Contacts of the strand formed by residues 87 - 96 (chain C) in PDB entry 3RT0


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 87 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76C  GLU*     4.5    13.7    -      -       -      +
     77C  VAL      3.1    13.2    -      -       -      +
     78C  ASP*     4.3    11.4    -      -       -      +
     79C  LEU*     4.1     6.2    -      -       -      +
     85C  ALA*     3.8     0.4    -      -       -      +
     86C  THR*     1.3    89.4    +      -       -      +
     88C  SER*     1.3    62.9    +      -       -      +
    109C  GLY*     3.3     8.0    -      -       -      -
    110C  ASP*     3.2    50.8    +      -       -      +
    111C  HIS*     3.5     5.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 88 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75C  ARG      3.8     1.4    -      -       -      +
     76C  GLU*     3.1     8.2    -      -       -      +
     77C  VAL*     2.9    40.5    +      -       -      +
     79C  LEU*     5.3     7.6    -      -       -      -
     87C  LYS*     1.3    77.8    -      -       -      +
     89C  THR*     1.3    60.4    +      -       -      +
     90C  GLU*     2.9    27.1    +      -       -      -
    106C  ILE*     3.6     8.5    -      -       -      +
    108C  GLY      3.6     6.1    -      -       -      -
    109C  GLY*     3.9     1.1    -      -       -      -
    111C  HIS*     3.2    21.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 89 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74C  VAL*     3.9    22.9    -      -       +      -
     75C  ARG      3.6     1.6    -      -       -      +
     76C  GLU*     2.2    30.9    +      -       +      +
     88C  SER*     1.3    71.5    +      -       -      +
     90C  GLU*     1.3    64.7    +      -       -      +
    106C  ILE*     3.4     5.5    -      -       -      +
    107C  VAL*     2.8    44.8    +      -       +      -
    108C  GLY*     2.9    28.6    +      -       -      -
    109C  GLY*     4.1     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 90 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  PHE*     3.6     3.7    -      -       +      -
     56C  LYS*     5.5     1.3    +      -       -      -
     59C  ILE*     5.8     0.7    -      -       -      +
     74C  VAL*     3.4     4.5    -      -       -      +
     75C  ARG*     2.7    81.9    +      -       +      +
     77C  VAL*     4.0    11.0    -      -       -      +
     88C  SER*     2.9    25.3    +      -       -      +
     89C  THR*     1.3    79.8    -      -       -      +
     91C  VAL*     1.3    59.5    +      -       -      +
    104C  ILE*     4.2    11.4    -      -       +      -
    105C  ARG      3.3     6.7    -      -       -      +
    106C  ILE*     3.7    26.9    -      -       +      +
    107C  VAL*     4.5     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 91 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  PHE*     3.9     3.4    -      -       -      -
     72C  GLY*     3.6    21.5    -      -       -      +
     73C  SER      3.3    12.3    -      -       -      +
     74C  VAL*     4.0    10.8    -      -       +      -
     90C  GLU*     1.3    74.1    -      -       -      +
     92C  LEU*     1.3    69.9    +      -       -      +
     93C  GLU*     3.4     9.5    +      -       +      +
    104C  ILE*     3.4     3.5    -      -       -      +
    105C  ARG*     2.9    56.1    +      -       +      +
    107C  VAL*     4.0    19.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 92 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  PHE*     3.4    42.5    -      -       +      -
     69C  LEU*     4.3     2.2    -      -       +      -
     70C  GLU*     3.7    36.8    -      -       -      +
     71C  VAL*     3.7     5.0    -      -       -      +
     72C  GLY*     2.9    27.2    +      -       -      -
     73C  SER      2.9    13.4    +      -       -      +
     91C  VAL*     1.3    73.4    -      -       -      +
     93C  GLU*     1.3    59.7    +      -       -      +
     94C  ILE      3.3    27.1    -      -       -      +
     95C  LEU*     4.0    20.0    -      -       +      -
    102C  LEU*     3.5    18.8    -      -       +      -
    103C  GLY      3.4    10.5    -      -       -      +
    104C  ILE*     4.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 93 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71C  VAL*     3.5    24.5    -      -       -      +
     91C  VAL*     3.4    10.5    +      -       +      +
     92C  LEU*     1.3    77.1    -      -       -      +
     94C  ILE*     1.3    69.7    +      -       +      +
    103C  GLY*     2.8    17.1    +      -       -      +
    104C  ILE      4.2     4.7    -      -       -      +
    105C  ARG*     3.3    50.5    +      -       +      +
    117C  SER*     4.3     7.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 94 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71C  VAL*     4.5     1.3    -      -       -      -
     92C  LEU*     3.3    10.3    -      -       -      +
     93C  GLU*     1.3    91.7    -      -       +      +
     95C  LEU*     1.3    63.5    +      -       -      +
     96C  ASP*     4.1    17.5    -      -       +      +
    101C  ILE*     4.1    23.3    -      -       +      +
    102C  LEU*     3.3     5.5    -      -       -      -
    103C  GLY*     2.8    38.5    +      -       -      +
    119C  THR*     5.3     7.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  TRP*     4.2    19.7    -      -       +      -
     47C  ARG*     4.0    32.5    -      -       +      +
     69C  LEU*     4.4    23.1    -      -       +      +
     70C  GLU*     4.6     4.5    -      -       -      -
     71C  VAL*     4.3    13.7    -      -       +      +
     92C  LEU*     4.0    24.5    -      -       +      -
     94C  ILE*     1.3    75.6    -      -       -      +
     96C  ASP*     1.3    59.4    +      -       -      +
     97C  ASP*     3.5    14.0    +      -       -      +
    101C  ILE      3.8     1.3    -      -       -      -
    102C  LEU*     3.8    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  TRP*     3.4     4.5    -      -       -      -
     94C  ILE*     4.0     8.7    -      -       +      -
     95C  LEU*     1.3    72.2    -      -       -      +
     97C  ASP*     1.3    57.6    +      -       -      +
     98C  ASN*     2.7    42.5    +      -       -      +
     99C  GLU*     3.0    29.5    +      -       -      +
    100C  HIS*     2.8    31.2    +      -       -      -
    101C  ILE*     2.9    31.8    +      -       +      +
----------------------------------------------------------
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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