Contacts of the strand formed by residues 94 - 103 (chain C) in PDB entry 6P59


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 LYS 94 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88C  LEU*     3.6    12.5    -      -       -      +
     91C  GLU*     3.2    57.7    +      -       +      +
     92C  ALA      3.3     4.1    -      -       -      +
     93C  GLY*     1.3    82.1    +      -       -      +
     95C  VAL*     1.3    59.0    +      -       -      +
     96C  TYR*     4.5    20.0    +      -       +      +
    113C  TRP*     4.9    24.4    -      -       +      -
    114C  ILE      3.5     9.2    -      -       -      +
    115C  ASP*     5.0     8.3    -      -       -      +
    116C  LEU*     3.3    13.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  PHE*     3.9    20.2    -      -       +      -
     48C  CYS*     5.3     0.9    -      -       -      -
     86C  VAL*     4.2    15.0    -      -       +      -
     87C  ASP      3.6    10.5    -      -       -      +
     88C  LEU*     3.5    22.9    -      -       +      -
     94C  LYS*     1.3    75.6    -      -       -      +
     96C  TYR*     1.3    76.3    +      -       -      +
     97C  LEU*     4.4     8.6    -      -       +      +
    113C  TRP*     3.0     4.5    -      -       -      -
    114C  ILE*     2.9    55.3    +      -       +      +
    116C  LEU*     3.6    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85C  TYR      3.9     0.6    -      -       -      +
     86C  VAL*     3.8     2.1    -      -       -      -
     87C  ASP*     3.0    36.1    +      -       +      +
     90C  ARG*     3.5    48.2    -      -       +      +
     91C  GLU*     3.4    29.4    +      -       +      -
     94C  LYS*     4.5    16.4    +      -       +      +
     95C  VAL*     1.3    81.6    -      -       -      +
     97C  LEU*     1.3    64.9    +      -       -      +
    111C  LYS*     6.4     0.9    -      -       +      -
    112C  GLY      3.2    15.3    -      -       -      -
    113C  TRP*     4.2    27.5    -      +       +      -
----------------------------------------------------------
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Residues in contact with LEU 97 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  ILE*     4.2    13.7    -      -       +      -
     57C  PHE*     3.6    47.8    -      -       +      -
     68C  PHE*     4.2    11.0    -      -       +      -
     85C  TYR      3.3     4.5    -      -       -      -
     86C  VAL*     4.0    27.6    -      -       +      -
     95C  VAL*     4.4     9.0    -      -       +      +
     96C  TYR*     1.3    83.3    -      -       -      +
     98C  LYS*     1.3    61.2    -      -       -      +
    110C  TRP*     3.7    27.8    -      -       +      -
    111C  LYS*     3.3     8.5    -      -       -      +
    112C  GLY      2.6    32.9    +      -       -      +
    114C  ILE*     4.3     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68C  PHE*     3.6     7.0    -      -       -      -
     84C  GLU*     4.6    14.8    +      -       +      +
     85C  TYR*     2.8    64.1    +      -       +      +
     97C  LEU*     1.3    74.9    -      -       -      +
     99C  ALA*     1.3    64.8    +      -       -      +
    100C  PRO*     4.5     5.6    -      -       +      -
    109C  ILE*     4.5    23.6    -      -       +      -
    110C  TRP      3.3     7.4    -      -       -      +
    111C  LYS*     5.2     7.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 99 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66C  LEU*     4.3    11.2    -      -       +      -
     68C  PHE*     4.3     4.7    -      -       +      -
     98C  LYS*     1.3    77.9    -      -       -      +
    100C  PRO*     1.3    65.9    -      -       -      +
    101C  MET*     3.7    10.0    +      -       +      +
    109C  ILE*     3.7     3.1    -      -       -      -
    110C  TRP*     2.8    46.9    +      -       +      +
      8F  VAL*     3.6    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 100 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79C  GLN*     3.9    10.2    +      -       -      -
     80C  THR*     6.0     0.4    -      -       -      +
     85C  TYR*     3.0    48.9    -      -       +      +
     98C  LYS*     4.5     6.7    -      -       +      -
     99C  ALA*     1.3    83.5    -      -       -      +
    101C  MET*     1.3    65.2    +      -       -      +
    108C  VAL      3.6     6.5    -      -       -      +
    109C  ILE*     3.5    20.9    -      -       +      -
    128C  ASP*     5.0     2.2    -      -       -      +
    131C  ARG*     3.6    14.1    +      -       -      +
      8F  VAL*     4.0     8.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 101 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21C  LEU*     5.3     4.3    -      -       +      -
     66C  LEU*     3.6    36.8    -      -       +      -
     79C  GLN*     4.1    16.4    -      -       -      +
     99C  ALA*     3.9    12.3    -      -       +      +
    100C  PRO*     1.3    76.6    -      -       -      +
    102C  ILE*     1.3    65.3    +      -       -      +
    103C  LEU*     4.0    20.6    -      -       +      -
    107C  CYS*     3.8     1.4    -      -       -      -
    108C  VAL*     2.9    42.4    +      -       +      +
    110C  TRP*     4.0    20.0    -      -       +      -
    125C  LEU*     6.0     0.7    -      -       +      -
    131C  ARG*     3.3    10.2    +      -       -      +
      8F  VAL*     4.8     4.7    -      -       -      +
     10F  PRO*     3.5    29.8    -      -       +      -
    104F  ASP*     4.4     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 102 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78C  ARG*     5.5     1.6    -      -       +      +
     79C  GLN*     5.5     0.2    +      -       -      -
    101C  MET*     1.3    75.3    -      -       -      +
    103C  LEU*     1.3    59.8    +      -       -      +
    105C  GLY*     3.8    21.1    -      -       -      +
    106C  VAL      3.5     6.3    -      -       -      +
    107C  CYS*     4.2    10.3    -      -       -      +
    131C  ARG*     3.4    42.8    -      -       -      +
    135C  GLU*     4.3    20.4    -      -       +      +
    101F  TYR*     3.9     7.6    -      -       +      +
    102F  PHE*     3.1    24.0    -      -       +      +
    103F  THR*     3.2    21.5    -      -       -      +
    104F  ASP*     2.6    41.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 103 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17C  PHE*     3.9     6.6    -      -       +      -
     18C  PHE*     3.7    41.1    -      -       +      -
     21C  LEU*     4.0    27.1    -      -       +      -
    101C  MET*     4.3    13.2    -      -       +      -
    102C  ILE*     1.3    76.1    -      -       -      +
    104C  ASN*     1.3    72.8    +      -       -      +
    105C  GLY      3.2     0.2    -      -       -      -
    106C  VAL*     2.8    31.4    +      -       -      +
    108C  VAL*     3.7    24.2    -      -       +      -
    125C  LEU*     4.4     6.1    -      -       +      -
     10F  PRO*     3.7    29.2    -      -       +      -
    104F  ASP*     3.3     4.7    -      -       +      -
----------------------------------------------------------
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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