Contacts of the strand formed by residues 73 - 84 (chain C) 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 C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45C  ASP*     3.5    29.4    +      -       -      +
     47C  GLY*     3.8    13.2    -      -       -      +
     70C  GLN*     3.9    34.2    +      -       +      +
     71C  LYS      3.1    19.8    +      -       -      +
     72C  ALA*     1.3   103.7    +      -       -      +
     74C  PHE*     1.3    59.8    +      -       -      +
     75C  TYR*     3.4    23.3    -      -       +      -
    319C  TRP*     3.3     9.5    -      -       -      -
    320C  GLN      3.0    29.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 74 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  LYS*     4.5    26.0    -      -       +      -
     45C  ASP*     5.2     1.6    +      -       -      -
     46C  PHE*     3.3    27.5    -      -       +      -
     47C  GLY      2.8    31.2    +      -       -      -
     73C  ARG*     1.3    74.9    -      -       -      +
     75C  TYR*     1.3    58.1    +      -       -      +
    317C  ASP*     6.1     0.7    -      -       -      -
    318C  LEU*     3.3     8.1    -      -       -      -
    319C  TRP*     3.7    44.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 75 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  PHE*     4.3     3.5    -      -       -      -
     47C  GLY*     3.5    33.0    -      -       -      -
     48C  LYS      3.6    12.6    -      -       -      -
     49C  PHE*     3.7    31.0    -      +       +      -
     68C  THR*     3.5    30.4    -      -       +      -
     69C  SER      3.4     2.4    +      -       -      -
     70C  GLN*     2.5    42.2    +      -       -      -
     73C  ARG*     3.4    25.6    -      -       +      -
     74C  PHE*     1.3    77.2    -      -       -      +
     76C  ALA*     1.3    65.7    +      -       -      +
    316C  LEU      3.8     2.2    -      -       -      +
    317C  ASP*     3.3     4.9    -      -       -      +
    318C  LEU*     2.8    45.7    +      -       +      +
    320C  GLN*     4.1     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 76 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39C  GLU*     3.8     4.7    -      -       -      +
     40C  SER*     3.1    41.8    +      -       -      +
     46C  PHE*     3.7    27.3    -      -       +      +
     47C  GLY      5.2     1.6    +      -       -      -
     49C  PHE*     4.6     1.6    -      -       -      -
     75C  TYR*     1.3    80.2    -      -       -      +
     77C  LEU*     1.3    60.5    +      -       -      +
    122C  MET*     3.4    19.3    -      -       +      +
    123C  HIS*     5.2     0.7    -      -       -      -
    316C  LEU      3.3     5.4    -      -       -      -
    317C  ASP*     5.0     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 77 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33C  TRP*     4.1    17.0    -      -       +      -
     37C  TRP*     3.8    32.5    -      -       +      -
     38C  ILE      3.5    18.8    -      -       -      +
     39C  GLU*     3.5    30.3    -      -       +      +
     49C  PHE*     3.8    36.1    -      -       +      -
     66C  LEU*     3.8    17.3    -      -       +      -
     76C  ALA*     1.3    75.3    -      -       -      +
     78C  SER*     1.3    63.1    +      -       -      +
    122C  MET*     3.2     2.3    -      -       -      +
    316C  LEU*     2.8    33.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 78 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37C  TRP*     3.2     9.5    -      -       -      -
     38C  ILE      2.8    34.4    +      -       -      -
     77C  LEU*     1.3    77.0    -      -       -      +
     79C  ALA*     1.3    60.0    +      -       -      +
    119C  GLN*     3.0    41.1    +      -       -      +
    122C  MET*     3.9    12.4    -      -       -      +
    313C  VAL*     3.4    13.9    -      -       -      +
    314C  LEU      3.3    13.0    -      -       -      -
    315C  GLY*     3.8     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 79 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  PHE*     3.6    23.8    -      -       +      -
     36C  ARG*     3.6    17.0    -      -       +      +
     37C  TRP*     3.6    28.5    -      -       +      +
     78C  SER*     1.3    75.1    -      -       -      +
     80C  SER*     1.3    61.7    +      -       -      +
     81C  PHE*     3.9     4.3    -      -       -      -
    119C  GLN*     3.9     0.2    -      -       -      +
    313C  VAL*     3.3     5.1    -      -       -      -
    314C  LEU*     2.9    38.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 80 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  PHE*     4.4     8.3    -      -       -      -
     36C  ARG      4.2     6.2    +      -       -      +
     79C  ALA*     1.3    75.9    -      -       -      +
     81C  PHE*     1.3    66.4    +      -       -      +
    115C  ASN*     5.2     5.2    -      -       -      -
    119C  GLN*     3.6    25.6    +      -       -      +
    312C  GLY      3.2    12.3    -      -       -      -
    313C  VAL*     4.3     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 81 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  TYR*     3.4    23.1    -      -       +      +
     23C  PHE*     4.0    24.9    -      +       +      -
     79C  ALA      3.9     4.3    -      -       -      -
     80C  SER*     1.3    80.1    -      -       -      +
     82C  GLU*     1.3    77.8    +      -       -      +
     83C  PRO*     3.1     9.9    -      -       -      +
     84C  PHE*     3.7    20.2    -      +       -      -
    112C  LEU*     5.4     3.1    -      -       +      -
    115C  ASN*     4.6     1.7    -      -       -      +
    311C  PHE*     3.4    30.5    -      -       +      -
    312C  GLY*     2.9    23.5    +      -       -      +
    313C  VAL*     3.6     7.9    -      -       -      -
    314C  LEU*     3.5    29.8    -      -       +      -
    332C  ILE*     4.4    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 82 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  TYR*     4.8     6.6    +      -       -      +
     81C  PHE*     1.3    82.0    -      -       -      +
     83C  PRO*     1.3    82.9    -      -       +      +
     84C  PHE*     3.7     4.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 83 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81C  PHE      3.1     7.8    -      -       -      +
     82C  GLU*     1.3    99.4    -      -       +      +
     84C  PHE*     1.3    61.1    +      -       -      +
    115C  ASN*     3.5    31.6    -      -       -      +
    310C  ASN*     3.9    20.4    -      -       -      +
    311C  PHE      3.0    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 84 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  TYR*     3.5    69.3    -      +       +      -
     81C  PHE*     3.7    21.1    -      +       -      -
     82C  GLU      4.3     1.3    -      -       -      -
     83C  PRO*     1.3    77.3    -      -       -      +
     85C  SER*     1.3    76.1    +      -       -      +
     86C  ASN*     4.2     3.4    -      -       -      -
     89C  GLN*     5.8     0.2    -      -       -      -
     91C  LEU*     3.6    26.7    -      -       +      -
    112C  LEU*     5.6     0.7    -      -       +      -
    309C  ASP      4.3     2.5    -      -       -      -
    310C  ASN*     3.4     3.0    -      -       -      -
    311C  PHE*     2.7    66.1    +      +       +      +
    332C  ILE*     3.9     7.2    -      -       +      -
----------------------------------------------------------
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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