Contacts of the strand formed by residues 101 - 108 (chain C) in PDB entry 2VM8


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 THR 101 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69C  GLY      3.4     9.4    -      -       -      +
     71C  ASP*     3.8    20.4    -      -       +      -
     96C  ALA*     3.2    29.0    +      -       +      +
     97C  LEU*     3.3    25.3    +      -       -      +
     99C  GLY      4.6     0.9    +      -       -      -
    100C  GLY*     1.3    75.2    -      -       -      +
    102C  THR*     1.3    59.7    +      -       -      +
    103C  MET      3.2    24.6    +      -       -      +
    104C  ILE*     4.3     0.7    -      -       +      -
    133C  CYS*     4.8     0.7    -      -       -      -
    358C  THR*     4.3     8.7    +      -       -      +
    361C  ARG*     3.1    21.7    +      -       -      +
    362C  MET*     3.6    11.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 102 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68C  GLY*     3.2    31.7    -      -       -      -
     69C  GLY      3.1     4.9    +      -       -      +
     97C  LEU*     3.9    11.4    -      -       +      -
    100C  GLY      4.5     1.6    -      -       -      +
    101C  THR*     1.3    74.2    -      -       -      +
    103C  MET*     1.3    60.3    +      -       -      +
    133C  CYS*     3.1    22.2    -      -       -      +
    134C  ASP*     3.7     6.6    +      -       -      +
    408C  ASP*     3.5    28.4    +      -       -      +
    409C  LEU      4.6     1.1    -      -       -      +
    410C  VAL*     4.7     0.2    -      -       +      -
    446C  VAL*     3.5    32.3    -      -       +      -
    447C  ILE      3.5    14.4    -      -       -      +
    448C  SER*     4.2     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 103 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69C  GLY      3.3     3.0    +      -       -      +
     70C  ILE*     4.1    25.4    -      -       +      -
     71C  ASP      3.2    11.7    +      -       -      -
    101C  THR*     3.2    20.9    +      -       -      +
    102C  THR*     1.3    80.8    -      -       -      +
    104C  ILE*     1.3    66.5    +      -       -      +
    105C  ILE*     4.9     2.2    -      -       +      -
    133C  CYS*     4.1     0.6    -      -       -      -
    134C  ASP*     3.2    21.8    -      -       +      +
    135C  TYR      4.1     4.7    -      -       -      -
    136C  SER*     4.0    19.3    -      -       -      -
    394C  LEU*     4.0    24.5    -      -       +      -
    398C  LYS*     3.8    29.8    -      -       +      -
    408C  ASP*     5.0     5.4    -      -       -      +
    469C  ILE*     3.6    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 104 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71C  ASP*     3.7     6.7    -      -       +      -
     74C  THR*     3.3    37.9    -      -       +      +
     76C  PHE*     4.0    17.9    -      -       +      -
     89C  PHE*     4.3     7.9    -      -       +      -
     93C  THR*     3.9    16.2    -      -       +      -
     96C  ALA*     4.1    21.5    -      -       +      -
    101C  THR*     4.3     3.8    -      -       +      -
    103C  MET*     1.3    81.6    -      -       -      +
    105C  ILE*     1.3    65.3    +      -       -      +
    106C  ASP*     4.1    14.6    -      -       +      +
    133C  CYS*     4.1    13.0    -      -       -      -
    134C  ASP      3.2     2.2    +      -       -      -
    135C  TYR*     3.1    28.6    -      -       +      -
    136C  SER      3.0    21.2    +      -       -      +
    358C  THR*     4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 105 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70C  ILE*     3.9    26.2    -      -       +      -
     71C  ASP      3.2     5.9    +      -       -      -
     72C  VAL*     3.5    18.5    -      -       -      +
     73C  HIS*     3.6     0.3    -      -       -      -
     74C  THR*     3.2    20.4    +      -       -      -
    103C  MET*     4.9     3.6    -      -       +      -
    104C  ILE*     1.3    78.8    -      -       -      +
    106C  ASP*     1.3    61.9    +      -       -      +
    136C  SER*     3.2    26.2    -      -       -      +
    137C  LEU      3.9     1.6    -      -       -      +
    138C  HIS*     3.1    35.7    -      -       +      +
    392C  PHE*     3.8    36.1    -      -       +      -
    394C  LEU*     4.7    11.2    -      -       +      -
    471C  ARG*     4.6     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 106 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74C  THR*     2.9    29.9    +      -       -      +
     75C  ARG*     3.5     8.8    -      -       -      -
     76C  PHE*     2.9    31.1    +      -       -      +
     78C  MET*     6.0     0.2    -      -       -      +
     89C  PHE*     3.8    18.1    -      -       +      -
    104C  ILE*     4.1     4.0    -      -       +      -
    105C  ILE*     1.3    72.1    -      -       -      +
    107C  HIS*     1.3    73.0    +      -       -      +
    123C  TRP*     3.4    16.5    +      -       -      -
    136C  SER      3.0     7.9    +      -       -      +
    137C  LEU*     3.5    19.2    -      -       +      -
    138C  HIS*     2.8    30.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 107 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72C  VAL      4.3     0.6    +      -       -      -
     73C  HIS*     3.7    38.9    +      +       -      -
     74C  THR      3.8     3.8    -      -       -      -
     75C  ARG*     3.6    32.9    +      -       +      +
     78C  MET*     5.9     0.3    -      -       -      +
    105C  ILE      4.4     1.3    -      -       -      -
    106C  ASP*     1.3    85.8    +      -       -      +
    108C  VAL*     1.3    63.7    +      -       -      +
    109C  VAL*     3.5     4.0    +      -       -      +
    123C  TRP*     3.1    25.1    +      -       -      -
    138C  HIS*     3.0    30.7    +      +       +      +
    140C  ASP*     2.8    21.4    +      -       -      +
    165C  LEU*     4.0    11.9    -      -       +      -
    196C  GLN*     3.1    29.0    +      -       -      -
    253C  THR*     5.0     0.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 108 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107C  HIS*     1.3    68.8    -      -       -      +
    109C  VAL*     1.3    61.8    +      -       -      +
    110C  PRO*     3.2     9.0    -      -       +      +
    116C  LEU      4.6     0.2    -      -       -      +
    119C  ALA*     3.5    33.0    -      -       +      -
    120C  PHE*     3.7    17.0    -      -       +      +
    123C  TRP*     3.9    28.9    -      -       +      -
    137C  LEU*     4.1    13.5    -      -       +      -
    138C  HIS      2.8    21.1    +      -       -      +
    139C  VAL*     3.9    24.2    -      -       +      -
    140C  ASP*     2.8    33.6    +      -       -      +
----------------------------------------------------------
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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