Contacts of the strand formed by residues 179 - 185 (chain I) in PDB entry 6A3V


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 LEU 179 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143I  VAL*     3.6    35.9    -      -       +      +
    144I  PHE      4.2     2.5    -      -       -      -
    145I  PHE*     3.6    32.8    -      -       +      -
    164I  ALA*     3.3     3.6    -      -       -      +
    165I  LEU*     2.6    49.5    +      -       +      +
    177I  ALA*     3.4     2.5    -      -       -      +
    178I  ALA*     1.3    78.1    -      -       -      +
    180I  ALA*     1.3    61.1    +      -       -      +
    200I  GLN*     3.6    27.1    -      -       +      +
    201I  GLY*     4.3     3.8    -      -       -      -
    202I  ARG*     3.6    35.0    -      -       +      +
    204I  LEU*     4.9     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 180 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148G  GLU*     5.3    10.8    -      -       -      +
    197G  PHE*     5.3     2.1    -      -       -      -
    145I  PHE*     4.9     1.3    -      -       -      -
    163I  LEU      3.2     8.1    -      -       -      +
    164I  ALA*     4.9     3.4    -      -       +      -
    177I  ALA*     4.9    12.8    -      -       +      +
    179I  LEU*     1.3    78.4    -      -       -      +
    181I  LEU*     1.3    63.2    +      -       -      +
    182I  THR*     5.9     0.7    -      -       -      +
    200I  GLN*     3.5    28.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 181 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197G  PHE*     3.5    35.2    -      -       +      -
    145I  PHE*     3.8    27.1    -      -       +      +
    147I  LEU*     4.5    14.8    -      -       +      -
    161I  VAL      4.6     0.4    -      -       -      -
    162I  SER*     3.2     6.1    -      -       -      -
    163I  LEU*     2.7    47.2    +      -       +      +
    180I  ALA*     1.3    72.0    -      -       -      +
    182I  THR*     1.3    78.8    +      -       -      +
    183I  VAL*     5.0     2.5    -      -       +      -
    198I  GLY*     3.8    30.3    -      -       -      +
    199I  PHE      3.8     7.9    -      -       -      +
    200I  GLN*     3.5    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 182 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193G  ARG*     3.9    27.2    +      -       -      +
    195G  SER*     5.1    16.7    -      -       -      -
    197G  PHE*     5.3    10.8    -      -       -      +
    160I  SER*     4.1    15.0    -      -       -      +
    161I  VAL      3.7     3.1    -      -       -      +
    162I  SER*     3.9    18.2    +      -       -      +
    180I  ALA*     5.9     0.7    -      -       -      +
    181I  LEU*     1.3    87.1    +      -       -      +
    183I  VAL*     1.3    65.8    +      -       -      +
    184I  ASP      4.2     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 183 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193G  ARG*     4.4     2.9    -      -       -      -
    147I  LEU*     3.7    30.1    -      -       +      +
    149I  LEU*     3.8    11.9    -      -       +      -
    160I  SER*     3.5     4.3    -      -       -      -
    161I  VAL*     3.0    37.0    +      -       +      +
    181I  LEU*     5.0     3.4    -      -       +      -
    182I  THR*     1.3    78.7    -      -       -      +
    184I  ASP*     1.3    62.8    +      -       -      +
    185I  LEU*     3.9     3.0    +      -       +      +
    196I  ALA*     3.6    29.6    -      -       +      -
    197I  PHE      3.6    33.2    -      -       -      +
    198I  GLY*     3.9     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 184 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191G  GLU*     3.7     7.1    -      -       -      +
    193G  ARG*     3.6    46.0    +      -       -      +
    159I  GLY      3.6     7.2    -      -       -      +
    182I  THR      4.2     0.8    +      -       -      -
    183I  VAL*     1.3    73.9    -      -       -      +
    185I  LEU*     1.3    77.1    +      -       -      +
    186I  PRO*     3.8    10.2    -      -       -      +
    196I  ALA*     3.5    20.8    -      -       -      +
    197I  PHE      5.5     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 185 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191G  GLU*     3.7     5.7    -      -       -      +
    102I  LEU*     4.9     2.9    -      -       +      -
    149I  LEU*     3.8    12.1    -      -       +      -
    158I  SER*     3.7     4.8    -      -       -      -
    159I  GLY      2.8    43.5    +      -       -      +
    161I  VAL*     3.8    23.6    -      -       +      -
    183I  VAL*     4.5     3.8    -      -       +      +
    184I  ASP*     1.3    89.2    +      -       -      +
    186I  PRO*     1.3    67.2    -      -       -      +
    187I  PRO*     3.8     0.7    -      -       -      +
    196I  ALA*     3.8     8.7    -      -       +      -
    220I  ALA*     5.1     5.6    -      -       +      -
    226I  TRP*     3.6    65.5    -      -       +      +
----------------------------------------------------------
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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