Contacts of the strand formed by residues 67 - 76 (chain L) in PDB entry 6O81


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 ASN 67 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20L  MET*     4.4    13.4    -      -       +      +
     21L  VAL      3.2     7.4    -      -       -      +
     22L  ASN*     3.4    16.6    -      -       -      +
     36L  LEU*     3.6    26.9    -      -       -      +
     65L  GLY      4.2     4.7    +      -       -      +
     66L  ARG*     1.3    87.9    +      -       -      +
     68L  GLU*     1.3    61.7    +      -       -      +
    101L  PHE*     4.3    13.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 68 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20L  MET*     3.5     6.9    -      -       -      +
     21L  VAL*     2.9    43.0    +      -       +      +
     23L  VAL*     5.7     5.6    -      -       +      -
     45L  ILE*     5.8     1.8    -      -       +      -
     66L  ARG*     3.8    12.1    +      -       -      +
     67L  ASN*     1.3    75.6    -      -       -      +
     69L  CYS*     1.3    62.9    +      -       -      +
     70L  VAL*     6.1     0.2    -      -       +      -
     86L  LYS*     4.3    29.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 69 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18L  VAL*     3.7    22.0    -      -       +      -
     19L  VAL      3.4     5.4    -      -       -      +
     20L  MET*     3.8    20.5    -      -       +      -
     68L  GLU*     1.3    73.4    -      -       -      +
     70L  VAL*     1.3    60.1    +      -       -      +
     86L  LYS*     4.2     9.7    -      -       -      +
     89L  VAL*     3.5    19.8    -      -       +      +
     94L  ALA*     4.3    21.5    -      -       +      +
     97L  CYS*     4.1     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 70 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18L  VAL*     4.1     4.5    -      -       -      +
     19L  VAL*     2.9    37.3    +      -       -      +
     21L  VAL*     4.4     9.9    -      -       +      -
     45L  ILE*     4.2    17.5    -      -       +      -
     68L  GLU*     3.9     1.0    +      -       +      -
     69L  CYS*     1.3    75.0    -      -       -      +
     71L  VAL*     1.3    61.2    +      -       -      +
     84L  LEU*     4.0    24.7    -      -       +      -
     85L  SER      3.4    17.7    -      -       -      +
     86L  LYS*     4.6     1.8    -      -       +      +
     89L  VAL*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 71 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16L  GLU*     5.1     6.7    -      -       -      -
     17L  ASP      3.9     5.4    -      -       -      -
     18L  VAL*     4.1    19.3    -      -       +      +
     70L  VAL*     1.3    72.8    -      -       -      +
     72L  VAL*     1.3    64.8    +      -       -      +
     73L  ILE      3.5     0.7    +      -       -      -
     84L  LEU*     3.5     2.2    -      -       -      -
     85L  SER*     2.9    38.1    +      -       -      +
     88L  ARG*     4.2    23.1    -      -       +      -
     89L  VAL*     4.7     7.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 72 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13L  PRO*     5.0     6.7    -      -       +      -
     14L  GLU      3.5    23.6    -      -       -      +
     15L  VAL*     4.6     0.8    -      -       -      +
     16L  GLU*     2.9    27.0    +      -       -      +
     17L  ASP      3.3    17.5    +      -       -      +
     19L  VAL*     5.7     0.4    -      -       +      -
     70L  VAL      4.0     0.6    +      -       -      -
     71L  VAL*     1.3    72.9    -      -       -      +
     73L  ILE*     1.3    60.1    +      -       -      +
     75L  VAL*     4.3    16.4    -      -       +      -
     83L  ASP      3.6     6.7    -      -       -      +
     84L  LEU*     3.8    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 73 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15L  VAL*     5.1     9.3    -      -       -      +
     46L  LEU*     5.9     4.0    -      -       +      -
     49L  GLU*     6.1     3.1    -      -       +      -
     71L  VAL      3.5     4.3    +      -       -      +
     72L  VAL*     1.3    73.9    -      -       -      +
     74L  ARG*     1.3    63.0    +      -       +      +
     83L  ASP*     2.9    18.8    +      -       +      +
     84L  LEU      5.2     0.7    -      -       -      +
     85L  SER*     4.8    12.6    -      -       -      -
     88L  ARG*     5.6    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 74 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247E  GLU*     3.6    25.1    -      -       -      -
    289E  SER*     5.3     3.9    +      -       -      -
     15L  VAL*     6.3     0.4    -      -       -      -
     73L  ILE*     1.3    81.4    -      -       +      +
     75L  VAL*     1.3    73.4    +      -       -      +
     76L  ASP*     5.0    10.3    -      -       +      -
     81L  TYR*     3.9    30.5    -      -       -      +
     82L  ILE*     3.6     0.7    -      -       -      -
     83L  ASP*     2.7    48.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 75 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12L  PHE*     4.3    26.5    -      -       +      -
     13L  PRO*     3.7    28.9    -      -       +      +
     14L  GLU      4.5     5.4    -      -       -      +
     15L  VAL*     5.1     4.5    -      -       +      +
     72L  VAL*     4.3    20.2    -      -       +      -
     74L  ARG*     1.3    86.9    -      -       -      +
     76L  ASP*     1.3    69.2    +      -       -      +
     77L  LYS*     4.7     2.5    -      -       +      +
     81L  TYR      3.5     4.9    -      -       -      -
     82L  ILE*     4.6    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 76 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247E  GLU*     5.8     0.2    -      -       -      +
     12L  PHE*     4.7     3.3    -      -       -      -
     74L  ARG*     5.0     8.9    -      -       +      -
     75L  VAL*     1.3    78.8    -      -       -      +
     77L  LYS*     1.3    61.0    +      -       -      +
     78L  GLU*     3.4    18.0    +      -       -      +
     79L  LYS*     3.4    33.2    +      -       +      +
     80L  GLY*     2.9    29.3    +      -       -      -
     81L  TYR*     2.9    21.3    +      -       +      +
----------------------------------------------------------
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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