Contacts of the strand formed by residues 43 - 47 (chain A) in PDB entry 1II7


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 PHE 43 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     3.8    23.8    -      -       +      -
      2A  LYS      3.8     0.6    +      -       -      -
      3A  PHE*     3.3    41.0    -      +       +      -
      4A  ALA      3.1    22.0    +      -       -      -
     41A  VAL*     3.4     3.2    -      -       -      +
     42A  ASP*     1.3    85.9    -      -       +      +
     44A  ILE*     1.3    67.7    +      -       -      +
     45A  LEU*     3.9    22.7    -      -       +      -
     76A  ILE*     3.7     3.6    -      -       -      -
     77A  PRO*     3.4    26.9    -      -       +      +
     79A  PHE*     3.8    18.6    -      +       +      -
    135A  TYR*     3.8    24.5    -      +       +      -
    138A  LEU*     3.8    18.8    -      -       +      -
    140A  ILE*     4.0     9.2    -      -       +      -
    169A  ILE*     4.2     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  ALA*     3.5    12.8    -      -       +      +
      6A  LEU*     4.4    12.8    -      -       +      -
     33A  LEU*     4.1    19.1    -      -       +      +
     36A  ALA*     4.0    18.6    -      -       +      -
     37A  VAL*     5.5     0.2    -      -       +      -
     41A  VAL*     4.0     7.9    -      -       +      -
     43A  PHE*     1.3    82.2    -      -       -      +
     45A  LEU*     1.3    68.9    +      -       -      +
     46A  ILE*     4.2    14.4    -      -       +      -
     71A  PRO*     3.8    29.6    -      -       +      -
     76A  ILE*     3.8    13.9    -      -       +      -
     77A  PRO      2.9     9.0    +      -       -      +
     78A  VAL*     3.4    10.9    -      -       +      -
     79A  PHE*     2.7    35.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     3.5    28.3    -      -       +      -
      4A  ALA      2.8    13.6    +      -       -      +
      5A  HIS*     4.4     6.7    -      -       +      -
      6A  LEU*     2.8    34.5    +      -       -      +
     43A  PHE*     3.9    21.8    -      -       +      -
     44A  ILE*     1.3    74.4    -      -       -      +
     46A  ILE*     1.3    60.8    +      -       -      +
     47A  ALA      3.9     0.9    -      -       -      -
     79A  PHE*     3.3    25.8    -      -       +      -
    140A  ILE*     4.0    10.5    -      -       +      -
    169A  ILE*     4.2    13.9    -      -       +      -
    171A  MET*     3.8    20.4    -      -       +      -
    203A  ALA*     3.8    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LEU*     3.5     8.1    -      -       +      -
      7A  ALA*     4.6     6.5    -      -       -      -
      9A  ILE*     4.1    20.6    -      -       +      -
     29A  PHE*     3.7    32.1    -      -       +      -
     33A  LEU*     5.5     0.4    -      -       +      -
     44A  ILE*     4.2    10.1    -      -       +      -
     45A  LEU*     1.3    77.0    -      -       -      +
     47A  ALA*     1.3    58.0    +      -       -      +
     48A  GLY      2.9    13.9    +      -       -      +
     50A  LEU*     4.1    30.5    -      -       +      -
     68A  LEU*     4.7     2.2    -      -       +      -
     78A  VAL*     3.9    26.0    -      -       +      -
     79A  PHE      2.9     9.7    +      -       -      -
     80A  ALA*     3.3    13.4    -      -       +      +
     81A  ILE      3.3    20.5    +      -       -      +
    171A  MET*     3.9     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  HIS*     4.1     5.4    -      -       -      +
      6A  LEU      3.0    16.0    +      -       -      +
      7A  ALA*     4.0     1.6    -      -       +      -
     45A  LEU      3.9     0.2    -      -       -      -
     46A  ILE*     1.3    68.3    -      -       -      +
     48A  GLY*     1.3    61.1    +      -       -      +
     81A  ILE*     3.7     9.6    -      -       -      -
    171A  MET*     3.7    26.4    -      -       +      -
    172A  LEU      4.3     1.6    -      -       -      +
    173A  HIS*     2.8    21.3    +      -       -      +
    203A  ALA      4.1     0.2    -      -       -      +
    204A  LEU      3.4    31.9    -      -       -      +
    205A  GLY*     3.5     8.4    -      -       -      +
----------------------------------------------------------
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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