Contacts of the helix formed by residues 919 - 930 (chain B) in PDB entry 3H44


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 ASP 919 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547B  TYR*     2.6    38.3    +      -       +      -
    917B  ASN*     3.3     6.7    +      -       -      +
    918B  PHE*     1.3    76.1    -      -       -      +
    920B  ARG*     1.3    64.7    +      -       -      +
    921B  ASP      3.2     4.0    +      -       -      -
    922B  ASN*     2.7    32.8    +      -       -      +
    923B  THR*     3.4    20.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 920 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    800B  GLN*     5.4     2.2    +      -       -      -
    805B  ASN*     3.5    13.1    +      -       -      -
    893B  ARG*     3.9     8.3    -      -       -      +
    910B  GLU*     2.8    38.9    +      -       -      +
    913B  SER*     5.4     0.2    +      -       -      -
    915B  GLN*     2.6    37.8    +      -       -      +
    917B  ASN*     3.1    39.5    +      -       -      +
    918B  PHE      3.2     3.2    +      -       -      +
    919B  ASP*     1.3    75.3    -      -       -      +
    921B  ASP*     1.3    58.5    +      -       -      +
    923B  THR*     3.1     7.4    +      -       -      -
    924B  GLU*     2.8    78.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 921 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    893B  ARG*     3.1    56.2    +      -       -      +
    894B  LEU*     3.8    13.4    -      -       +      -
    896B  LYS*     5.7     2.9    +      -       -      +
    906B  LYS*     2.3    35.8    +      -       -      -
    918B  PHE      5.3     0.5    +      -       -      +
    919B  ASP      3.3     0.8    -      -       -      -
    920B  ARG*     1.3    78.3    -      -       -      +
    922B  ASN*     1.3    60.4    -      -       -      +
    925B  VAL*     2.9    37.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 922 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547B  TYR*     3.4     8.8    +      -       -      -
    894B  LEU*     3.4    23.2    -      -       -      +
    896B  LYS*     4.9     6.5    -      -       -      +
    919B  ASP*     2.7    34.4    +      -       -      +
    921B  ASP*     1.3    78.4    -      -       -      +
    923B  THR*     1.3    58.2    +      -       +      +
    925B  VAL*     4.2     1.1    -      -       -      +
    926B  ALA*     3.0    29.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 923 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    802B  THR*     4.8     8.9    +      -       -      +
    917B  ASN*     4.6     6.4    +      -       -      -
    919B  ASP*     3.4    21.2    +      -       +      +
    920B  ARG*     3.1    17.2    +      -       -      -
    922B  ASN*     1.3    79.1    -      -       -      +
    924B  GLU*     1.3    59.0    +      -       -      +
    926B  ALA*     3.3     6.3    +      -       -      +
    927B  TYR*     2.9    30.4    +      -       -      +
   1011B  HIS*     5.9     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 924 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    802B  THR*     4.2    26.4    +      -       +      +
    805B  ASN*     3.0    29.9    -      -       -      +
    806B  MET*     3.5    29.5    -      -       +      +
    809B  GLU*     4.4     2.4    -      -       -      +
    893B  ARG*     2.6    39.6    +      -       -      +
    917B  ASN*     5.1     1.9    +      -       -      +
    920B  ARG*     2.8    44.9    +      -       +      +
    921B  ASP      4.2     1.6    -      -       -      +
    923B  THR*     1.3    72.6    -      -       -      +
    925B  VAL*     1.3    54.0    +      -       -      +
    927B  TYR      3.4     0.7    +      -       -      -
    928B  LEU*     2.8    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 925 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    806B  MET*     5.4     1.1    -      -       +      -
    890B  ALA*     4.1    19.1    -      -       +      +
    893B  ARG*     3.8    32.8    -      -       +      +
    894B  LEU*     3.9    29.8    -      -       +      -
    921B  ASP      2.9    22.1    +      -       -      +
    922B  ASN*     4.3     1.6    -      -       -      +
    924B  GLU*     1.3    73.4    -      -       -      +
    926B  ALA*     1.3    65.7    +      -       -      +
    927B  TYR      3.1     1.1    -      -       -      -
    928B  LEU*     3.2    10.6    +      -       +      +
    929B  LYS*     3.2    45.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 926 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    922B  ASN      3.0    19.7    +      -       -      +
    923B  THR*     3.6     6.3    -      -       -      +
    925B  VAL*     1.3    79.5    -      -       -      +
    927B  TYR*     1.3    61.7    +      -       -      +
    929B  LYS*     3.4    17.7    +      -       -      +
    930B  THR*     4.0     7.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 927 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    802B  THR*     3.9    18.6    -      -       +      -
    803B  SER*     3.1    40.5    -      -       -      -
    806B  MET*     4.0    20.0    -      -       +      -
    807B  PHE*     3.8    11.1    -      -       -      -
    923B  THR      2.9    16.2    +      -       -      +
    924B  GLU      3.8     2.7    -      -       -      +
    926B  ALA*     1.3    74.5    -      -       -      +
    928B  LEU*     1.3    67.1    +      -       -      +
    929B  LYS      3.1     1.8    -      -       -      -
    930B  THR*     3.1    25.5    +      -       -      -
    931B  LEU*     3.5    33.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 928 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    806B  MET*     3.5    21.5    -      -       +      +
    810B  LEU*     3.6    35.4    -      -       +      -
    886B  ILE*     3.5    42.3    -      -       +      +
    889B  LEU*     3.7    15.7    -      -       +      -
    890B  ALA*     3.9    15.9    -      -       +      +
    924B  GLU      2.8    21.2    +      -       -      +
    925B  VAL*     3.3    11.4    -      -       +      +
    927B  TYR*     1.3    76.8    -      -       -      +
    929B  LYS*     1.3    58.7    +      -       -      +
    931B  LEU*     3.0    34.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 929 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    883B  GLN*     4.4    18.3    +      -       -      +
    886B  ILE*     3.9    21.2    -      -       +      +
    887B  GLN*     5.0     8.6    +      -       -      +
    890B  ALA*     4.6    13.0    -      -       -      +
    894B  LEU*     5.6     2.6    -      -       -      +
    925B  VAL*     3.2    37.1    +      -       -      +
    926B  ALA*     3.4    11.6    +      -       -      +
    927B  TYR      3.1     1.4    -      -       -      -
    928B  LEU*     1.3    79.8    -      -       -      +
    930B  THR*     1.3    59.8    +      -       -      +
    931B  LEU      3.1     6.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 930 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    926B  ALA      4.0     4.9    +      -       -      +
    927B  TYR*     3.1    27.6    +      -       -      -
    929B  LYS*     1.3    75.0    -      -       -      +
    931B  LEU*     1.3    62.9    +      -       -      +
    932B  THR*     3.5    15.3    -      -       -      +
    935B  ASP*     4.3     3.3    -      -       -      +
----------------------------------------------------------
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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