Contacts of the strand formed by residues 73 - 84 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ASP*     3.5    34.1    +      -       -      +
     46A  PHE      4.7     3.0    +      -       -      -
     47A  GLY*     3.8    10.8    -      -       -      +
     70A  GLN*     2.8    44.2    +      -       +      +
     71A  LYS      3.3    13.9    +      -       -      +
     72A  ALA*     1.3    82.8    +      -       -      +
     74A  PHE*     1.3    60.1    +      -       -      +
     75A  TYR*     3.4    24.2    -      -       +      -
    319A  TRP*     3.3    10.0    -      -       -      -
    320A  GLN      3.0    28.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  LYS*     3.4    26.0    -      -       +      +
     45A  ASP      5.2     1.4    +      -       -      -
     46A  PHE*     3.3    27.9    -      +       +      -
     47A  GLY      2.8    29.1    +      -       -      -
     73A  ARG*     1.3    75.5    -      -       -      +
     75A  TYR*     1.3    57.9    +      -       -      +
    317A  ASP*     6.2     0.7    -      -       -      -
    318A  LEU      3.3     8.1    -      -       -      +
    319A  TRP*     3.7    43.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  PHE*     4.4     3.1    -      -       -      -
     47A  GLY*     3.5    34.1    -      -       -      -
     48A  LYS      3.7    12.6    -      -       -      -
     49A  PHE*     3.7    31.0    -      +       +      -
     68A  THR*     3.5    30.1    -      -       +      -
     69A  SER      3.4     2.6    +      -       -      -
     70A  GLN*     2.5    41.9    +      -       -      +
     73A  ARG*     3.4    24.7    -      -       +      -
     74A  PHE*     1.3    78.2    -      -       -      +
     76A  ALA*     1.3    64.4    +      -       -      +
    316A  LEU      3.7     2.7    -      -       -      +
    317A  ASP*     3.3     5.4    -      -       -      -
    318A  LEU*     2.7    47.3    +      -       +      +
    320A  GLN*     4.1    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  GLU*     3.8     5.0    -      -       -      +
     40A  SER*     3.1    43.2    +      -       -      +
     46A  PHE*     3.7    27.0    -      -       +      +
     47A  GLY      5.2     1.2    +      -       -      -
     49A  PHE*     4.5     1.6    -      -       -      -
     75A  TYR*     1.3    78.2    -      -       -      +
     77A  LEU*     1.3    61.5    +      -       -      +
    122A  MET*     4.0    11.4    -      -       +      +
    316A  LEU      3.3     5.4    -      -       -      -
    317A  ASP*     4.4    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  TRP*     4.1    17.0    -      -       +      -
     37A  TRP*     3.8    34.9    -      -       +      -
     38A  ILE      3.5    20.0    -      -       -      +
     39A  GLU*     3.5    30.7    -      -       +      +
     49A  PHE*     3.8    36.3    -      -       +      -
     66A  LEU*     3.8    16.6    -      -       +      -
     76A  ALA*     1.3    74.8    -      -       -      +
     78A  SER*     1.3    63.5    +      -       -      +
    122A  MET*     4.5     1.3    -      -       -      +
    315A  GLY*     3.5     0.2    -      -       -      -
    316A  LEU*     2.8    33.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  TRP*     3.2     8.7    -      -       -      -
     38A  ILE      2.8    33.8    +      -       -      -
     77A  LEU*     1.3    73.9    -      -       -      +
     79A  ALA*     1.3    61.2    +      -       -      +
    119A  GLN*     3.0    33.5    +      -       -      +
    122A  MET*     3.2    35.5    -      -       -      +
    313A  VAL*     3.4     6.3    -      -       -      -
    314A  LEU      3.3    11.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     3.6    29.2    -      -       +      -
     36A  ARG*     3.6    13.2    -      -       +      +
     37A  TRP*     3.6    26.2    -      -       +      +
     78A  SER*     1.3    75.1    -      -       -      +
     80A  SER*     1.3    60.9    +      -       -      +
     81A  PHE*     3.9     3.6    -      -       -      -
    119A  GLN*     3.9     2.7    -      -       -      +
    313A  VAL*     3.3     2.7    -      -       -      -
    314A  LEU*     2.9    38.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     4.3     8.3    -      -       -      -
     36A  ARG      4.2     5.3    +      -       -      +
     79A  ALA*     1.3    74.9    -      -       -      +
     81A  PHE*     1.3    67.0    +      -       -      +
    115A  ASN*     5.2     3.0    +      -       -      -
    119A  GLN*     2.8    30.3    +      -       -      +
    312A  GLY      3.3     8.9    +      -       -      -
    313A  VAL*     4.0     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  TYR*     3.4    23.6    -      -       +      +
     23A  PHE*     3.9    23.1    -      +       +      -
     79A  ALA      3.9     4.3    -      -       -      -
     80A  SER*     1.3    81.8    -      -       -      +
     82A  GLU*     1.3    77.0    +      -       -      +
     83A  PRO*     3.1     9.5    -      -       -      +
     84A  PHE*     3.6    20.0    -      +       -      -
    112A  LEU*     5.4     2.9    -      -       +      -
    115A  ASN*     4.6     1.7    -      -       -      +
    311A  PHE*     3.4    30.3    -      -       +      -
    312A  GLY*     3.0    22.9    +      -       -      +
    313A  VAL      3.6     7.2    -      -       -      -
    314A  LEU*     3.5    30.5    -      -       +      -
    332A  ILE*     4.4    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  TYR*     4.8     6.6    -      -       -      +
     81A  PHE*     1.3    82.5    -      -       -      +
     83A  PRO*     1.3    88.0    -      -       -      +
     84A  PHE*     3.6     5.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  PHE      3.1     7.2    -      -       -      +
     82A  GLU*     1.3   108.4    -      -       -      +
     84A  PHE*     1.3    60.4    +      -       -      +
    115A  ASN*     3.5    34.3    -      -       +      +
    310A  ASN*     4.0    13.9    -      -       +      +
    311A  PHE      3.0    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  TYR*     3.5    67.1    -      +       +      -
     81A  PHE*     3.6    22.0    -      +       -      -
     82A  GLU      4.3     1.8    -      -       -      +
     83A  PRO*     1.3    77.9    -      -       -      +
     85A  SER*     1.3    74.8    -      -       -      +
     86A  ASN*     4.3     4.3    -      -       +      -
     91A  LEU*     3.6    22.9    -      -       +      -
    112A  LEU*     5.6     0.9    -      -       +      -
    309A  ASP      4.3     0.9    -      -       -      -
    310A  ASN*     3.1     5.6    -      -       -      -
    311A  PHE*     2.8    68.2    +      +       +      +
    332A  ILE*     3.9     7.4    -      -       +      -
----------------------------------------------------------
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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