Contacts of the strand formed by residues 38 - 48 (chain D) in PDB entry 1EJH


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 PRO 38 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35D  ILE*     5.6     1.1    -      -       +      -
     36D  LYS      3.0    12.9    -      -       -      +
     37D  HIS*     1.3    83.5    -      -       -      +
     39D  LEU*     1.3    66.2    +      -       -      +
     67D  ASP*     3.7     7.9    -      -       -      +
     68D  THR*     4.4     5.4    -      -       +      -
    624H  TYR*     3.1    27.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 39 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  PRO*     1.3    81.0    -      -       -      +
     40D  GLN*     1.3    65.7    +      -       -      +
     41D  ASN*     3.2    17.9    +      -       -      +
     43D  TRP*     4.2     1.8    -      -       +      +
     66D  PHE*     3.9    23.6    -      -       +      -
     67D  ASP*     2.8    26.9    +      -       -      +
     68D  THR      3.6    21.8    -      -       -      +
     69D  VAL*     3.6    31.6    -      -       +      +
     72D  PHE*     5.0     0.2    -      -       +      -
    138D  ILE*     3.7    38.8    -      -       +      +
    624H  TYR*     4.7     7.4    -      -       +      -
    629H  LEU*     5.1     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 40 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39D  LEU*     1.3    75.0    -      -       -      +
     41D  ASN*     1.3    75.7    +      -       -      +
    138D  ILE      4.7     3.8    +      -       -      -
    140D  GLU*     3.5    34.5    -      -       +      +
    147D  ASP*     5.9     2.9    -      -       -      +
    624H  TYR*     5.6     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 41 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39D  LEU*     3.2    16.9    -      -       -      +
     40D  GLN*     1.3    96.4    +      -       -      +
     42D  ARG*     1.3    65.1    +      -       -      +
     43D  TRP*     3.1    36.0    +      -       +      +
     67D  ASP*     4.1     4.0    -      -       -      -
     95D  LYS*     3.9    33.7    +      -       +      +
    140D  GLU*     3.5    16.6    +      -       -      +
    147D  ASP*     5.5     2.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 42 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  ASN*     1.3    76.7    -      -       -      +
     43D  TRP*     1.3    65.8    +      -       -      +
     65D  LYS*     4.5    11.2    -      -       +      -
     66D  PHE      3.3    19.3    -      -       -      +
     67D  ASP*     3.6    30.7    +      -       +      +
     95D  LYS*     3.7     4.0    -      -       -      -
     96D  ASP*     2.8    58.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 43 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39D  LEU*     4.2     3.5    -      -       +      +
     41D  ASN*     3.1    40.0    +      -       +      +
     42D  ARG*     1.3    77.1    -      -       -      +
     44D  ALA*     1.3    62.6    +      -       -      +
     45D  LEU      4.3     0.2    -      -       -      -
     64D  SER      4.0     0.4    -      -       -      +
     65D  LYS*     3.1     8.4    -      -       -      +
     66D  PHE*     2.8    55.0    +      +       +      -
     93D  LEU*     3.8    20.0    -      -       +      -
     94D  PHE      3.5    22.7    -      -       -      -
     95D  LYS*     3.6    37.5    -      -       +      -
     96D  ASP*     4.6     1.3    -      -       -      -
    137D  LEU*     3.2    53.8    -      -       +      -
    138D  ILE*     3.7    30.1    +      -       +      +
    140D  GLU*     3.7    10.4    +      -       -      -
    149D  VAL*     4.5     4.9    -      -       +      -
    150D  CYS      4.0     4.0    -      -       -      -
    151D  GLY*     4.2     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 44 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43D  TRP*     1.3    76.4    -      -       -      +
     45D  LEU*     1.3    60.3    +      -       -      +
     46D  TRP*     3.3    21.5    -      -       +      +
     62D  LEU*     3.6    20.4    -      -       +      -
     64D  SER      3.4     4.7    -      -       -      -
     65D  LYS*     3.8    17.9    -      -       +      -
     92D  SER      3.3     1.2    -      -       -      +
     93D  LEU*     3.4     4.6    -      -       -      -
     94D  PHE      2.9    32.1    +      -       -      +
     95D  LYS      5.4     0.2    -      -       -      +
     96D  ASP*     4.9     7.4    -      -       -      -
     97D  GLY      5.9     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 45 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44D  ALA*     1.3    72.8    -      -       -      +
     46D  TRP*     1.3    56.1    +      -       -      +
     62D  LEU*     3.2     4.9    -      -       -      +
     63D  ILE*     2.7    47.7    +      -       +      +
     64D  SER      2.9     8.6    +      -       -      +
     66D  PHE*     5.0     0.4    -      -       -      -
     75D  LEU*     3.7    35.2    -      -       +      -
     79D  ILE*     3.3    33.4    -      -       +      -
     91D  TYR*     4.0    23.8    -      -       +      -
     92D  SER      3.2    19.1    -      -       -      +
     93D  LEU*     4.0    15.8    -      -       +      +
    130D  TRP*     5.1     6.1    -      -       +      +
    134D  LEU*     5.8     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 46 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  LYS      4.5     3.1    -      -       -      -
     55B  THR*     3.9    28.5    -      -       +      -
     44D  ALA*     3.3    31.3    +      -       +      +
     45D  LEU*     1.3    75.8    -      -       -      +
     47D  PHE*     1.3    60.7    +      -       -      +
     60D  LEU*     4.1    14.6    -      -       +      -
     61D  ARG      3.3     8.7    -      -       -      +
     62D  LEU*     3.7    48.7    -      -       +      -
     63D  ILE*     4.7     0.4    -      -       -      -
     65D  LYS*     5.8     1.6    -      -       -      -
     90D  ASP      3.9     0.2    -      -       -      +
     91D  TYR*     3.4    10.3    -      -       -      -
     92D  SER*     2.7    47.8    +      -       -      +
     94D  PHE*     4.6     5.4    -      -       +      +
     98D  ILE      4.1     9.2    +      -       -      -
     99D  GLU*     4.3    27.1    -      -       +      -
    100D  PRO*     3.6    34.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 47 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46D  TRP*     1.3    74.7    -      -       -      +
     48D  PHE*     1.3    79.9    +      -       -      +
     49D  LYS*     4.1    16.6    -      -       +      -
     59D  ASN      3.6     2.6    -      -       -      +
     60D  LEU*     3.7     4.1    -      -       -      +
     61D  ARG*     2.7    43.3    +      -       +      +
     63D  ILE*     3.4    29.6    -      -       +      +
     85D  LEU*     3.6    28.5    -      -       +      -
     89D  CYS*     3.7    21.5    -      -       +      -
     90D  ASP      3.3    12.6    -      -       -      -
     91D  TYR*     3.8    15.0    -      +       +      -
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Residues in contact with PHE 48 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47D  PHE*     1.3    80.8    -      -       -      +
     49D  LYS*     1.3    74.5    +      -       -      +
     50D  ASN*     4.1    12.3    -      -       -      -
     56D  TRP*     3.6    44.2    -      +       -      -
     59D  ASN*     3.5    31.2    -      -       +      -
     60D  LEU*     4.1    22.2    -      -       +      -
     88D  GLY      3.4    24.5    -      -       -      -
     89D  CYS*     3.1    27.5    -      -       -      +
     90D  ASP*     2.8    41.3    +      -       +      +
    157D  ARG*     5.3     2.2    -      -       -      -
----------------------------------------------------------
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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