Contacts of the strand formed by residues 61 - 68 (chain A) in PDB entry 6J7Z


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
----------------------------------------------------------
     48A  LEU*     4.3    22.9    -      -       +      -
     49A  GLU      3.5     6.5    -      -       -      +
     50A  MET*     3.6    31.4    -      -       +      -
     60A  ILE*     1.3    77.4    -      -       -      +
     62A  GLU*     1.3    73.3    +      -       -      +
     63A  MET*     4.0     3.5    +      -       +      +
     81A  LEU      3.8     0.5    -      -       -      +
     82A  ILE*     3.4     7.0    -      -       -      -
     83A  ILE*     2.9    43.5    +      -       +      +
     84A  LYS      4.5    12.1    -      -       -      +
    150A  PHE*     3.7    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  ASP      3.8     0.7    -      -       -      +
     48A  LEU*     3.2     4.9    -      -       -      -
     49A  GLU*     2.9    40.9    +      -       +      +
     60A  ILE      4.3     0.4    -      -       -      -
     61A  ILE*     1.3    75.2    -      -       -      +
     63A  MET*     1.3    62.8    +      -       -      +
     80A  ASN*     3.2    15.9    -      -       -      +
     81A  LEU      3.4     4.7    -      -       -      +
     82A  ILE*     3.6    22.3    -      -       +      +
    194A  HIS      4.2     4.0    -      -       -      +
    195A  ARG*     3.0    56.9    +      -       -      +
    196A  ALA*     3.3    21.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  VAL*     4.7     9.9    -      -       +      -
     47A  ASP      3.4     3.4    -      -       -      -
     48A  LEU*     3.6    31.0    -      -       +      -
     61A  ILE*     4.9     2.0    -      -       +      -
     62A  GLU*     1.3    75.8    -      -       -      +
     64A  ALA*     1.3    64.0    +      -       -      +
     80A  ASN*     3.4     4.5    -      -       -      +
     81A  LEU      2.9    32.6    +      -       -      -
     83A  ILE*     4.3    12.3    -      -       +      -
    124A  PHE*     3.4    50.7    -      -       +      -
    150A  PHE*     6.2     0.2    -      -       -      -
    151A  LEU*     3.8    23.8    -      -       +      -
    155A  MET*     3.9    21.8    -      -       -      +
    158A  PHE*     4.3    14.4    -      -       +      -
    196A  ALA*     4.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  VAL*     3.3     5.2    -      -       -      +
     47A  ASP      2.9    31.3    +      -       -      +
     63A  MET*     1.3    76.6    -      -       -      +
     65A  CYS*     1.3    61.7    +      -       -      +
     79A  PRO      3.7     5.6    -      -       -      +
     80A  ASN*     3.8    18.2    -      -       +      +
    124A  PHE*     4.4     1.3    -      -       -      -
    196A  ALA*     3.6    19.9    -      -       +      +
    197A  LEU*     3.8    19.7    -      -       +      +
    200A  ILE*     3.7     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  VAL*     3.7    30.1    -      -       -      -
     45A  TRP      3.2     8.1    -      -       -      +
     46A  VAL*     3.9     9.2    -      -       +      -
     64A  ALA*     1.3    77.8    -      -       -      +
     66A  LEU*     1.3    63.6    +      -       -      +
     77A  GLU*     4.2     0.5    -      -       -      +
     78A  GLY*     2.8    31.8    +      -       -      +
     79A  PRO      3.6     5.0    +      -       -      +
    124A  PHE*     3.7    25.6    -      -       +      -
    127A  PHE*     4.0    22.4    -      -       -      -
    128A  VAL*     4.4     4.7    -      -       -      -
    158A  PHE*     4.8     2.0    -      -       -      -
    197A  LEU*     5.1     4.0    -      -       -      +
    200A  ILE*     3.9     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  VAL*     3.7     0.5    -      -       -      -
     45A  TRP*     2.9    38.0    +      -       +      +
     65A  CYS*     1.3    76.8    -      -       -      +
     67A  ILE*     1.3    76.5    +      -       -      +
     68A  THR*     3.7    26.2    -      -       +      -
     74A  ILE*     4.0    22.9    -      -       +      -
     76A  ALA      3.3    15.0    -      -       -      +
     77A  GLU*     4.0    13.7    -      -       +      -
     78A  GLY      4.1     2.2    -      -       -      +
    127A  PHE*     4.3     0.9    -      -       -      -
    197A  LEU*     4.1    20.2    -      -       +      -
    200A  ILE*     3.6    24.0    -      -       +      -
    201A  SER*     5.5     3.4    -      -       -      +
    204A  ILE*     3.7    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ARG*     4.1    23.3    -      -       +      -
     43A  MET      3.4     6.3    -      -       -      +
     44A  VAL*     3.8    31.2    -      -       +      -
     66A  LEU*     1.3    83.7    -      -       -      +
     68A  THR*     1.3    74.8    +      -       -      +
     74A  ILE*     3.5     4.9    -      -       -      -
     75A  LEU*     2.8    29.3    +      -       +      -
     76A  ALA      2.9    15.4    +      -       -      +
    127A  PHE*     3.5    27.6    -      -       +      -
    128A  VAL*     4.5     3.4    -      -       +      -
    131A  GLN*     3.6    33.9    -      -       +      +
    132A  THR*     4.2     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ARG*     3.3     8.7    -      -       -      +
     43A  MET*     2.9    36.5    +      -       -      +
     45A  TRP*     2.7    39.1    +      -       +      +
     66A  LEU*     3.7    11.4    -      -       +      -
     67A  ILE*     1.3    79.1    -      -       -      +
     69A  ASP*     1.3    69.3    +      -       -      +
     72A  LEU*     3.9    17.4    -      -       -      +
     73A  ASN      3.2    12.3    -      -       -      +
     74A  ILE*     4.1     4.3    -      -       +      -
     75A  LEU*     4.0     5.8    -      -       -      +
    204A  ILE*     3.8    12.6    -      -       +      -
----------------------------------------------------------
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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