Contacts of the strand formed by residues 343 - 349 (chain D) in PDB entry 6CIM


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 PHE 343 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    549C  PRO*     5.4     5.2    -      -       +      -
     12D  ILE*     3.9    19.8    -      -       +      +
     15D  ILE      4.2    20.2    -      -       -      -
     16D  GLN*     5.0     0.9    -      -       +      -
     17D  PRO*     4.1    16.4    -      -       +      -
    316D  ILE*     6.4     0.7    -      -       +      -
    318D  PHE*     3.3    33.9    -      +       -      -
    331D  ILE      3.3    16.8    -      -       -      -
    332D  PRO*     4.0    17.7    -      -       +      -
    333D  GLY      4.3     0.4    -      -       -      +
    341D  GLU*     3.4     7.3    -      -       -      +
    342D  ALA*     1.3    92.8    -      -       +      +
    344D  TYR*     1.3    73.3    +      -       -      +
    345D  PHE*     3.5    28.5    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 344 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  MET*     5.1    13.2    -      -       +      -
    310D  ASP*     6.0     7.6    -      -       +      -
    330D  GLY*     3.4     1.0    -      -       -      -
    331D  ILE*     2.9    42.5    +      -       +      +
    332D  PRO      4.9     3.8    -      -       -      -
    333D  GLY*     4.3    19.1    -      -       -      -
    334D  ASP*     4.6     9.9    +      -       +      +
    341D  GLU*     3.5    40.6    +      -       +      -
    343D  PHE*     1.3    81.2    -      -       -      +
    345D  PHE*     1.3    60.7    +      -       -      +
    346D  TYR*     3.9    18.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 345 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  MET*     3.7     4.9    -      -       -      +
      6D  VAL*     2.9    37.8    +      -       +      +
      8D  VAL*     3.5    21.3    -      -       +      -
     12D  ILE*     3.7    25.6    -      -       +      -
     15D  ILE*     3.8    38.6    -      -       +      -
    318D  PHE*     3.9    10.3    -      +       -      -
    328D  PHE*     3.6    28.7    -      +       +      -
    329D  LEU      3.2    17.0    -      -       -      +
    330D  GLY*     3.5    15.5    -      -       -      -
    343D  PHE*     3.5    32.3    -      +       +      -
    344D  TYR*     1.3    73.0    -      -       -      +
    346D  TYR*     1.3    70.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 346 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3D  LEU*     3.6    33.0    -      -       +      -
      4D  GLN      3.1     7.6    -      -       -      +
      5D  MET*     3.2    46.4    -      -       +      +
      6D  VAL*     3.8     2.2    -      -       -      -
    308D  THR*     3.8    26.5    +      -       +      -
    310D  ASP*     3.9    18.5    +      -       +      +
    311D  ILE*     4.0    24.0    -      -       +      -
    328D  PHE*     3.6     3.3    -      -       -      -
    329D  LEU*     2.8    42.3    +      -       +      +
    331D  ILE*     4.0    10.8    -      -       +      -
    344D  TYR*     3.9    25.5    -      -       +      +
    345D  PHE*     1.3    76.6    -      -       -      +
    347D  THR*     1.3    66.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 347 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2D  SER      3.6     3.8    -      -       -      +
      3D  LEU*     3.7     2.2    -      -       -      -
      4D  GLN*     2.8    48.2    +      -       -      +
      6D  VAL*     3.6    19.9    -      -       +      +
     50D  ILE*     3.7    26.1    -      -       +      +
     53D  ASN*     5.2     0.7    +      -       -      -
    322D  MET*     4.3     7.9    -      -       -      -
    326D  THR*     5.7     2.5    -      -       -      -
    327D  ILE      3.2     9.2    -      -       -      +
    328D  PHE*     3.8     9.2    -      -       +      -
    346D  TYR*     1.3    75.0    -      -       -      +
    348D  LEU*     1.3    60.2    +      -       -      +
    349D  ARG*     4.0    19.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 348 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1D  MET*     3.6    34.1    -      -       +      -
      2D  SER      3.8    17.3    -      -       -      +
      3D  LEU*     4.2    16.4    -      -       +      +
    274D  VAL*     3.9    22.0    -      -       +      -
    305D  PRO*     4.0    23.6    -      -       +      -
    307D  TRP*     3.7    26.2    -      -       +      -
    326D  THR*     3.6     0.5    -      -       -      -
    327D  ILE*     2.9    45.0    +      -       +      +
    329D  LEU*     4.9     7.8    -      -       +      +
    346D  TYR      4.2     0.6    -      -       -      -
    347D  THR*     1.3    72.1    -      -       -      +
    349D  ARG*     1.3    64.4    +      -       -      +
    350D  CYS*     4.4     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 349 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1D  MET*     3.0    28.9    -      -       -      +
      2D  SER*     3.3    26.6    +      -       -      +
      4D  GLN*     4.5    11.1    -      -       -      +
     50D  ILE*     6.1     2.6    -      -       -      +
     53D  ASN*     3.7    21.2    +      -       -      -
    326D  THR*     3.7    25.9    -      -       +      +
    347D  THR*     4.2    21.5    +      -       -      +
    348D  LEU*     1.3    76.0    -      -       -      +
    350D  CYS*     1.3    66.7    +      -       -      +
----------------------------------------------------------
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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