Contacts of the strand formed by residues 143 - 149 (chain C) in PDB entry 6VVT


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 VAL 143 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98C  PHE*     5.4     2.2    -      -       +      -
    125C  PHE*     3.4     5.4    -      -       -      +
    126C  VAL*     2.9    38.3    +      -       +      +
    141C  GLN*     4.0    10.3    +      -       +      +
    142C  THR*     1.3    81.9    -      -       -      +
    144C  PHE*     1.3    58.4    +      -       -      +
    145C  MET*     3.4    28.8    +      -       -      -
    405C  PRO*     4.4    12.6    -      -       +      +
    406C  GLN*     4.5     5.2    -      -       +      +
    409C  ILE*     3.6    30.1    -      -       +      -
    411C  ILE*     4.1     4.3    -      -       +      -
    326F  GLN*     2.9    30.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 144 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123C  PRO*     3.3    22.7    -      -       +      -
    124C  LEU      3.5     7.2    -      -       -      -
    125C  PHE*     3.2    35.2    -      +       +      -
    143C  VAL*     1.3    68.0    -      -       -      +
    145C  MET*     1.3    58.7    +      -       -      +
    146C  GLY*     3.2    34.5    -      -       -      -
    147C  ASP*     3.6    10.5    -      -       -      -
    411C  ILE*     2.9    22.1    -      -       +      +
    325F  LEU*     3.2    38.4    -      -       +      -
    326F  GLN*     2.4    39.3    +      -       -      +
    327F  ASP      6.0     0.2    -      -       -      +
    329F  GLY*     3.0    38.6    -      -       -      -
    330F  ARG*     4.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 145 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98C  PHE*     6.1     4.9    -      -       +      -
    124C  LEU*     3.2    31.3    +      -       +      -
    126C  VAL*     3.4    34.3    -      -       +      -
    143C  VAL*     3.4    27.6    -      -       -      +
    144C  PHE*     1.3    73.6    -      -       -      +
    146C  GLY*     1.3    56.5    +      -       -      +
    384C  LEU*     4.6    11.9    -      -       +      -
    409C  ILE*     4.8     6.1    -      -       +      -
    411C  ILE*     3.1    44.6    -      -       +      +
    414C  VAL*     4.0    30.3    -      -       +      +
    415C  VAL*     4.1    13.7    +      -       -      +
    418C  ILE*     5.8     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 146 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  LEU*     2.9    31.4    +      -       -      +
    144C  PHE*     3.2    26.7    -      -       -      -
    145C  MET*     1.3    80.2    -      -       -      +
    147C  ASP*     1.3    66.5    +      -       -      -
    411C  ILE*     4.8     0.9    -      -       -      -
    415C  VAL*     4.8    11.2    -      -       -      -
    418C  ILE*     5.8     2.5    -      -       -      -
    325F  LEU*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 147 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107C  LYS*     2.9    32.8    +      -       +      -
    119C  THR*     5.7     5.2    -      -       +      -
    121C  ALA*     3.9    17.1    -      -       +      +
    123C  PRO*     3.9    11.5    -      -       +      +
    144C  PHE*     4.2    10.5    -      -       -      -
    146C  GLY*     1.3    71.9    -      -       -      -
    148C  PHE*     1.3    59.5    +      -       -      +
    149C  PRO*     3.6     9.2    -      -       -      +
    415C  VAL*     5.2    10.1    -      -       -      +
    418C  ILE*     4.2    10.7    -      -       -      +
    325F  LEU*     5.8     1.4    -      -       -      +
    329F  GLY      4.5     1.6    -      -       -      +
    330F  ARG*     5.1     3.5    -      -       -      -
    331F  GLU      5.7     2.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 148 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  PHE*     4.5     2.7    -      +       -      -
     55C  LEU*     4.3    18.6    -      -       +      -
     56C  VAL*     4.3    17.0    -      -       +      -
     77C  LEU*     4.8     7.2    -      -       +      -
    103C  PHE*     3.2    34.3    -      +       +      -
    121C  ALA*     3.3     3.4    -      -       -      -
    122C  ALA      2.6    45.7    +      -       -      +
    124C  LEU*     4.6    14.8    -      -       +      -
    146C  GLY      3.3     4.9    +      -       -      +
    147C  ASP*     1.3    71.8    -      -       -      +
    149C  PRO*     1.3    91.2    -      -       +      +
    150C  MET*     3.3     7.7    -      -       +      +
    376C  ILE*     4.8     4.9    -      -       +      -
    380C  ILE*     3.6    33.4    -      -       +      -
    418C  ILE*     4.5    18.8    -      -       +      -
    422C  PHE*     6.5     0.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with PRO 149 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  PHE*     3.4     8.3    -      -       -      -
    119C  THR*     4.6     5.6    -      -       -      +
    120C  TYR      3.3    12.6    -      -       -      +
    121C  ALA*     3.6     3.3    -      -       +      -
    147C  ASP      3.6     8.3    -      -       -      +
    148C  PHE*     1.3   107.3    -      -       +      +
    150C  MET*     1.3    68.1    +      -       -      +
    157C  PHE*     4.2     2.7    -      -       +      -
    159C  ILE*     4.0    16.6    -      -       +      -
    418C  ILE*     4.7    11.9    -      -       +      -
    422C  PHE*     3.4    42.8    -      -       +      -
----------------------------------------------------------
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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