Contacts of the helix formed by residues 354 - 363 (chain A) in PDB entry 4DSI


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 354 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    306A  ARG*     5.9     0.2    +      -       -      -
    307A  VAL*     3.5    35.5    +      -       +      +
    350A  THR*     3.2    10.2    +      -       +      +
    351A  ALA      3.1    13.8    +      -       -      +
    352A  LEU      3.3     0.2    -      -       -      -
    353A  ALA*     1.3    76.8    -      -       -      +
    355A  PRO*     1.4    66.3    -      -       -      +
    356A  GLN*     2.8    40.9    +      -       -      +
    357A  PHE*     3.0    10.3    +      -       +      +
    358A  VAL*     2.9    29.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  ALA      3.3    10.9    -      -       -      +
    354A  ASP*     1.4    86.5    -      -       -      +
    356A  GLN*     1.3    66.9    +      -       -      +
    358A  VAL*     3.9     9.1    -      -       +      +
    359A  ALA*     3.0    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 356 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307A  VAL*     5.1     4.5    -      -       +      +
    309A  GLU*     3.1    24.3    -      -       -      +
    312A  LEU*     4.0    19.0    -      -       +      +
    354A  ASP*     2.8    20.7    +      -       -      +
    355A  PRO*     1.3    82.6    -      -       -      +
    357A  PHE*     1.3    59.8    +      -       -      +
    359A  ALA*     3.3     5.8    +      -       -      +
    360A  TRP*     2.9    28.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 357 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307A  VAL*     4.2    10.2    -      -       +      +
    311A  MET*     5.3     1.8    -      -       +      -
    312A  LEU*     4.0    19.2    -      -       +      +
    318A  LEU*     4.5     2.9    -      -       +      -
    320A  VAL*     5.8     0.2    -      -       +      -
    335A  ILE*     3.9    32.1    -      -       +      -
    337A  VAL*     4.3     8.3    -      -       +      -
    346A  LEU*     4.1    20.0    -      -       +      -
    351A  ALA*     3.3    41.3    -      -       +      +
    352A  LEU*     4.1     2.5    -      -       +      -
    354A  ASP*     3.0    14.9    +      -       +      +
    356A  GLN*     1.3    76.6    -      -       -      +
    358A  VAL*     1.3    56.4    +      -       -      +
    360A  TRP*     3.2    32.4    +      +       -      +
    361A  LEU*     2.9    55.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 358 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352A  LEU*     3.4    32.8    -      -       -      +
    353A  ALA      5.2     0.2    -      -       -      -
    354A  ASP      2.9    18.8    +      -       -      +
    355A  PRO*     4.0     7.4    -      -       +      +
    357A  PHE*     1.3    75.6    -      -       -      +
    359A  ALA*     1.3    62.8    +      -       -      +
    361A  LEU*     3.2    14.0    +      -       +      +
    362A  GLY*     3.1    19.1    +      -       -      -
    385A  ILE*     4.3    29.2    -      -       +      -
    386A  GLU      4.7     1.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 359 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  PRO      3.0    20.2    +      -       -      +
    356A  GLN*     3.7     6.7    -      -       -      +
    358A  VAL*     1.3    74.6    -      -       -      +
    360A  TRP*     1.3    66.2    +      -       -      +
    362A  GLY*     3.3     2.8    +      -       -      +
    363A  ASP*     3.0    25.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 360 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311A  MET      4.5     5.6    -      -       -      -
    312A  LEU*     3.4    43.9    -      -       +      -
    313A  ALA      2.9    22.4    +      -       -      -
    316A  ALA*     3.9    27.4    -      -       +      -
    318A  LEU*     4.1    17.0    -      -       +      -
    337A  VAL*     4.5     6.5    -      -       +      -
    356A  GLN      2.9    17.3    +      -       -      +
    357A  PHE*     3.2    33.0    +      +       -      +
    359A  ALA*     1.3    77.4    -      -       -      +
    361A  LEU*     1.3    88.3    +      -       +      +
    363A  ASP*     3.3    14.1    +      -       -      +
    366A  LYS*     3.7    25.0    -      -       +      +
    367A  LYS      5.5     1.1    -      -       -      -
    368A  LYS*     2.8    49.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 361 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  LEU*     3.8    29.2    -      -       +      -
    320A  VAL*     4.9     2.7    -      -       +      -
    352A  LEU*     3.8    18.8    -      -       +      -
    357A  PHE*     2.9    43.3    +      -       +      +
    358A  VAL*     3.3    10.5    -      -       -      +
    360A  TRP*     1.3    88.4    -      -       +      +
    362A  GLY*     1.3    56.2    +      -       -      +
    368A  LYS*     3.0    14.1    +      -       -      +
    380A  LEU*     4.5    11.7    -      -       +      -
    385A  ILE*     4.0    17.9    -      -       +      -
    386A  GLU      3.7     9.6    -      -       -      +
    387A  LEU*     3.6    12.9    -      -       +      +
    388A  CYS      2.8    22.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 362 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  VAL      3.1    13.1    +      -       -      -
    359A  ALA*     3.3     4.5    +      -       -      -
    360A  TRP      3.2     0.2    -      -       -      -
    361A  LEU*     1.3    73.8    -      -       -      +
    363A  ASP*     1.3    60.4    +      -       -      +
    364A  GLU      3.5     1.2    +      -       -      -
    386A  GLU*     3.5    19.2    +      -       -      -
    388A  CYS*     3.5    22.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 363 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359A  ALA      3.0    16.1    +      -       -      +
    360A  TRP*     3.3     3.0    +      -       -      +
    361A  LEU      3.4     0.2    -      -       -      -
    362A  GLY*     1.3    76.0    -      -       -      +
    364A  GLU*     1.3    61.7    +      -       -      +
    365A  THR*     2.5    37.9    +      -       -      +
    366A  LYS*     3.0    42.7    +      -       +      -
    368A  LYS*     3.1    17.1    +      -       -      -
    388A  CYS*     4.4     0.4    -      -       -      -
----------------------------------------------------------
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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