Contacts of the strand formed by residues 180 - 189 (chain A) in PDB entry 1XHU


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 180 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  GLN      4.0     0.2    -      -       -      +
     20A  VAL*     2.8    35.7    +      -       +      +
     21A  LYS      4.1     4.0    +      -       -      +
     22A  ARG*     4.6     0.4    -      -       -      -
     23A  PRO*     3.5    27.6    -      -       +      -
     28A  LEU*     4.1     3.8    -      -       +      -
     33A  ALA      3.4    25.1    -      -       -      +
     34A  GLY*     4.2     1.6    -      -       -      -
     36A  PRO*     5.1     1.1    -      -       +      -
     37A  PHE*     3.1    32.3    -      -       +      -
    173A  TRP*     3.1    43.1    -      -       +      -
    174A  GLU      3.5     2.9    -      -       -      -
    175A  LEU*     3.5    23.1    -      -       +      -
    179A  ASP*     1.3    70.5    -      -       -      +
    181A  VAL*     1.3    61.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  GLY*     3.9    18.4    -      -       -      +
     18A  GLN      3.5    16.6    -      -       -      +
     19A  LYS*     4.4    16.6    -      -       +      +
    173A  TRP*     3.1     5.3    -      -       -      +
    174A  GLU*     2.7    58.1    +      -       +      +
    176A  ASN*     3.4    32.1    -      -       +      +
    179A  ASP      3.7     3.2    +      -       -      -
    180A  LEU*     1.3    76.3    -      -       -      +
    182A  CYS*     1.3    78.7    +      -       -      +
    183A  VAL*     4.6     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LEU*     4.1    20.6    -      -       -      +
     16A  ILE*     3.6    25.0    -      -       -      +
     17A  GLY*     3.2    20.6    +      -       -      -
     18A  GLN*     3.6     4.5    +      -       +      +
     37A  PHE*     3.7    22.0    -      -       +      -
    171A  VAL*     4.6     9.2    -      -       +      -
    172A  ASP      3.3    15.3    -      -       -      +
    173A  TRP*     3.8     2.2    -      -       +      +
    180A  LEU      4.0     0.6    +      -       -      -
    181A  VAL*     1.3    83.9    -      -       -      +
    183A  VAL*     1.3    64.9    +      -       -      +
    184A  SER      3.5    15.7    -      -       -      -
    185A  THR*     4.7     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ILE*     3.1    25.6    -      -       -      +
    133A  ILE*     3.6    28.9    -      -       +      -
    172A  ASP*     2.9    12.7    +      -       +      +
    173A  TRP      4.5     0.2    -      -       -      +
    174A  GLU*     3.7    37.9    -      -       +      +
    181A  VAL*     4.6     3.6    -      -       +      -
    182A  CYS*     1.3    77.9    -      -       -      +
    184A  SER*     1.3    76.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ILE*     3.3     8.3    -      -       -      -
    133A  ILE*     5.0     0.9    -      -       -      +
    172A  ASP*     2.2    55.1    +      -       -      +
    182A  CYS*     3.5     8.0    -      -       -      -
    183A  VAL*     1.3    84.7    -      -       -      +
    185A  THR*     1.3    66.4    +      -       -      +
    186A  SER*     6.1     0.2    -      -       -      -
    213A  ARG*     3.6     8.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  TYR*     2.6    49.3    +      -       +      +
     11A  ILE*     6.3     0.9    -      -       +      -
     12A  ASN*     3.2    32.1    +      -       +      +
     15A  LEU*     4.1    11.8    -      -       -      +
     16A  ILE*     3.9     3.6    -      -       -      +
    169A  LEU*     3.8     9.8    -      -       +      +
    170A  GLU      3.2    11.1    +      -       -      -
    171A  VAL*     3.9    13.7    -      -       -      +
    172A  ASP*     4.3     2.0    -      -       -      -
    184A  SER*     1.3    81.1    +      -       -      +
    186A  SER*     1.3    63.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  TYR*     3.2     6.3    -      -       -      -
    169A  LEU*     3.3     6.1    -      -       -      +
    170A  GLU*     2.6    47.3    +      -       -      +
    172A  ASP*     4.9     1.9    +      -       -      -
    184A  SER*     6.1     0.2    -      -       -      -
    185A  THR*     1.3    78.2    +      -       -      +
    187A  PHE*     1.3    60.5    -      -       -      +
    212A  VAL*     3.8     2.2    -      -       -      +
    213A  ARG*     3.6    45.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  SER*     3.8    11.7    -      -       -      -
      4A  ILE*     3.4    23.8    -      -       +      -
      5A  LYS*     3.9    28.0    -      -       +      -
      8A  TYR*     3.6    30.8    +      +       +      -
    124A  GLU*     4.3     0.2    -      -       -      -
    126A  LEU*     4.4     6.3    -      -       +      -
    167A  ASN*     3.5    37.7    -      -       +      -
    168A  TYR      3.3    15.9    -      -       -      -
    169A  LEU*     4.4    11.9    -      -       +      -
    186A  SER*     1.3    75.6    -      -       -      +
    188A  ALA*     1.3    77.7    +      -       -      +
    189A  GLU*     3.9    26.0    -      -       +      -
    212A  VAL*     3.7     3.4    -      -       -      +
    217A  GLN*     5.4     1.4    -      -       -      +
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Residues in contact with ALA 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  ASN*     3.4     2.8    -      -       -      +
    168A  TYR*     2.8    38.4    +      -       +      +
    187A  PHE*     1.3    86.1    -      -       -      +
    189A  GLU*     1.3    62.3    +      -       -      +
    212A  VAL*     3.5    23.6    -      -       +      +
    215A  LEU*     3.6    17.5    -      -       +      +
    217A  GLN*     3.2    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  SER*     4.0    17.0    +      -       -      -
      5A  LYS*     4.3    13.0    +      -       -      +
    165A  ASP*     3.3    15.8    -      -       -      +
    167A  ASN*     3.1    26.7    +      -       -      +
    187A  PHE*     3.9    18.7    -      -       +      -
    188A  ALA*     1.3    75.7    -      -       -      +
    190A  LEU*     1.3    66.1    +      -       -      +
    191A  PHE      4.7     0.4    -      -       -      +
    192A  LYS*     3.4    46.1    +      -       +      +
    193A  SER      3.8     0.9    +      -       -      -
    215A  LEU*     3.7     4.8    -      -       -      +
    217A  GLN*     2.9    23.6    +      -       -      +
----------------------------------------------------------
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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