Contacts of the strand formed by residues 46 - 51 (chain A) in PDB entry 1VH7


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 GLU 46 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ARG*     2.9    38.0    +      -       -      -
      6A  ILE      3.6     2.8    +      -       -      -
      7A  ILE*     3.4    23.9    -      -       +      +
      8A  ALA      3.2    12.0    +      -       -      -
     44A  ILE*     2.9    18.0    -      -       -      +
     45A  ASP*     1.3    88.3    -      -       +      +
     47A  LEU*     1.3    67.2    +      -       -      +
     48A  VAL*     6.1     0.5    -      -       -      +
     75A  ILE*     4.0     2.0    -      -       -      -
     76A  PRO*     3.3    31.8    -      -       +      +
     78A  THR*     4.7     3.1    +      -       -      -
     99A  LYS*     2.8    31.7    +      -       -      -
    199A  ILE*     5.7     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ALA*     3.4    18.4    -      -       +      +
     10A  LEU*     4.1    11.4    -      -       +      -
     36A  GLY*     3.7    28.3    -      -       -      +
     39A  TYR*     4.2    13.9    -      -       +      -
     44A  ILE*     3.9    13.9    -      -       +      -
     46A  GLU*     1.3    84.6    -      -       -      +
     48A  VAL*     1.3    68.7    +      -       -      +
     49A  PHE*     3.8    23.3    -      -       +      -
     73A  ILE*     3.5    28.7    -      -       +      -
     75A  ILE*     4.0     8.5    -      -       +      -
     76A  PRO      3.1     5.1    +      -       -      -
     77A  PHE*     3.2     6.8    -      -       +      -
     78A  THR*     2.9    24.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ILE*     3.7    21.3    -      -       +      -
      8A  ALA      2.9     9.9    +      -       -      +
      9A  CYS*     3.3    12.9    -      -       -      -
     10A  LEU*     2.7    35.0    +      -       -      +
     46A  GLU*     6.1     0.9    -      -       -      +
     47A  LEU*     1.3    79.7    -      -       -      +
     49A  PHE*     1.3    59.9    +      -       -      +
     50A  LEU*     3.9    30.7    -      -       +      -
     78A  THR*     3.4    27.1    -      -       +      +
    101A  SER*     5.7     0.7    -      -       -      -
    169A  LEU*     4.8    12.1    -      -       +      -
    199A  ILE*     5.8     3.4    -      -       +      -
    222A  LEU*     4.0    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU*     3.4    38.4    -      -       +      +
     12A  VAL*     4.3     7.0    -      -       +      -
     32A  PRO*     3.8    17.9    -      -       +      -
     33A  VAL*     5.6     0.2    -      -       -      -
     36A  GLY*     4.9     0.9    -      -       -      -
     47A  LEU*     3.8    34.5    -      -       +      -
     48A  VAL*     1.3    75.1    -      -       -      +
     50A  LEU*     1.3    63.0    +      -       -      +
     51A  ASP      4.0     0.7    -      -       -      -
     65A  LEU*     4.1    28.7    -      -       +      -
     69A  VAL*     3.7    38.4    -      -       +      -
     73A  ILE*     6.0     0.2    -      -       +      -
     77A  PHE*     3.9    20.4    -      +       +      -
     78A  THR      2.9    11.2    +      -       -      +
     79A  VAL*     3.4    10.1    -      -       +      +
     80A  GLY      2.9    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  CYS*     3.8    20.2    -      -       -      -
     10A  LEU      3.0     8.9    +      -       -      +
     11A  ASP*     3.5    19.1    -      -       -      +
     12A  VAL*     2.9    26.1    +      -       -      +
     48A  VAL*     3.9    20.2    -      -       +      -
     49A  PHE*     1.3    80.8    -      -       -      +
     51A  ASP*     1.3    61.1    +      -       -      +
     52A  ILE*     4.1     5.1    +      -       +      +
     80A  GLY*     3.3    23.8    -      -       -      +
     81A  GLY*     4.2     4.5    -      -       -      +
    101A  SER*     4.9     9.9    -      -       -      +
    169A  LEU*     5.9     5.2    -      -       +      -
    222A  LEU*     6.3     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  VAL*     3.4    23.0    -      -       +      +
     13A  LYS*     4.3     0.7    -      -       -      -
     14A  ASP      4.4     0.2    +      -       -      -
     15A  GLY      5.2     0.3    +      -       -      -
     49A  PHE      4.0     1.2    -      -       -      +
     50A  LEU*     1.3    73.4    -      -       -      +
     52A  ILE*     1.4    67.9    +      -       -      +
     53A  THR*     2.6    45.1    +      -       -      -
     58A  LYS*     3.0    29.5    +      -       -      +
     61A  THR*     4.2     7.3    -      -       -      +
     62A  MET*     3.5    36.8    -      -       +      +
     65A  LEU*     5.5     3.1    -      -       +      +
     79A  VAL*     5.7     0.9    -      -       +      -
     80A  GLY      2.9     8.7    +      -       -      +
     81A  GLY*     3.6    12.5    -      -       -      -
----------------------------------------------------------
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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