Contacts of the strand formed by residues 5 - 14 (chain D) in PDB entry 6B0Z


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 ILE 5 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3D  LYS      3.7     2.4    +      -       -      +
      4D  LYS*     1.3    71.7    -      -       -      +
      6D  SER*     1.3    75.5    +      -       -      +
     34D  TYR*     2.7    18.0    +      -       +      +
     35D  VAL*     3.1    26.4    -      -       +      -
     36D  GLU      3.3     4.9    +      -       -      -
    351D  GLU*     3.4    32.8    -      -       +      +
    352D  LEU*     3.9    28.9    -      -       +      +
    354D  PHE*     6.0     2.2    -      -       +      -
    355D  PHE*     3.7    22.7    -      -       +      -
    409D  LEU*     6.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 6 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  LYS      3.4     5.7    +      -       -      -
      5D  ILE*     1.3    82.4    -      -       -      +
      7D  GLY*     1.3    60.9    +      -       -      +
      8D  GLY*     4.2     5.9    +      -       -      -
     36D  GLU      3.9     5.6    +      -       -      +
    349D  ASN*     3.1    25.6    +      -       -      -
    351D  GLU*     5.8     0.6    -      -       -      +
    352D  LEU*     4.1     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 7 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  ILE      3.6     0.6    +      -       -      -
      6D  SER*     1.3    75.2    +      -       -      +
      8D  GLY*     1.3    58.5    +      -       -      +
     35D  VAL*     4.0     5.4    -      -       -      -
     36D  GLU      2.9    13.3    +      -       -      -
     37D  LEU*     3.4    25.6    -      -       -      -
    343D  ARG*     3.4    12.8    -      -       -      +
    347D  ASP*     4.7     1.6    -      -       -      +
    349D  ASN*     4.1     5.6    +      -       -      -
    352D  LEU*     3.4    24.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 8 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  SER*     3.9     5.3    +      -       -      -
      7D  GLY*     1.3    77.7    -      -       -      +
      9D  SER*     1.3    59.7    +      -       -      -
     10D  VAL*     4.4     1.8    -      -       -      -
     36D  GLU      4.3     0.2    +      -       -      -
     37D  LEU*     3.3    11.3    -      -       -      +
     38D  ASP*     2.4    35.8    +      -       -      +
    343D  ARG*     4.8     4.7    -      -       -      -
    347D  ASP*     4.9     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 9 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8D  GLY*     1.3    71.4    -      -       -      -
     10D  VAL*     1.3    60.1    +      -       -      +
     38D  ASP*     2.9    31.9    +      -       -      +
     40D  HIS*     4.3     1.1    -      -       -      -
     67D  HIS*     4.0    24.5    -      -       -      +
     69D  VAL*     4.4     1.4    -      -       -      +
    343D  ARG*     3.1    38.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 10 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8D  GLY      3.7     2.0    +      -       -      +
      9D  SER*     1.3    79.4    -      -       -      +
     11D  VAL*     1.3    72.5    +      -       -      +
     37D  LEU*     4.0    33.4    -      -       +      -
     38D  ASP      3.1     7.1    +      -       -      +
     39D  LEU*     3.4    11.5    -      -       +      +
     40D  HIS*     3.0    24.2    +      -       -      -
     69D  VAL*     3.8    24.5    -      -       +      +
     71D  VAL*     4.3    16.4    -      -       +      -
    336D  TRP*     5.1     1.6    -      -       +      -
    340D  LEU*     4.2    19.5    -      -       +      -
    343D  ARG*     4.4    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 11 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  VAL*     1.3    75.4    -      -       -      +
     12D  GLU*     1.3    61.7    +      -       -      +
     13D  MET*     4.7     6.3    -      -       +      -
     40D  HIS*     3.4    16.2    -      -       +      +
     42D  TYR*     4.0    21.8    -      -       +      -
     60D  ALA      4.3     2.2    -      -       -      +
     63D  ALA*     3.8    27.8    -      -       +      +
     64D  ILE*     4.2    16.4    -      -       +      +
     67D  HIS*     3.8    22.0    -      -       +      -
     69D  VAL      2.9    18.3    +      -       -      +
     70D  GLY*     3.2     4.8    -      -       -      -
     71D  VAL*     2.7    36.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 12 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  VAL      3.9     1.0    +      -       -      -
     11D  VAL*     1.3    75.0    -      -       -      +
     13D  MET*     1.3    65.2    +      -       -      +
     14D  GLN*     3.0    22.0    +      -       -      +
     23D  TRP*     2.8    28.1    +      -       -      -
     27D  LYS*     2.5    39.2    +      -       -      +
     39D  LEU*     4.0    18.7    -      -       +      +
     40D  HIS      2.9     8.8    +      -       -      +
     41D  SER*     3.8    23.7    +      -       -      +
     42D  TYR*     3.0    27.7    +      -       -      +
     71D  VAL*     3.3    14.1    -      -       +      +
    336D  TRP*     3.5     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 13 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11D  VAL*     4.7     5.8    -      -       +      +
     12D  GLU*     1.3    77.9    -      -       -      +
     14D  GLN*     1.3    62.7    +      -       -      +
     23D  TRP*     4.2     5.0    -      -       -      -
     42D  TYR*     3.2     4.0    -      -       +      +
     44D  LEU*     3.4    26.2    -      -       +      -
     60D  ALA*     3.7    24.7    -      -       +      -
     64D  ILE*     3.7    30.1    -      -       +      -
     70D  GLY*     4.6     0.9    -      -       -      -
     71D  VAL      3.0    31.0    +      -       -      +
     72D  LYS*     3.7    25.8    -      -       +      -
     73D  CYS*     2.9    30.8    +      -       -      +
     99D  ILE*     4.4    18.2    -      -       -      -
    304D  GLU*     4.1     6.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 14 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12D  GLU*     3.0    28.2    +      -       -      +
     13D  MET*     1.3    74.1    -      -       -      +
     15D  GLY*     1.3    60.6    +      -       -      +
     20D  ARG*     5.7     5.6    -      -       +      -
     23D  TRP*     4.5     5.8    -      -       +      +
     24D  GLU*     4.1    16.2    +      -       -      +
     27D  LYS*     4.0     4.8    -      -       -      +
     41D  SER*     4.4    13.9    -      -       -      -
     42D  TYR      2.9    10.5    +      -       -      +
     43D  ASP*     3.6    34.2    -      -       -      +
     44D  LEU*     3.1    28.7    +      -       -      +
     45D  GLY      4.2     0.7    -      -       -      -
     73D  CYS*     4.2     3.5    -      -       -      +
     75D  THR*     4.1     2.1    -      -       -      +
----------------------------------------------------------
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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