Contacts of the strand formed by residues 234 - 244 (chain C) in PDB entry 4AEJ


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 GLU 234 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91C  ARG      4.8     1.6    -      -       -      +
     92C  LYS*     3.6    12.7    +      -       -      +
     93C  HIS*     3.7    27.7    -      -       +      +
     94C  TRP      5.3     0.4    -      -       -      +
    152C  LYS*     3.0    53.6    +      -       +      +
    154C  SER*     3.8     7.3    -      -       -      -
    203C  TRP*     3.1    31.9    +      -       +      -
    228C  ILE*     5.7     0.2    -      -       -      -
    231C  PRO      5.1     3.7    -      -       -      +
    232C  ASP      4.1     5.9    -      -       -      +
    233C  GLN*     1.3    79.7    -      -       -      +
    235C  PHE*     1.3    68.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 235 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89C  VAL*     4.6     4.9    -      -       +      -
     91C  ARG*     4.1     5.4    -      -       -      -
     92C  LYS      3.0    24.2    +      -       -      -
     94C  TRP*     3.1    44.4    -      +       +      -
     95C  TRP      5.3     1.1    -      -       -      -
    107C  PHE*     4.5     9.6    -      +       +      -
    111C  MSE      3.8    24.9    -      -       +      -
    149C  TYR*     3.4    39.9    -      +       +      +
    150C  HIS      3.0    15.9    -      -       -      +
    203C  TRP*     3.9     4.5    -      -       -      -
    223C  ILE*     5.3     1.3    -      -       +      -
    225C  PRO*     3.9    19.1    -      -       +      -
    228C  ILE*     4.2    15.7    -      -       +      -
    234C  GLU*     1.3    81.2    -      -       -      +
    236C  GLY*     1.3    68.3    +      -       -      +
    237C  VAL*     4.1    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 236 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89C  VAL*     3.4    13.9    -      -       -      -
     90C  PRO      3.8     8.1    -      -       -      -
     91C  ARG*     4.1     4.9    -      -       -      -
    149C  TYR*     3.7     2.3    -      -       -      -
    150C  HIS*     2.8    43.0    +      -       -      +
    203C  TRP*     4.3     0.8    -      -       -      -
    235C  PHE*     1.3    79.4    -      -       -      +
    237C  VAL*     1.3    66.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 237 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88C  ASN*     3.1     9.0    -      -       -      +
     89C  VAL*     2.8    54.3    +      -       +      +
    117C  PHE*     4.9     1.6    -      -       +      -
    147C  ILE*     3.5    33.7    -      -       +      -
    148C  THR      3.2    12.1    -      -       -      +
    149C  TYR*     4.6     1.6    -      -       +      -
    150C  HIS*     4.4     2.2    -      -       -      -
    223C  ILE*     4.2    23.8    -      -       +      -
    235C  PHE*     4.1    18.2    -      -       +      -
    236C  GLY*     1.3    79.6    -      -       -      +
    238C  ASP*     1.3    69.7    +      -       -      +
    239C  VAL*     3.9     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 238 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  LEU      4.1     4.0    -      -       -      +
     88C  ASN*     3.5    15.6    +      -       -      +
    147C  ILE*     3.6     0.7    -      -       -      -
    148C  THR*     2.8    49.5    +      -       -      +
    150C  HIS*     2.5    32.8    +      -       -      -
    237C  VAL*     1.3    78.7    -      -       -      +
    239C  VAL*     1.3    65.0    +      -       -      +
    240C  GLY      3.5     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 239 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  ALA*     4.1    19.6    +      -       +      +
     86C  PRO      5.0     1.1    -      -       -      +
     87C  LEU*     3.1    33.6    +      -       -      +
     88C  ASN*     5.3     1.8    -      -       -      -
     89C  VAL*     5.3     0.9    -      -       +      -
    117C  PHE*     3.9    40.6    -      -       +      -
    119C  TYR*     3.3    15.0    -      -       -      +
    145C  GLN*     3.3    24.9    -      -       -      +
    146C  GLN      4.8     0.2    -      -       -      +
    147C  ILE*     4.1    19.7    -      -       +      -
    220C  ILE*     5.5     1.1    -      -       +      -
    237C  VAL*     4.1     7.2    -      -       +      +
    238C  ASP*     1.3    72.2    -      -       -      +
    240C  GLY*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 240 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  ALA      5.4     0.7    -      -       -      -
    119C  TYR*     4.6     1.9    -      -       -      -
    145C  GLN*     2.8    24.6    -      -       -      +
    146C  GLN*     3.1    24.9    +      -       -      -
    238C  ASP*     3.5     4.6    +      -       -      -
    239C  VAL*     1.3    75.8    -      -       -      +
    241C  PRO*     1.3    74.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 241 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72C  PHE*     6.0     3.4    -      -       +      -
     81C  CYS*     3.9    18.8    -      -       +      -
     82C  ILE      3.2    22.9    -      -       -      +
     83C  SER*     4.1    13.4    -      -       -      +
     84C  ALA      4.9     0.7    -      -       -      +
     87C  LEU*     6.3     2.7    -      -       +      -
    144C  SER      4.0     1.9    -      -       -      +
    145C  GLN*     3.4    10.6    -      -       -      +
    146C  GLN      4.5     1.6    +      -       -      -
    239C  VAL      4.8     0.7    -      -       -      +
    240C  GLY*     1.3    87.3    -      -       -      +
    242C  VAL*     1.3    62.1    +      -       -      +
    243C  CYS*     3.7    17.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 242 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80C  THR      3.6     1.4    -      -       -      +
     81C  CYS*     3.2     1.4    -      -       -      -
     82C  ILE*     2.8    47.5    +      -       +      +
    119C  TYR*     4.0    10.7    -      -       +      -
    133C  LEU*     5.1     1.1    -      -       +      -
    143C  ALA*     5.1     0.2    -      -       +      -
    144C  SER      3.7     8.7    -      -       -      +
    145C  GLN*     4.0    10.0    +      -       -      +
    218C  LEU*     3.9    16.2    -      -       +      -
    219C  PRO*     3.6    43.1    -      -       +      -
    240C  GLY      3.6     1.2    +      -       -      -
    241C  PRO*     1.3    72.3    -      -       -      +
    243C  CYS*     1.3    62.5    +      -       -      +
    244C  PHE*     4.0    28.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 243 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79C  GLU*     3.7    21.8    -      -       -      +
     80C  THR      3.2     2.9    -      -       -      -
     81C  CYS*     2.1    46.9    -      -       -      -
    143C  ALA*     3.1     5.6    -      -       -      +
    144C  SER*     2.8    46.5    +      -       -      +
    241C  PRO*     3.9    16.8    -      -       -      -
    242C  VAL*     1.3    76.2    -      -       -      +
    244C  PHE*     1.3    61.1    +      -       -      +
    245C  LEU      4.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 244 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78C  GLY      4.4     0.7    -      -       -      +
     79C  GLU*     3.3     4.8    -      -       -      -
     80C  THR*     2.8    47.4    +      -       -      +
     82C  ILE*     4.0    21.3    -      -       +      -
    133C  LEU*     4.3    14.4    -      -       +      -
    136C  LEU*     4.1    30.7    -      -       +      +
    137C  ARG*     4.0    28.7    -      -       +      -
    140C  SER*     3.1    22.9    -      -       -      +
    142C  ARG      3.6     2.9    -      -       -      -
    143C  ALA*     3.7    22.0    -      -       +      -
    215C  ALA*     4.0    14.4    -      -       +      -
    218C  LEU      4.7     4.9    -      -       -      -
    219C  PRO      5.2     0.2    -      -       -      -
    242C  VAL*     4.0    27.6    -      -       +      -
    243C  CYS*     1.3    74.6    -      -       -      +
    245C  LEU*     1.3    59.2    +      -       -      +
----------------------------------------------------------
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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