Contacts of the strand formed by residues 6 - 13 (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 HIS 6 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A    A      3.7    21.7    +      -       -      +
    275A    A      4.6     7.0    +      -       -      +
      4E  PHE*     3.6    25.3    +      -       +      +
      5E  LYS*     1.3    77.0    +      -       -      +
      7E  ARG*     1.3    70.8    +      -       -      +
      8E  TYR*     3.8    25.1    -      +       +      -
     52E  GLY      5.2     3.6    +      -       -      -
     68E  ARG*     3.3    33.0    +      -       +      +
     69E  CYS      3.6    13.2    +      -       -      +
     70E  ARG*     3.3    34.6    +      -       -      -
    104E  GLY      3.9     1.0    -      -       -      -
    105E  GLY*     3.3    20.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 7 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A    G      5.2     7.1    +      -       -      -
     25A    U      5.7     3.8    -      -       -      -
    275A    A      4.4     0.4    +      -       -      -
    276A    U      3.0    29.4    +      -       -      -
      5E  LYS      6.2     0.2    -      -       -      -
      6E  HIS*     1.3    81.2    +      -       -      +
      8E  TYR*     1.3    64.7    +      -       -      +
     67E  LEU      3.7     2.8    -      -       -      +
     68E  ARG*     4.0     0.7    -      -       -      -
     69E  CYS*     2.9    48.8    +      -       -      +
     70E  ARG      3.3    20.6    -      -       -      +
     71E  LYS*     3.1    31.9    -      -       -      +
     74E  TYR*     4.1    20.0    +      -       +      -
    102E  HIS*     4.0    21.4    +      -       -      +
    104E  GLY*     3.4    26.8    -      -       -      -
    105E  GLY      3.7     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 8 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273A    C      3.4    21.0    +      -       -      -
    274A    A      3.5    14.6    +      -       -      -
      6E  HIS*     3.8    25.0    -      -       +      +
      7E  ARG*     1.3    73.2    -      -       -      +
      9E  LEU*     1.3    60.9    +      -       -      +
     10E  LEU      4.2     0.3    +      -       -      -
     56E  ARG*     4.7     8.3    -      -       +      -
     66E  LEU*     3.8    21.5    -      -       +      -
     67E  LEU      3.6    13.7    -      -       -      -
     68E  ARG*     3.6    35.4    +      -       +      -
    102E  HIS*     4.7     1.1    -      -       -      -
    103E  VAL*     2.9    42.6    +      -       -      +
    105E  GLY*     3.5    33.2    -      -       -      +
    106E  THR      4.8     0.2    -      -       -      -
    107E  ILE*     3.6    31.0    -      -       +      -
    110E  CYS*     4.7     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 9 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8E  TYR*     1.3    74.3    -      -       -      +
     10E  LEU*     1.3    62.0    +      -       -      +
     11E  CYS*     3.8    25.6    -      -       -      -
     65E  VAL      3.5     3.6    -      -       -      +
     66E  LEU*     3.7     2.5    -      -       -      +
     67E  LEU*     3.4    46.7    +      -       +      +
     69E  CYS*     4.0    21.8    -      -       +      -
     74E  TYR      4.9     0.2    -      -       -      +
     77E  VAL*     3.8    24.9    -      -       +      -
     78E  TRP*     4.4    22.7    -      -       +      +
     81E  LEU*     3.9    12.1    -      -       +      -
     99E  ASN*     6.4     0.7    -      -       +      -
    102E  HIS*     3.6    24.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 10 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  LEU*     1.3    76.5    -      -       -      +
     11E  CYS*     1.3    70.7    +      -       -      +
     57E  TYR*     5.7     0.9    -      -       +      -
     64E  ILE*     4.1    23.3    -      -       +      -
     65E  VAL      3.4     3.1    -      -       -      +
     66E  LEU*     3.8    26.0    -      -       +      -
     99E  ASN*     3.4    22.4    -      -       -      +
    100E  THR*     3.3    27.0    +      -       +      +
    101E  LEU      4.1    15.7    +      -       -      +
    103E  VAL*     5.0     2.0    -      -       +      -
    110E  CYS*     3.9    33.4    -      -       -      +
    111E  GLN*     5.6     1.3    -      -       -      +
    113E  PHE*     4.3    15.3    -      -       +      -
    114E  LEU*     4.9    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 11 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  LEU*     3.8    15.0    -      -       -      -
     10E  LEU*     1.3    82.2    -      -       -      +
     12E  GLU*     1.3    63.0    +      -       -      +
     64E  ILE*     3.5    11.4    -      -       -      +
     65E  VAL*     2.9    43.5    +      -       +      -
     67E  LEU*     5.0     1.6    -      -       -      -
     81E  LEU*     3.7    35.2    -      -       -      -
     97E  PHE*     3.6    25.6    -      -       +      -
     98E  PHE      3.4     9.0    -      -       -      +
     99E  ASN*     5.1     0.9    -      -       -      -
    100E  THR*     5.3     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 12 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  CYS*     1.3    78.4    -      -       -      +
     13E  LEU*     1.3    66.8    +      -       -      +
     14E  VAL*     3.5    15.2    +      -       +      +
     62E  THR      5.8     1.1    -      -       -      +
     63E  GLY      3.4    12.6    -      -       -      +
     64E  ILE*     4.5     7.4    -      -       +      -
     65E  VAL*     5.8     0.2    -      -       -      -
     97E  PHE*     3.6     3.9    -      -       -      -
     98E  PHE*     2.8    43.6    +      -       +      +
    100E  THR*     4.1    11.1    -      -       +      +
    117E  TYR*     2.6    43.6    +      -       -      -
    121E  GLN*     5.1     5.2    +      -       -      +
     27I  HIS*     3.2    20.9    +      -       -      -
     28I  LEU*     6.0     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 13 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12E  GLU*     1.3    73.8    -      -       -      +
     14E  VAL*     1.3    62.4    +      -       -      +
     15E  SER*     3.9     6.0    +      -       -      +
     20E  CYS*     5.7     3.4    -      -       -      +
     21E  ARG*     4.9    24.4    +      -       +      -
     24E  LEU*     3.9    38.1    -      -       +      -
     62E  THR      5.6     0.7    -      -       -      +
     63E  GLY*     3.6    16.0    +      -       -      +
     65E  VAL*     5.2     6.5    -      -       +      +
     87E  LEU*     6.0     0.2    -      -       +      -
     95E  PRO*     3.8    32.1    -      -       +      -
     96E  CYS      3.9    13.2    -      -       -      +
     97E  PHE*     3.7    42.2    -      -       +      -
----------------------------------------------------------
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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