Contacts of the strand formed by residues 190 - 198 (chain A) 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 ASP 190 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  PRO*     3.6     3.6    -      -       -      +
     26A  LEU      3.1    31.8    +      -       -      +
     27A  GLU      4.0     3.1    -      -       -      +
     28A  PRO*     2.8    43.0    -      -       -      +
     29A  GLY*     3.3     9.2    +      -       -      +
     30A  PHE      4.8     0.3    +      -       -      -
     31A  GLY*     5.1    10.8    -      -       -      +
    178A  VAL*     5.6     6.0    -      -       +      +
    180A  ALA*     3.2    29.2    -      -       +      +
    183A  VAL*     5.9     0.2    -      -       -      +
    189A  PHE*     1.3    83.8    -      -       -      +
    191A  LYS*     1.3    63.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  VAL*     3.4    18.8    -      -       +      -
     23A  ILE      3.2    11.9    -      -       -      +
     24A  GLU*     3.0    55.0    -      -       +      +
     31A  GLY*     5.8     0.4    -      -       -      -
    178A  VAL*     3.8     3.0    -      -       -      +
    179A  GLU*     2.4    74.8    +      -       +      +
    180A  ALA*     4.5     4.9    -      -       -      +
    181A  THR*     6.3     1.1    -      -       -      -
    189A  PHE*     4.8     8.7    -      -       +      -
    190A  ASP*     1.3    74.4    -      -       -      +
    192A  LEU*     1.3    59.9    +      -       -      +
    193A  ILE*     4.0    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  PHE      4.8     0.2    -      -       -      +
     22A  VAL*     3.5     1.7    -      -       -      +
     23A  ILE*     3.1    55.7    +      -       +      +
     30A  PHE      4.5     0.2    -      -       -      +
     31A  GLY*     3.3    41.5    -      -       -      +
     34A  LEU*     4.0    15.3    -      -       +      -
     35A  GLY*     3.9    15.0    -      -       -      +
    176A  TYR*     5.9     2.2    -      -       +      -
    177A  LYS      3.8     8.1    -      -       -      +
    178A  VAL*     4.3     5.6    -      -       +      +
    191A  LYS*     1.3    72.4    -      -       -      +
    193A  ILE*     1.3    72.8    +      -       -      +
    194A  ILE*     3.6    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ARG*     4.5    21.5    -      -       +      +
     21A  PHE      3.2     8.7    -      -       -      +
     22A  VAL*     4.0    19.7    -      -       +      -
    175A  THR*     6.4     0.2    -      -       +      -
    176A  TYR*     3.3     6.1    -      -       -      +
    177A  LYS*     3.2    66.8    +      -       +      +
    179A  GLU*     5.2     4.5    -      -       +      +
    191A  LYS*     4.0    14.6    -      -       -      +
    192A  LEU*     1.3    81.5    -      -       -      +
    194A  ILE*     1.3    70.4    +      -       -      +
    195A  ASP*     4.8     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ARG*     3.2     7.8    -      -       -      +
     21A  PHE*     2.7    43.7    +      -       +      +
     23A  ILE*     5.1     6.5    -      -       +      -
     35A  GLY*     5.1     9.6    -      -       -      +
     38A  LEU*     3.6    33.2    -      -       +      -
     39A  ARG      6.0     0.2    -      -       -      +
     42A  LEU*     5.2     3.1    -      -       +      -
    174A  VAL*     4.4     9.0    -      -       +      -
    175A  THR      3.5    13.5    -      -       -      +
    176A  TYR*     4.3    10.5    -      -       +      -
    192A  LEU*     3.6    23.8    -      -       +      -
    193A  ILE*     1.3    80.8    -      -       -      +
    195A  ASP*     1.3    61.2    +      -       -      +
    196A  VAL*     3.8    21.3    +      -       +      -
    208A  LEU*     4.9    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  VAL*     4.7     1.2    -      -       -      +
     18A  ARG*     2.8    49.6    +      -       -      +
     19A  SER      4.9     0.3    -      -       -      +
     20A  ARG*     3.8    34.0    +      -       +      +
    173A  LYS      3.6     2.1    -      -       -      +
    174A  VAL*     3.3     8.0    -      -       -      -
    175A  THR*     3.1    50.0    +      -       +      +
    176A  TYR*     4.8     0.2    -      -       -      +
    193A  ILE*     4.3     4.7    +      -       +      -
    194A  ILE*     1.3    71.4    -      -       -      +
    196A  VAL*     1.3    61.2    +      -       -      +
    197A  GLU*     5.2     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  ARG*     2.8    24.4    -      -       -      +
     19A  SER      3.1    12.1    +      -       -      -
     21A  PHE*     4.2    18.4    -      -       +      -
     42A  LEU*     3.6    33.9    -      -       +      -
    171A  VAL*     4.8     2.2    -      -       +      -
    174A  VAL*     4.2     6.7    -      -       +      -
    194A  ILE*     3.8    17.5    -      -       +      -
    195A  ASP*     1.3    74.5    +      -       -      +
    197A  GLU*     1.3    68.3    +      -       -      +
    198A  THR*     4.8     0.7    -      -       +      -
    204A  PRO*     3.9    31.1    -      -       +      +
    207A  ALA*     4.7     9.0    -      -       +      -
    208A  LEU*     5.0     7.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  ASN*     3.3    27.8    +      -       -      +
     18A  ARG*     3.3    24.3    +      -       +      -
    171A  VAL*     3.3    11.3    -      -       -      +
    172A  LEU*     2.8    58.1    +      -       +      +
    173A  LYS*     3.3    21.3    +      -       -      +
    174A  VAL*     4.4     0.2    -      -       -      +
    195A  ASP*     5.2     0.2    -      -       -      +
    196A  VAL*     1.3    73.4    -      -       -      +
    198A  THR*     1.3    65.3    +      -       -      +
    987C  ARG*     2.3    40.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  ASN*     2.8    38.1    +      -       -      +
    170A  PRO      3.1    15.0    -      -       -      +
    171A  VAL*     4.7     1.1    -      -       -      -
    172A  LEU*     4.0     6.8    -      -       -      +
    196A  VAL*     4.8     1.6    -      -       +      -
    197A  GLU*     1.3    85.3    -      -       -      +
    199A  LYS*     1.3    61.9    +      -       -      +
    200A  ASN*     3.3     7.1    +      -       -      -
    202A  ILE*     2.5    38.8    +      -       +      +
    203A  SER      3.7     4.5    -      -       -      +
    204A  PRO*     3.7    24.9    -      -       +      +
    207A  ALA*     4.3     9.9    -      -       +      -
----------------------------------------------------------
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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