Contacts of the helix formed by residues 46 - 57 (chain D) in PDB entry 3T79


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 SER 46 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43D  LEU      3.9     5.2    -      -       -      -
     44D  PHE      3.6     3.4    +      -       -      -
     45D  LEU*     1.3    74.5    -      -       -      +
     47D  GLN*     1.3    70.8    +      -       -      +
     48D  LYS*     2.9    22.0    +      -       -      +
     49D  TYR*     3.0    38.3    +      -       -      -
     50D  ILE*     3.2    16.8    +      -       -      +
     88D  LEU*     5.1     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 47 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46D  SER*     1.3    72.8    +      -       -      +
     48D  LYS*     1.3    65.5    +      -       +      +
     50D  ILE*     4.7     7.2    -      -       -      -
     51D  VAL*     2.9    34.5    +      -       +      +
     87D  VAL*     3.7    27.9    -      -       -      +
     88D  LEU*     4.1    21.1    -      -       +      +
     91D  ARG*     3.9    37.4    -      -       +      +
     92D  LEU*     5.9     1.3    -      -       -      -
    280D  ASP      5.4     1.6    -      -       -      +
    281D  PHE*     4.8    14.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 48 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46D  SER*     2.9    20.4    +      -       -      +
     47D  GLN*     1.3    75.6    -      -       +      +
     49D  TYR*     1.3    90.8    +      -       +      +
     51D  VAL*     3.8     3.5    -      -       -      +
     52D  LYS*     2.9    30.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 49 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  TYR*     3.5    17.5    -      -       +      +
     29D  TRP*     3.4    13.6    -      +       +      -
     30D  LEU*     6.3     0.2    -      -       +      -
     33D  MET*     5.6    15.5    -      -       +      -
     35D  ASP      5.4    11.7    -      -       -      -
     43D  LEU      4.3     8.5    -      -       -      -
     44D  PHE*     3.9    27.1    -      +       +      +
     46D  SER*     3.0    30.9    +      -       -      +
     48D  LYS*     1.3   104.0    +      -       +      +
     50D  ILE*     1.3    61.1    +      -       -      +
     52D  LYS*     4.4     6.3    -      -       +      -
     53D  TYR*     2.9    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 50 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  TYR*     3.5    25.1    -      -       +      +
     45D  LEU*     4.5     8.5    -      -       +      -
     46D  SER      3.2    21.9    +      -       -      +
     47D  GLN*     4.0     3.6    -      -       -      +
     49D  TYR*     1.3    77.4    -      -       -      +
     51D  VAL*     1.3    57.2    +      -       -      +
     53D  TYR*     3.3     3.1    +      -       +      +
     54D  ILE*     2.9    51.6    +      -       +      +
     67D  THR*     5.4     0.9    -      -       +      -
     71D  MET*     3.9    39.9    -      -       +      -
     88D  LEU*     3.9    29.4    -      -       +      -
     92D  LEU*     4.2    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 51 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47D  GLN*     2.9    33.5    +      -       +      +
     48D  LYS*     3.8     3.1    -      -       -      +
     50D  ILE*     1.3    73.3    -      -       -      +
     52D  LYS*     1.3    66.2    +      -       -      +
     54D  ILE*     3.4     1.5    +      -       -      +
     55D  ALA*     3.0    24.9    +      -       -      +
     91D  ARG*     3.4    49.8    -      -       +      +
     92D  LEU*     4.5    12.1    -      -       +      -
     95D  LEU*     4.1    13.0    -      -       +      +
    303D  PRO*     4.4     8.5    -      -       +      -
    305D  PHE*     4.0    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 52 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  TRP*     3.6    16.5    -      -       +      -
     33D  MET*     4.0    26.2    -      -       +      -
     48D  LYS      2.9    19.4    +      -       -      +
     49D  TYR*     3.7     8.7    -      -       +      +
     51D  VAL*     1.3    75.8    -      -       -      +
     53D  TYR*     1.3    54.0    +      -       -      +
     55D  ALA*     4.2     1.9    -      -       -      +
     56D  SER*     2.7    49.6    +      -       -      -
    297D  GLU*     3.1    31.6    +      -       -      +
    305D  PHE*     6.0     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 53 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  ILE*     4.7     5.6    +      -       +      +
     25D  LYS*     3.3    27.6    -      -       +      +
     26D  TYR*     3.5    37.2    -      +       +      +
     29D  TRP*     3.4    40.5    -      +       +      -
     49D  TYR      2.9    19.3    +      -       -      +
     50D  ILE*     3.4     4.7    -      -       +      +
     52D  LYS*     1.3    76.0    -      -       -      +
     54D  ILE*     1.3    74.9    +      -       +      +
     56D  SER*     3.1     6.3    +      -       -      -
     57D  HIS*     2.9    47.3    +      +       -      +
     60D  ILE*     3.9    31.3    -      -       +      +
     67D  THR*     4.4    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 54 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50D  ILE*     2.9    41.3    +      -       +      +
     51D  VAL      3.9     2.9    -      -       -      +
     53D  TYR*     1.3    81.4    -      -       +      +
     55D  ALA*     1.3    63.1    +      -       -      +
     57D  HIS      3.2    18.7    -      -       -      +
     60D  ILE*     3.9    11.3    -      -       +      +
     61D  ALA*     3.5     8.3    +      -       -      +
     64D  PRO*     4.0    22.7    -      -       +      +
     67D  THR*     4.0    24.9    -      -       +      -
     68D  CYS*     3.8    29.2    -      -       -      +
     92D  LEU*     4.6     5.6    -      -       +      -
     95D  LEU*     4.0    18.8    -      -       +      -
     99D  LEU*     4.3     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 55 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51D  VAL      3.0    13.0    +      -       -      +
     52D  LYS      4.2     2.0    -      -       -      +
     54D  ILE*     1.3    80.0    -      -       -      +
     56D  SER*     1.3    61.1    +      -       -      +
     57D  HIS      3.1     5.4    +      -       -      +
     58D  ASP*     4.8     0.5    +      -       -      -
     61D  ALA*     4.3    10.4    -      -       -      +
     95D  LEU*     5.1     2.0    -      -       +      -
     99D  LEU*     5.1     6.1    -      -       +      -
    305D  PHE*     3.3    49.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 56 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  TRP*     4.0     5.7    +      -       -      -
     52D  LYS*     2.7    37.3    +      -       -      -
     53D  TYR*     3.1     3.5    +      -       -      -
     55D  ALA*     1.3    76.0    -      -       -      +
     57D  HIS*     1.3    87.3    +      -       -      +
     58D  ASP      4.1     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 57 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  TRP*     3.4    35.0    -      +       -      +
     53D  TYR*     2.9    33.7    +      +       -      +
     54D  ILE      3.2     1.2    -      -       -      +
     55D  ALA      3.1     1.1    -      -       -      -
     56D  SER*     1.3   110.0    +      -       -      +
     58D  ASP*     1.3    51.5    +      -       -      +
     59D  ASP*     2.9    22.2    -      -       -      +
     60D  ILE*     3.4    18.8    -      -       +      -
     61D  ALA*     2.7    37.1    +      -       -      +
----------------------------------------------------------
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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