B  VAL      2.7    29.7    +      -       -      +
     31B  TRP*     5.4     2.0    -      -       +      -
     32B  ARG*     3.5    18.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     3.7    25.4    -      -       +      -
     15A  HIS      3.4     4.3    -      -       -      -
     16A  THR*     3.7     9.0    -      -       +      -
    137A  GLY*     3.2     3.1    -      -       -      -
    138A  VAL*     2.8    52.5    +      -       +      +
    167A  ILE*     4.1     0.6    -      -       +      -
    168A  THR*     1.3    78.8    -      -       -      +
    170A  GLU*     1.3    65.6    +      -       -      +
    201A  OTP      4.0    14.7    -      -       +      +
     29B  SER*     4.3     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     3.5     3.4    -      -       -      -
     12A  ASP*     2.9    31.7    +      -       +      +
     15A  HIS*     3.3    29.9    +      -       +      +
     16A  THR*     3.3     5.3    +      -       -      -
    128A  HIS*     5.2     4.0    +      -       -      -
    135A  VAL*     4.1    10.7    -      -       +      +
    136A  CYS      3.3     5.8    -      -       -      +
    137A  GLY*     4.3     0.2    -      -       -      -
    169A  ALA*     1.3    81.2    -      -       -      +
    171A  ALA*     1.3    61.7    +      -       -      +
     24B  HIS*     2.7    32.8    +      -       -      -
     25B  PHE*     4.9     1.0    -      -       -      -
     28B  LEU*     3.3    27.3    -      -       +      +
     29B  SER*     2.5    31.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  TYR*     3.5    27.1    -      -       +      -
     10A  GLN      3.3    15.0    -      -       -      +
     11A  PHE*     3.9    16.8    -      -       +      -
     42A  VAL*     4.3     5.4    -      -       +      -
    135A  VAL*     3.4     2.1    -      -       -      -
    136A  CYS*     2.8    33.9    +      -       +      +
    170A  GLU*     1.3    76.6    -      -       -      +
    172A  VAL*     1.3    63.2    +      -       -      +
    201A  OTP      4.3     8.2    -      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
      9A  TYR*     3.8     2.0    -      -       -      -
     10A  GLN*     2.9    37.9    +      -       +      +
     12A  ASP*     4.5    17.3    -      -       +      -
    128A  HIS*     4.3     5.8    -      -       +      -
    131A  LEU*     3.8    30.3    -      -       +      -
    133A  ARG*     3.7    37.7    +      -       +      +
    134A  GLU      3.5    10.3    -      -       -      +
    135A  VAL*     4.2    14.1    -      -       +      +
    171A  ALA*     1.3    75.6    -      -       -      +
    173A  LYS*     1.3    69.6    +      -       -      +
    174A  GLN*     3.4     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ALA*     4.1    18.8    -      -       +      +
      8A  THR      3.5    11.2    -      -       -      +
      9A  TYR*     3.4    22.2    +      -       +      -
    133A  ARG*     2.8    28.3    +      -       +      +
    134A  GLU*     2.8    52.9    +      -       +      +
    172A  VAL*     1.3    72.3    -      -       -      +
    174A  GLN*     1.3    71.8    +      -       -      +
----------------------------------------------------------
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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