Contacts of the helix formed by residues 42 - 55 (chain A) in PDB entry 2EBJ


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 42 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  PRO*     2.9    18.6    +      -       +      +
     41A  VAL*     1.3    76.7    -      -       -      +
     43A  ALA*     1.3    59.3    +      -       -      +
     44A  GLU*     3.2    11.1    +      -       -      +
     45A  ALA*     3.1    34.1    +      -       +      +
     46A  LEU*     2.9    29.1    +      -       -      +
     89A  ASP*     3.9     5.0    -      -       -      +
     91A  ARG*     3.0    45.6    +      -       -      +
     93A  ARG*     5.8     0.3    +      -       -      +
    138A  LEU*     3.3     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ASP*     1.3    73.2    +      -       -      +
     44A  GLU*     1.3    62.1    +      -       -      +
     45A  ALA      3.6     0.2    +      -       -      -
     46A  LEU*     3.7     4.3    +      -       -      +
     47A  GLY      4.5     1.7    +      -       -      -
     83A  LEU*     5.7     0.2    -      -       +      -
     85A  PHE*     3.8    16.2    -      -       +      -
     89A  ASP*     3.1    20.0    +      -       -      +
     93A  ARG*     5.3     2.5    -      -       +      +
     95A  LEU*     3.6    30.7    -      -       +      -
    138A  LEU*     3.8     3.1    -      -       +      +
    141A  GLN*     3.1    33.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ASP*     3.2     7.8    +      -       -      +
     43A  ALA*     1.3    80.2    -      -       -      +
     45A  ALA*     1.3    59.9    +      -       -      +
     46A  LEU      3.5     0.2    -      -       -      -
     47A  GLY      4.6     3.6    +      -       -      -
     48A  GLU*     5.1     2.8    +      -       -      +
     89A  ASP*     4.7     0.6    +      -       -      -
     93A  ARG*     4.0    26.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  PRO*     4.5     7.6    -      -       +      -
     42A  ASP*     3.1    32.6    +      -       +      +
     44A  GLU*     1.3    74.8    -      -       -      +
     46A  LEU*     1.3    65.0    +      -       -      +
     47A  GLY      3.3     2.5    -      -       -      -
     48A  GLU*     3.3    10.8    +      -       +      +
     49A  ALA*     3.0    22.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PHE*     4.3     4.0    -      -       +      -
     39A  LEU*     4.0    33.7    -      -       +      -
     40A  PRO*     4.2    17.7    -      -       +      +
     42A  ASP      2.9    17.3    +      -       -      +
     44A  GLU      3.5     1.0    -      -       -      -
     45A  ALA*     1.3    77.0    -      -       -      +
     47A  GLY*     1.3    58.6    +      -       -      +
     49A  ALA*     3.1     4.9    +      -       -      +
     50A  LEU*     2.8    39.2    +      -       +      +
    138A  LEU*     3.8    10.1    -      -       +      +
    141A  GLN*     3.4    46.0    -      -       +      +
    142A  ALA*     3.6    20.2    -      -       +      +
    145A  LEU*     4.2     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  ALA      4.5     3.8    +      -       -      -
     44A  GLU      4.6     2.7    +      -       -      -
     45A  ALA      3.3     1.0    -      -       -      -
     46A  LEU*     1.3    78.7    -      -       -      +
     48A  GLU*     1.3    56.0    +      -       -      +
     50A  LEU*     3.6     1.0    +      -       -      +
     51A  GLU*     3.0    23.6    +      -       -      +
    141A  GLN*     4.8     0.8    +      -       -      -
    145A  LEU*     4.2    13.7    -      -       -      +
    149A  ARG*     3.2    30.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  GLU      5.1     2.7    +      -       -      +
     45A  ALA*     3.3    12.1    +      -       +      +
     46A  LEU      3.2     0.4    -      -       -      -
     47A  GLY*     1.3    72.4    -      -       -      +
     49A  ALA*     1.3    71.5    +      -       -      +
     51A  GLU*     3.2     8.4    +      -       +      +
     52A  ASP*     3.0    49.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  LEU*     4.2     9.2    -      -       +      -
     40A  PRO*     3.7    29.8    -      -       +      -
     45A  ALA      3.0    16.1    +      -       -      +
     46A  LEU      3.6     4.0    -      -       -      +
     48A  GLU*     1.3    84.3    +      -       -      +
     50A  LEU*     1.3    62.4    +      -       -      +
     52A  ASP*     3.5     7.3    +      -       -      +
     53A  LEU*     3.4    24.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  LEU*     5.6     0.7    -      -       +      -
     39A  LEU*     4.2    12.1    -      -       +      -
     46A  LEU*     2.8    26.5    +      -       +      +
     47A  GLY*     3.8     4.5    -      -       -      +
     49A  ALA*     1.3    75.6    -      -       -      +
     51A  GLU*     1.3    59.9    +      -       -      +
     53A  LEU*     3.0    12.2    +      -       +      +
     54A  HIS*     2.8    53.8    +      -       +      +
     63A  HIS*     3.7    27.6    -      -       +      -
    142A  ALA*     3.7    32.8    -      -       +      +
    145A  LEU*     3.8    28.3    -      -       +      -
    146A  SER*     3.9     2.5    -      -       -      +
    149A  ARG*     4.7     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  GLY      3.0    19.0    +      -       -      +
     48A  GLU*     3.2    10.7    +      -       +      +
     50A  LEU*     1.3    77.4    -      -       -      +
     52A  ASP*     1.3    67.1    +      -       -      +
     54A  HIS*     4.3    11.9    +      -       -      +
     55A  ARG*     2.9    45.4    +      -       -      +
    149A  ARG*     4.1    15.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  GLU*     3.0    44.2    +      -       -      +
     49A  ALA*     3.5     9.8    -      -       -      +
     50A  LEU      3.2     0.2    -      -       -      -
     51A  GLU*     1.3    80.0    -      -       -      +
     53A  LEU*     1.3    64.6    +      -       +      +
     55A  ARG*     3.7    10.5    +      -       -      +
     56A  GLU*     3.6    19.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     5.3     0.2    -      -       -      +
      3A  LEU*     3.9    20.5    -      -       +      +
      5A  THR*     4.2    11.7    -      -       +      -
     35A  ARG*     3.7    37.5    -      -       -      +
     37A  ALA*     3.8    23.3    -      -       +      -
     39A  LEU*     3.7    30.5    -      -       +      -
     49A  ALA      3.5     9.9    -      -       -      +
     50A  LEU*     3.0    11.5    +      -       +      +
     52A  ASP*     1.3    78.0    -      -       +      +
     54A  HIS*     1.3    66.5    +      -       +      +
     55A  ARG      3.2     0.2    -      -       -      -
     56A  GLU*     3.0    24.4    +      -       -      +
     58A  PRO*     3.5     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  LEU*     5.1     8.5    -      -       +      -
     50A  LEU*     2.8    42.9    +      -       +      +
     51A  GLU*     3.7    14.2    +      -       -      +
     53A  LEU*     1.3    75.7    -      -       +      +
     55A  ARG*     1.3    57.0    +      -       -      +
     57A  GLY*     2.9    19.8    +      -       -      -
     58A  PRO*     3.5    10.4    -      -       +      +
     61A  VAL*     5.3     0.6    -      -       +      +
    145A  LEU      4.2     7.0    -      -       -      -
    146A  SER*     2.9    44.7    +      -       -      -
    149A  ARG*     4.2    21.5    -      -       +      +
    150A  LEU*     3.8    34.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  GLU*     2.9    33.7    +      -       -      +
     52A  ASP*     3.9     8.5    -      -       -      +
     53A  LEU      3.2     0.6    -      -       -      -
     54A  HIS*     1.3    71.5    -      -       -      +
     56A  GLU*     1.3    61.2    +      -       -      +
     57A  GLY*     3.0     7.2    +      -       -      -
----------------------------------------------------------
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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