Contacts of the strand formed by residues 73 - 84 (chain J) in PDB entry 5LK5


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 ARG 73 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45J  ASP*     3.5    28.9    +      -       -      +
     47J  GLY*     3.8    13.2    -      -       -      +
     70J  GLN*     3.9    35.5    +      -       +      +
     71J  LYS      3.1    20.7    +      -       -      +
     72J  ALA*     1.3   103.4    +      -       -      +
     74J  PHE*     1.3    60.0    +      -       -      +
     75J  TYR*     3.4    24.1    -      -       +      -
    319J  TRP*     3.3     9.1    -      -       -      -
    320J  GLN      3.0    28.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 74 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45J  ASP      5.2     1.4    +      -       -      +
     46J  PHE*     3.3    28.3    -      +       +      -
     47J  GLY      2.8    29.8    +      -       -      -
     73J  ARG*     1.3    74.5    -      -       -      +
     75J  TYR*     1.3    57.5    +      -       -      +
    124J  GLY*     6.5     0.9    -      -       -      -
    317J  ASP*     6.1     0.7    -      -       -      -
    318J  LEU      3.4     7.6    -      -       -      +
    319J  TRP*     3.7    43.5    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 75 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46J  PHE*     4.4     3.5    -      -       -      -
     47J  GLY*     3.5    34.3    -      -       -      -
     48J  LYS      3.6    12.8    -      -       -      -
     49J  PHE*     3.7    30.7    -      +       +      -
     68J  THR*     3.5    29.6    -      -       +      -
     69J  SER      3.4     2.8    +      -       -      -
     70J  GLN*     2.5    41.9    +      -       -      +
     73J  ARG*     3.4    28.3    -      -       +      -
     74J  PHE*     1.3    74.0    -      -       -      +
     76J  ALA*     1.3    65.2    +      -       -      +
    316J  LEU      3.7     2.2    -      -       -      -
    317J  ASP*     3.3     5.2    -      -       -      -
    318J  LEU*     2.8    45.4    +      -       +      +
    320J  GLN*     4.2     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 76 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39J  GLU*     3.8     4.2    -      -       -      +
     40J  SER*     3.0    44.0    +      -       -      +
     46J  PHE*     3.8    27.1    -      -       +      +
     47J  GLY      5.2     1.2    +      -       -      -
     49J  PHE*     4.5     1.8    -      -       -      -
     75J  TYR*     1.3    78.7    -      -       -      +
     77J  LEU*     1.3    60.7    +      -       -      +
    122J  MET*     4.0    11.0    -      -       +      +
    316J  LEU      3.3     5.6    -      -       -      -
    317J  ASP*     4.4     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 77 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33J  TRP*     4.2    16.8    -      -       +      -
     37J  TRP*     3.7    34.7    -      -       +      -
     38J  ILE      3.5    18.8    -      -       -      +
     39J  GLU*     3.5    31.0    -      -       +      -
     49J  PHE*     3.7    32.8    -      -       +      -
     66J  LEU*     3.8    21.5    -      -       +      -
     76J  ALA*     1.3    76.2    -      -       -      +
     78J  SER*     1.3    63.1    +      -       -      +
    122J  MET*     4.7     1.3    -      -       -      -
    315J  GLY*     3.6     0.3    -      -       -      -
    316J  LEU*     2.8    33.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 78 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37J  TRP*     3.2     8.6    -      -       -      -
     38J  ILE      2.8    37.3    +      -       -      -
     77J  LEU*     1.3    74.2    -      -       -      +
     79J  ALA*     1.3    60.3    +      -       -      +
    119J  GLN*     3.0    33.6    +      -       -      +
    122J  MET*     3.2    35.9    -      -       -      +
    313J  VAL*     3.4    10.8    -      -       -      -
    314J  LEU      3.3     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 79 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23J  PHE*     3.6    30.1    -      -       +      -
     36J  ARG      3.6    12.8    -      -       -      +
     37J  TRP*     3.6    26.4    -      -       +      +
     78J  SER*     1.3    75.7    -      -       -      +
     80J  SER*     1.3    60.2    +      -       -      +
     81J  PHE*     3.8     4.4    -      -       -      -
    119J  GLN*     3.8     2.9    -      -       -      +
    313J  VAL*     3.3     2.1    -      -       -      -
    314J  LEU*     2.9    38.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 80 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23J  PHE*     4.3     8.7    -      -       -      -
     36J  ARG      4.2     5.4    +      -       -      +
     79J  ALA*     1.3    75.2    -      -       -      +
     81J  PHE*     1.3    65.3    +      -       -      +
    115J  ASN*     5.2     4.3    -      -       -      -
    119J  GLN*     3.6    25.8    +      -       -      +
    312J  GLY      3.2    11.7    -      -       -      -
    313J  VAL*     4.1     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 81 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22J  TYR*     3.4    23.1    -      -       +      +
     23J  PHE*     4.0    22.7    -      +       +      -
     79J  ALA      3.8     4.9    -      -       -      -
     80J  SER*     1.3    79.8    -      -       -      +
     82J  GLU*     1.3    78.5    +      -       -      +
     83J  PRO*     3.0     9.4    -      -       -      +
     84J  PHE*     3.7    20.4    -      +       -      -
    112J  LEU*     4.8     2.9    -      -       +      -
    115J  ASN*     4.7     1.6    -      -       -      +
    311J  PHE*     3.4    29.4    -      -       +      -
    312J  GLY*     3.0    23.2    +      -       -      +
    313J  VAL      3.6     8.1    -      -       -      -
    314J  LEU*     3.5    29.4    -      -       +      -
    332J  ILE*     4.4    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 82 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22J  TYR*     4.8     7.2    -      -       -      +
     81J  PHE*     1.3    82.4    -      -       -      +
     83J  PRO*     1.3    89.8    -      -       -      +
     84J  PHE*     3.6     5.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 83 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81J  PHE      3.0     7.8    -      -       -      +
     82J  GLU*     1.3   107.4    -      -       -      +
     84J  PHE*     1.3    61.8    +      -       -      +
    115J  ASN*     3.5    32.5    -      -       -      +
    310J  ASN*     4.0    20.6    -      -       -      +
    311J  PHE      3.0    14.8    -      -       -      +
    312J  GLY*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 84 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22J  TYR*     3.6    67.3    -      +       +      -
     81J  PHE*     3.7    21.1    -      +       -      -
     82J  GLU      4.2     1.8    -      -       -      +
     83J  PRO*     1.3    77.3    -      -       -      +
     85J  SER*     1.3    75.6    +      -       -      +
     86J  ASN*     4.3     4.5    -      -       +      -
     89J  GLN*     5.8     0.2    -      -       -      +
     91J  LEU*     3.6    25.8    -      -       +      -
    112J  LEU*     5.7     0.7    -      -       +      -
    309J  ASP      4.3     2.7    -      -       -      -
    310J  ASN*     3.4     3.8    -      -       -      -
    311J  PHE*     2.8    67.6    +      +       +      +
    332J  ILE*     3.9     8.5    -      -       +      -
----------------------------------------------------------
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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