Contacts of the strand formed by residues 61 - 66 (chain A) in PDB entry 3E6D


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 ILE 61 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  VAL*     3.7    32.3    -      -       +      -
     56A  LEU*     3.5    28.6    -      -       +      +
     60A  LYS*     1.3    80.6    -      -       -      +
     62A  LYS*     1.3    65.7    +      -       -      +
     63A  LEU*     3.6    20.8    +      -       +      -
     77A  TYR*     3.4     6.6    -      -       -      -
     78A  ALA*     2.8    39.4    +      -       +      +
     84A  ILE*     4.2    11.0    -      -       +      -
     96A  ALA*     3.9    12.8    -      -       +      -
     97A  THR      3.6    13.7    -      -       -      +
     98A  ALA*     4.4     2.9    -      -       -      -
     99A  MET*     4.2     4.5    -      -       -      -
    102A  THR*     4.2    13.5    -      -       +      -
    104A  THR*     4.4     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  ILE*     1.3    71.2    -      -       -      +
     63A  LEU*     1.3    63.6    +      -       -      +
     64A  ASP*     4.0     5.4    -      -       -      +
     74A  LEU*     5.7     2.9    -      -       +      -
     77A  TYR*     3.9    16.4    -      -       +      -
     95A  TYR      3.8     1.2    -      -       -      +
     96A  ALA*     3.3     4.2    -      -       -      -
     97A  THR*     3.0    39.8    +      -       -      +
     99A  MET*     3.5    29.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  ILE*     5.3     2.7    -      -       +      -
     61A  ILE*     3.6    28.0    -      -       +      +
     62A  LYS*     1.3    70.8    -      -       -      +
     64A  ASP*     1.3    57.5    +      -       -      +
     74A  LEU*     4.5     1.9    -      -       -      +
     75A  LEU*     2.8    52.6    +      -       +      +
     76A  TYR*     2.9    52.4    +      -       +      +
     78A  ALA*     4.3     8.1    -      -       +      -
     84A  ILE*     4.0    27.1    -      -       +      -
     94A  ILE*     4.3    13.7    -      -       +      -
     95A  TYR      4.1     2.5    -      -       -      -
     96A  ALA*     4.0    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  LYS*     3.9     6.0    +      -       -      +
     63A  LEU*     1.3    76.7    -      -       -      +
     65A  ILE*     1.3    63.7    +      -       -      +
     66A  ILE*     4.3     0.7    -      -       -      -
     72A  GLU*     2.8    36.0    -      -       +      +
     73A  LYS      3.7     5.8    -      -       -      +
     74A  LEU*     3.2    30.1    +      -       -      +
     75A  LEU*     4.1     1.1    -      -       -      -
     94A  ILE*     3.7     9.7    -      -       -      +
     95A  TYR*     3.0    42.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ASP*     1.3    77.1    -      -       -      +
     66A  ILE*     1.3    68.8    +      -       -      +
     67A  PHE*     3.5    29.3    +      -       +      -
     72A  GLU*     3.8     1.7    -      -       -      -
     73A  LYS      3.1    23.7    +      -       -      +
     74A  LEU      3.9     5.4    -      -       -      +
     75A  LEU*     3.6    26.9    -      -       +      -
     92A  ASN*     3.4    42.6    -      -       +      +
     93A  ASN      3.4    14.6    -      -       -      +
     94A  ILE*     4.5     2.9    -      -       +      -
    138B  ARG*     3.6    26.0    -      -       +      +
    140B  VAL      6.2     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  PRO*     4.4    11.4    -      -       +      -
     65A  ILE*     1.3    75.5    -      -       -      +
     67A  PHE*     1.3    75.1    +      -       -      +
     68A  GLU      4.0     0.5    +      -       -      -
     70A  GLY*     4.2    14.6    -      -       -      +
     71A  SER      3.4     7.9    -      -       -      +
     72A  GLU*     3.5    31.2    -      -       +      +
     93A  ASN*     3.1    45.0    +      -       -      +
     95A  TYR*     3.6    35.2    -      -       +      +
    138B  ARG*     5.2     1.2    +      -       -      -
----------------------------------------------------------
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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