Contacts of the helix formed by residues 9 - 22 (chain P) in PDB entry 2X86


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 GLY 9 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6P  GLY      2.8    14.0    +      -       -      -
      8P  ALA*     1.3    79.3    -      -       -      +
     10P  PHE*     1.3    56.7    +      -       -      -
     11P  ILE      3.7     0.9    -      -       -      -
     13P  SER*     2.7    35.0    +      -       -      -
     31P  ASP*     3.2     3.0    +      -       -      -
    174P  ARG      4.2     0.4    -      -       -      -
    177P  HIS*     3.8     9.9    -      -       -      -
    400P  NAP      3.6    25.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 10 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9P  GLY*     1.3    70.6    -      -       -      -
     11P  ILE*     1.3    67.4    +      -       +      +
     13P  SER*     3.0     9.4    +      -       -      -
     14P  ASN*     2.8    28.1    +      -       -      -
    170P  VAL*     3.6    32.5    -      -       +      -
    171P  TYR*     3.5     5.6    -      -       -      -
    172P  GLY      3.2    33.9    -      -       -      -
    173P  PRO      3.1    22.4    -      -       -      -
    174P  ARG      3.1    24.0    -      -       -      +
    175P  GLU*     3.6    16.8    -      -       +      -
    177P  HIS*     3.5     1.8    -      -       +      -
    178P  LYS*     4.0     8.7    -      -       +      -
    214P  VAL*     3.6    12.3    -      -       +      -
    400P  NAP      3.0    42.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 11 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10P  PHE*     1.3    89.2    -      -       +      +
     12P  GLY*     1.3    62.4    +      -       -      +
     14P  ASN*     3.1     5.2    +      -       -      +
     15P  ILE*     3.0    28.7    +      -       +      +
     75P  GLU*     3.5    21.3    -      -       -      +
    167P  TYR*     3.5    38.6    -      -       +      +
    170P  VAL*     4.1    22.0    -      -       +      -
    214P  VAL*     4.5     8.5    -      -       +      -
    217P  VAL*     4.0    14.4    -      -       +      -
    400P  NAP      2.9    41.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 12 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4P  VAL*     3.7    16.2    -      -       -      +
      6P  GLY      3.5    19.0    +      -       -      -
      7P  GLY*     3.8     7.2    -      -       -      -
     10P  PHE      3.3     0.4    -      -       -      -
     11P  ILE*     1.3    80.9    -      -       -      +
     13P  SER*     1.3    61.1    +      -       -      +
     15P  ILE*     3.0     6.3    +      -       -      +
     16P  VAL*     2.9    24.1    +      -       -      +
     75P  GLU*     4.0    14.6    -      -       -      +
    400P  NAP      4.4     0.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 13 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7P  GLY      3.3    17.9    +      -       -      -
      9P  GLY      2.7    25.0    +      -       -      -
     10P  PHE      3.0     8.5    +      -       -      -
     12P  GLY*     1.3    74.9    -      -       -      +
     14P  ASN*     1.3    56.8    +      -       -      +
     16P  VAL*     3.2     8.0    +      -       -      +
     17P  LYS*     2.9    24.6    +      -       -      +
     41P  ASN*     3.6    29.9    -      -       -      +
     42P  LEU*     4.9     0.2    -      -       -      -
     45P  LEU*     3.4     7.3    -      -       -      +
    174P  ARG*     3.3    21.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 14 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10P  PHE*     2.8    23.0    +      -       -      -
     11P  ILE      3.1     8.2    +      -       -      +
     13P  SER*     1.3    79.9    +      -       -      +
     15P  ILE*     1.3    60.4    +      -       +      +
     17P  LYS*     3.4    12.8    +      -       -      +
     18P  ALA*     3.0    28.1    +      -       -      +
    173P  PRO*     2.9    30.9    +      -       -      +
    174P  ARG*     3.8    14.7    +      -       -      +
    214P  VAL*     3.5    36.4    -      -       +      +
    215P  GLY*     5.3     1.6    +      -       -      -
    218P  ALA*     3.9    11.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 15 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4P  VAL*     4.4     5.6    -      -       +      -
     11P  ILE*     3.0    20.5    +      -       +      +
     12P  GLY*     3.0     8.5    +      -       -      +
     14P  ASN*     1.3    75.6    -      -       -      +
     16P  VAL*     1.3    65.1    +      -       -      +
     18P  ALA*     3.2     6.9    +      -       -      +
     19P  LEU*     2.9    36.6    +      -       +      +
     73P  PHE*     4.0    27.1    -      -       +      -
     75P  GLU*     3.6    31.9    -      -       +      +
    218P  ALA*     4.6     8.7    -      -       -      -
    221P  ASN*     3.5    38.8    -      -       +      +
    222P  LEU*     4.4     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 16 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4P  VAL*     4.2    17.0    -      -       +      -
      7P  GLY      4.2     9.0    -      -       -      +
     12P  GLY      2.9    18.3    +      -       -      +
     13P  SER      3.3     7.6    -      -       -      +
     15P  ILE*     1.3    77.3    -      -       -      +
     17P  LYS*     1.3    58.3    +      -       -      +
     19P  LEU*     3.1    11.7    +      -       -      +
     20P  ASN*     2.8    30.2    +      -       -      +
     27P  ILE*     4.0    11.0    -      -       +      -
     29P  VAL*     4.1    22.2    -      -       +      -
     42P  LEU*     4.7     1.1    -      -       +      -
     45P  LEU*     3.7    21.8    -      -       +      -
     47P  ILE*     3.8    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 17 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13P  SER      2.9    13.3    +      -       -      +
     14P  ASN*     3.7    15.0    -      -       -      +
     15P  ILE      3.3     0.2    -      -       -      -
     16P  VAL*     1.3    74.6    -      -       -      +
     18P  ALA*     1.3    58.0    +      -       -      +
     20P  ASN*     3.1     6.6    +      -       +      +
     21P  ASP*     2.8    60.8    +      -       -      +
     45P  LEU*     3.9    27.8    -      -       +      +
    174P  ARG*     4.0    20.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 18 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14P  ASN      3.0    17.7    +      -       -      +
     15P  ILE*     3.5     5.8    -      -       -      +
     16P  VAL      3.2     0.2    -      -       -      -
     17P  LYS*     1.3    78.6    -      -       -      +
     19P  LEU*     1.3    60.4    +      -       -      +
     21P  ASP*     3.2    12.3    +      -       -      +
     22P  LYS*     3.1    18.7    +      -       -      +
    218P  ALA*     4.0    20.2    -      -       +      +
    219P  ASP*     5.3     4.3    -      -       -      +
    222P  LEU*     3.8    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 19 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2P  ILE*     3.9    45.3    -      -       +      -
      4P  VAL*     4.2     6.7    -      -       +      -
     15P  ILE*     2.9    32.6    +      -       +      +
     16P  VAL      3.4     6.1    -      -       -      +
     18P  ALA*     1.3    71.8    -      -       -      +
     20P  ASN*     1.3    67.8    +      -       -      +
     22P  LYS*     3.0    11.2    +      -       +      +
     23P  GLY      3.3     0.2    +      -       -      -
     24P  ILE*     2.9    39.2    +      -       +      +
     27P  ILE*     3.9    23.1    -      -       +      -
     73P  PHE*     4.4     3.6    -      -       +      -
    222P  LEU*     3.9    26.0    -      -       +      -
    225P  LEU*     5.1     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 20 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16P  VAL*     2.8    17.1    +      -       -      -
     17P  LYS*     3.3    12.3    -      -       +      +
     19P  LEU*     1.3    76.4    -      -       -      +
     21P  ASP*     1.3    56.6    +      -       -      +
     23P  GLY*     2.7    26.5    +      -       -      -
     24P  ILE      2.9    19.4    +      -       -      -
     25P  THR*     3.8     8.5    -      -       +      +
     27P  ILE*     3.8     4.4    -      -       -      +
     44P  ASP      5.0     0.2    -      -       -      +
     45P  LEU*     3.5    15.4    -      -       +      +
     46P  ASN*     2.8    55.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 21 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132H  GLU*     5.6     1.0    -      -       -      +
     17P  LYS*     2.8    51.7    +      -       -      +
     18P  ALA*     3.2    13.0    +      -       -      +
     20P  ASN*     1.3    78.6    -      -       -      +
     22P  LYS*     1.3    60.2    +      -       +      +
     23P  GLY      3.2     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 22 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  ASP*     6.2     0.2    -      -       -      +
    128H  ILE*     3.4    10.3    -      -       -      +
    132H  GLU*     5.3    13.3    +      -       -      +
    133H  TYR*     2.6    41.8    +      -       +      +
     18P  ALA      3.1    12.6    +      -       -      +
     19P  LEU*     3.0    10.9    +      -       +      +
     21P  ASP*     1.3    78.2    -      -       +      +
     23P  GLY*     1.3    60.6    +      -       -      +
     24P  ILE*     3.3    10.8    +      -       +      +
    222P  LEU*     3.8    23.8    -      -       +      -
    226P  GLU*     3.1    30.7    +      -       -      +
----------------------------------------------------------
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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