Contacts of the strand formed by residues 73 - 80 (chain C) in PDB entry 6S1M


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 SER 73 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  MET*     6.1     0.2    -      -       -      -
    448B  GLN*     3.3    34.9    +      -       -      +
    449B  PRO*     3.8     7.7    -      -       -      +
     66C  SER*     4.7     8.1    -      -       -      -
     67C  LEU      3.4     7.9    -      -       -      -
     68C  ILE*     4.0    11.0    -      -       -      -
     71C  GLY      3.8     1.4    +      -       -      -
     72C  HIS*     1.3    71.3    -      -       -      +
     74C  CYS*     1.3    60.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 74 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448B  GLN*     3.6     4.4    +      -       -      -
    449B  PRO*     3.8    25.1    -      -       +      +
    450B  ILE*     5.9     0.2    -      -       -      -
    451B  SER*     5.8     5.2    -      -       -      +
     66C  SER*     3.5     6.6    +      -       -      -
     67C  LEU*     2.9    51.9    +      -       -      +
     69C  GLN*     4.2    24.7    -      -       -      +
     72C  HIS*     3.6    11.6    +      -       +      -
     73C  SER*     1.3    75.3    -      -       -      +
     75C  HIS*     1.3    68.5    +      -       -      +
     76C  LYS*     4.4    11.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 75 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  PHE*     3.4    39.4    -      +       +      -
      3B  SER*     3.8    17.1    +      -       -      -
      6B  ALA*     4.9     4.7    -      -       +      -
    231B  GLU*     3.9    16.3    +      -       -      -
    448B  GLN*     3.6    13.9    -      -       -      +
    449B  PRO      3.5     9.5    +      -       -      +
    450B  ILE*     3.8    15.4    -      -       +      +
    451B  SER      3.3    24.9    +      -       -      +
     64C  SER*     3.0    24.7    +      -       -      -
     65C  GLY*     3.3    26.0    +      -       -      -
     66C  SER*     4.4     0.2    -      -       -      +
     74C  CYS*     1.3    78.1    -      -       -      +
     76C  LYS*     1.3    61.9    +      -       -      +
     77C  VAL*     4.3     6.1    -      -       +      +
     96C  ALA*     4.9     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 76 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    451B  SER*     4.0    24.7    -      -       -      +
    453B  SER*     4.1    19.5    -      -       -      +
     63C  VAL      4.1     0.9    -      -       -      +
     64C  SER*     3.4     3.1    -      -       -      -
     65C  GLY      2.9    36.1    +      -       -      +
     66C  SER      5.0     0.2    -      -       -      -
     67C  LEU*     4.0    26.7    -      -       +      +
     69C  GLN*     4.4    16.9    -      -       -      +
     74C  CYS*     4.1    11.8    -      -       -      -
     75C  HIS*     1.3    72.8    -      -       -      +
     77C  VAL*     1.3    65.4    +      -       -      +
     78C  ALA*     4.3     6.5    -      -       +      -
     92C  LEU*     4.9    12.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 77 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217B  LEU*     5.2     7.6    -      -       +      +
    221B  VAL*     5.1     7.6    -      -       +      -
    226B  LEU*     5.0     8.7    -      -       +      -
    231B  GLU*     5.2     3.8    -      -       -      +
    450B  ILE*     5.3     3.8    -      -       +      -
    451B  SER      3.5    13.0    +      -       -      +
    452B  PHE*     3.9    24.2    -      -       +      -
    453B  SER*     3.3    25.8    +      -       -      -
     62C  LEU*     4.5    21.5    -      -       +      -
     63C  VAL      3.7     3.1    -      -       -      -
     64C  SER*     3.3    28.0    -      -       -      +
     75C  HIS*     4.3    13.0    -      -       +      +
     76C  LYS*     1.3    76.9    -      -       -      +
     78C  ALA*     1.3    63.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 78 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217B  LEU*     5.8     0.4    -      -       -      -
    453B  SER*     3.4    18.2    -      -       -      +
     62C  LEU*     3.4     6.2    -      -       -      +
     63C  VAL      2.9    37.6    +      -       -      +
     76C  LYS*     5.1     7.0    -      -       +      -
     77C  VAL*     1.3    77.5    -      -       -      +
     79C  VAL*     1.3    64.3    +      -       -      +
     80C  VAL*     3.6    15.1    -      -       +      +
     88C  VAL*     5.2     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 79 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  LEU*     5.4     7.2    -      -       +      -
    217B  LEU*     3.8    27.4    -      -       +      -
    453B  SER      3.8     5.7    +      -       -      +
    454B  GLY*     4.3     7.8    -      -       -      -
    455B  PHE*     3.1    42.1    +      -       +      +
     60C  THR*     4.9     4.7    -      -       -      -
     61C  TYR      3.5    11.2    -      -       -      +
     62C  LEU*     3.7    24.0    -      -       +      -
     78C  ALA*     1.3    71.4    -      -       -      +
     80C  VAL*     1.3    63.9    +      -       -      +
    101C  TYR*     4.2    30.1    -      -       +      -
    111C  SER*     5.8     0.2    -      -       -      +
    114C  LEU*     5.1     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 80 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455B  PHE*     4.7     4.9    -      -       +      -
     60C  THR*     3.4     8.1    -      -       -      -
     61C  TYR*     2.9    34.7    +      -       +      +
     63C  VAL*     3.9    24.2    -      -       +      +
     78C  ALA*     3.6    26.7    -      -       +      +
     79C  VAL*     1.3    78.7    -      -       -      +
     81C  ARG*     1.3    70.5    +      -       -      +
     84C  LYS*     4.1    31.0    -      -       +      +
     85C  LEU*     4.5     7.4    -      -       +      -
     88C  VAL*     4.4    15.7    -      -       +      -
----------------------------------------------------------
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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