Contacts of the strand formed by residues 97 - 103 (chain E) in PDB entry 6AHU


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 97 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  CYS*     3.6    31.2    -      -       +      -
     12E  GLU      3.6     3.8    -      -       -      -
     13E  LEU*     3.7    30.7    -      -       +      -
     24E  LEU*     6.3     0.9    -      -       +      -
     29E  LEU*     3.9    22.4    -      -       +      -
     32E  LEU*     4.1    11.9    -      -       +      -
     33E  VAL*     5.4     3.1    -      -       +      -
     65E  VAL*     3.6    28.7    -      -       +      -
     81E  LEU*     4.4    25.9    +      -       +      +
     82E  PRO*     5.6     0.3    -      -       -      +
     84E  ILE*     3.6    47.0    +      -       +      -
     95E  PRO*     6.2     2.0    -      -       +      -
     96E  CYS*     1.3    76.2    -      -       -      +
     98E  PHE*     1.3    72.5    +      -       -      +
    198I  ARG*     5.1     5.7    -      -       -      -
    202I  ASP*     5.6     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 98 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  CYS*     3.4     4.4    -      -       -      -
     12E  GLU*     2.8    49.6    +      -       +      +
     14E  VAL*     3.7    31.9    -      -       +      -
     81E  LEU*     6.2     0.2    -      -       -      -
     96E  CYS*     3.4    43.5    -      -       -      -
     97E  PHE*     1.3    79.2    -      -       -      +
     99E  ASN*     1.3    67.3    +      -       -      +
     24I  THR*     5.0     5.2    -      -       +      -
     28I  LEU*     3.6    37.5    -      -       +      -
    195I  LEU*     5.3     1.8    -      -       +      -
    197I  ILE*     3.2    31.6    -      -       +      -
    198I  ARG*     3.6     7.6    -      -       -      -
    199I  GLY*     3.5    18.6    -      -       -      +
    202I  ASP*     6.0     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 99 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  LEU*     6.4     0.4    -      -       +      -
     10E  LEU      3.4    16.4    -      -       -      +
     11E  CYS*     4.5     1.5    -      -       -      +
     78E  TRP*     3.0    35.3    -      -       +      +
     81E  LEU*     4.8     8.1    -      -       +      +
     98E  PHE*     1.3    78.0    -      -       -      +
    100E  THR*     1.3    64.4    +      -       -      +
    101E  LEU*     5.0     2.5    -      -       -      +
    102E  HIS      6.0     0.4    -      -       -      +
     28I  LEU*     5.8     0.7    -      -       -      +
    199I  GLY*     4.2     4.9    -      -       -      -
    200I  PRO*     4.6    10.6    -      -       -      +
    201I  TYR*     3.3    17.9    +      -       -      +
    202I  ASP*     3.2    46.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 100 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10E  LEU*     3.3    35.7    +      -       +      +
     11E  CYS      5.3     1.1    -      -       -      -
     12E  GLU*     4.1    24.2    -      -       +      +
     64E  ILE*     5.9     3.1    -      -       +      -
     98E  PHE      4.4     4.7    -      -       -      +
     99E  ASN*     1.3    79.8    -      -       -      +
    101E  LEU*     1.3    71.2    +      -       -      +
    113E  PHE*     3.7    21.9    -      -       +      -
    117E  TYR*     4.8    17.3    -      -       +      -
    200I  PRO*     6.0     1.2    -      -       -      +
    201I  TYR*     3.3    23.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 101 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A    U      3.8    17.3    -      -       -      +
     26A    G      5.6     4.7    -      -       -      +
     10E  LEU*     4.1    16.1    +      -       -      +
     99E  ASN*     5.0     2.4    -      -       -      +
    100E  THR*     1.3    86.8    +      -       -      +
    102E  HIS*     1.3    79.7    +      -       -      +
    103E  VAL*     3.3    29.7    +      -       +      +
    113E  PHE*     3.7    42.8    -      -       +      -
    201I  TYR*     4.4    18.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 102 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A    G      4.9     1.8    -      -       -      +
     25A    U      3.6    22.8    +      -       -      +
      7E  ARG*     4.0    34.9    -      -       +      +
      8E  TYR      4.4     1.6    -      -       -      -
      9E  LEU*     3.6    35.5    -      -       +      +
     69E  CYS*     4.6     0.2    -      -       -      -
     74E  TYR*     3.6    39.3    -      +       +      -
     78E  TRP*     4.8    32.0    -      +       +      +
     99E  ASN*     6.0     1.2    -      -       -      +
    101E  LEU*     1.3    71.2    -      -       -      +
    103E  VAL*     1.3    66.5    +      -       -      +
    104E  GLY*     3.8     2.3    +      -       -      -
    201I  TYR*     5.3     2.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 103 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A    U      5.5     1.3    -      -       -      -
     26A    G      4.8     4.7    -      -       -      +
      7E  ARG*     3.9     2.6    -      -       -      +
      8E  TYR      2.9    40.9    +      -       -      +
     10E  LEU*     5.0     4.3    -      -       +      -
    101E  LEU*     3.6    30.3    -      -       +      +
    102E  HIS*     1.3    74.6    +      -       -      +
    104E  GLY*     1.3    60.7    +      -       -      +
    105E  GLY      3.1    20.9    +      -       -      +
    106E  THR*     3.8    16.4    -      -       +      +
    109E  THR*     4.3     6.5    -      -       +      +
    110E  CYS*     3.8    40.2    -      -       +      +
    113E  PHE*     5.5     3.4    -      -       +      -
----------------------------------------------------------
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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