Contacts of the helix formed by residues 1987 - 1994 (chain H) in PDB entry 2VKZ


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 PRO1987 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1738H  PHE*     5.4     3.1    -      -       +      -
   1739H  GLU*     3.0    71.6    -      -       +      +
   1740H  THR      4.8     0.4    -      -       -      +
   1741H  ILE*     5.2     0.2    -      -       +      -
   1746H  LEU*     5.1     3.4    -      -       +      -
   1833H  TYR*     4.3    13.3    +      -       -      +
   1983H  ASN      4.0     4.7    -      -       -      +
   1984H  GLY*     3.4    15.5    -      -       -      +
   1985H  VAL      3.3     1.1    -      -       -      +
   1986H  LYS*     1.3    92.5    -      -       +      +
   1988H  PHE*     1.3    61.3    +      -       -      +
   1990H  SER*     3.3     8.2    +      -       -      +
   1991H  PHE*     3.3    21.1    +      -       -      +
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Residues in contact with PHE1988 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  LEU      4.5     2.0    -      -       -      -
     19B  ALA*     4.3     8.3    -      -       -      -
     22B  PHE*     3.9    27.6    -      +       +      -
   1812H  TYR*     3.4    20.6    -      -       -      -
   1830H  VAL*     4.4     7.2    -      -       +      -
   1833H  TYR*     3.8    26.2    -      +       +      -
   1834H  ARG*     3.6    47.1    -      -       +      -
   1837H  THR*     4.6     3.4    -      -       +      -
   1984H  GLY      3.8    12.3    -      -       -      +
   1985H  VAL*     3.0     8.4    +      -       -      +
   1987H  PRO*     1.3    75.4    -      -       -      +
   1989H  LYS*     1.3    54.9    +      -       -      +
   1990H  SER      3.0     4.5    -      -       -      -
   1991H  PHE*     2.9     7.9    +      +       +      +
   1992H  LEU*     2.7    67.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS1989 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  THR*     4.2    12.1    -      -       -      +
     16B  GLU*     3.2    34.3    +      -       -      +
     19B  ALA*     4.0    22.6    -      -       +      +
     20B  TYR*     5.2     2.0    +      -       -      -
   1985H  VAL*     2.7    20.9    +      -       +      +
   1986H  LYS*     3.8    18.6    -      -       +      +
   1987H  PRO      3.4     0.2    -      -       -      -
   1988H  PHE*     1.3    76.9    -      -       -      +
   1990H  SER*     1.3    55.7    +      -       -      +
   1992H  LEU*     4.2     4.3    -      -       -      +
   1993H  LYS*     3.0    41.3    +      -       +      +
   2035H  SER*     3.9     4.9    +      -       -      -
   2037H  PRO*     3.4    29.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER1990 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1739H  GLU*     5.2     3.5    +      -       -      -
   1986H  LYS      3.4    13.8    +      -       -      -
   1987H  PRO*     3.3     9.9    +      -       -      +
   1988H  PHE      3.0     0.8    -      -       -      -
   1989H  LYS*     1.3    77.7    -      -       -      +
   1991H  PHE*     1.3    67.5    +      -       -      +
   1992H  LEU      3.2     1.6    -      -       -      -
   1993H  LYS*     3.1     7.0    +      -       -      +
   1994H  LYS*     2.9    48.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1991 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1736H  MET*     5.0     6.5    -      -       +      -
   1829H  GLU*     4.3    16.6    -      -       +      -
   1830H  VAL*     3.6    31.9    -      -       +      -
   1833H  TYR*     3.6    53.6    -      +       +      -
   1987H  PRO      3.3    12.0    +      -       -      +
   1988H  PHE*     2.9    17.9    +      +       +      +
   1990H  SER*     1.3    82.5    +      -       -      +
   1992H  LEU*     1.3    62.6    +      -       +      +
   1994H  LYS*     3.2    19.2    +      -       +      +
   1995H  ASN*     3.3    38.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1992 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  THR*     4.1    13.7    -      -       -      +
     18B  LEU*     3.7    17.7    -      -       +      -
     19B  ALA*     3.6    33.7    -      -       +      +
   1812H  TYR*     4.3     5.8    -      -       +      +
   1830H  VAL*     3.5    36.1    -      -       +      -
   1988H  PHE*     2.7    45.8    +      -       +      +
   1989H  LYS*     4.6     3.1    -      -       -      +
   1991H  PHE*     1.3    73.4    -      -       +      +
   1993H  LYS*     1.3    55.1    +      -       -      +
   1995H  ASN*     3.0     4.0    +      -       -      -
   1996H  ILE*     2.7    48.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS1993 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  HIS*     4.5    19.1    +      -       -      +
     12B  ILE*     4.9    12.0    -      -       -      +
     15B  THR*     3.8    20.2    -      -       +      +
   1989H  LYS*     3.0    39.9    +      -       -      +
   1990H  SER*     3.1     8.8    +      -       -      +
   1992H  LEU*     1.3    76.2    -      -       -      +
   1994H  LYS*     1.3    61.1    +      -       +      +
   1995H  ASN      3.2     0.6    +      -       -      -
   1996H  ILE*     3.8    16.2    -      -       -      +
   1997H  ILE*     4.9     2.9    +      -       -      +
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Residues in contact with LYS1994 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1990H  SER*     2.9    37.7    +      -       -      +
   1991H  PHE*     3.6    12.3    -      -       +      +
   1992H  LEU      3.1     0.4    -      -       -      -
   1993H  LYS*     1.3    76.7    -      -       +      +
   1995H  ASN*     1.3    66.8    +      -       -      +
   1997H  ILE*     5.3     5.4    -      -       -      +
----------------------------------------------------------
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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