Contacts of the strand formed by residues 130 - 137 (chain D) 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 ILE 130 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86D  ASN*     5.6     0.2    -      -       -      +
     91D  LEU*     3.9    27.8    -      -       +      -
     93D  VAL*     5.7     0.9    -      -       +      -
    111D  LYS*     3.4     2.3    -      -       -      -
    112D  LEU*     2.8    45.0    +      -       +      +
    128D  TYR*     3.8     5.4    -      -       -      -
    129D  ASN*     1.3    86.8    -      -       +      +
    131D  MET*     1.3    71.2    +      -       -      +
    132D  PHE*     4.3     2.5    -      -       +      +
    146D  VAL*     5.5     0.2    -      -       +      -
    147D  ILE      3.3    10.8    -      -       -      +
    148D  PHE*     4.0    26.0    -      -       +      -
    174D  LEU*     4.1    21.5    -      -       +      -
    176D  VAL*     5.0     4.9    -      -       +      -
    306D  TYR      5.3     1.6    -      -       -      +
    308D  TYR*     3.9    12.6    -      -       +      -
    311D  PHE*     3.9    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 131 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109D  TYR*     3.6    39.5    -      -       +      -
    110D  VAL      3.4    12.8    -      -       -      +
    111D  LYS*     4.1    21.1    -      -       +      -
    128D  TYR*     3.8    19.7    -      -       +      -
    130D  ILE*     1.3    76.0    -      -       -      +
    132D  PHE*     1.3    66.9    +      -       -      +
    145D  HIS*     3.5    39.6    -      -       +      +
    146D  VAL*     3.5     3.1    -      -       -      -
    147D  ILE*     2.8    56.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 132 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93D  VAL*     4.0    11.9    -      -       +      -
     95D  PHE*     3.6    16.0    -      +       -      -
    109D  TYR*     3.4     5.3    -      -       -      -
    110D  VAL*     2.9    37.4    +      -       +      +
    130D  ILE*     4.3     3.1    -      -       +      -
    131D  MET*     1.3    77.3    -      -       -      +
    133D  GLY*     1.3    63.2    +      -       -      +
    144D  VAL*     3.8    21.1    -      -       +      -
    145D  HIS      3.3    11.4    -      -       -      -
    146D  VAL*     4.0    11.4    -      -       +      -
    172D  TYR*     3.9    20.2    -      +       +      -
    173D  THR      3.5    32.1    -      -       -      -
    174D  LEU*     3.5    46.0    -      -       +      -
    184D  VAL*     4.0    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 133 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95D  PHE*     4.3     4.0    -      -       -      -
    109D  TYR*     3.6     8.3    -      -       -      +
    132D  PHE*     1.3    82.2    -      -       -      +
    134D  PRO*     1.3    77.1    -      -       -      +
    135D  ASP      3.7     0.2    +      -       -      -
    144D  VAL*     4.0    10.8    -      -       -      -
    145D  HIS*     3.0    37.8    +      -       -      +
    172D  TYR*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 134 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95D  PHE*     4.4     1.8    -      -       +      -
     97D  VAL*     4.2    10.3    -      -       +      -
     99D  HIS*     4.7     9.6    -      -       +      +
    108D  GLY*     2.8    54.6    +      -       -      +
    109D  TYR*     3.5     4.7    -      -       -      -
    133D  GLY*     1.3    85.4    -      -       -      +
    135D  ASP*     1.3    56.8    +      -       -      +
    136D  ILE*     5.2     1.3    -      -       +      -
    143D  LYS      3.4     6.7    -      -       -      +
    144D  VAL*     4.4     1.6    -      -       +      -
    163D  CYS*     3.8    15.5    -      -       +      -
    164D  LYS      5.2     0.7    -      -       -      +
    172D  TYR*     3.7    50.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 135 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106D  GLY      3.6     5.4    -      -       -      +
    107D  GLY*     3.5    16.3    +      -       -      -
    109D  TYR*     4.0    13.4    +      -       +      -
    134D  PRO*     1.3    74.5    -      -       -      +
    136D  ILE*     1.3    73.6    +      -       -      +
    137D  CYS*     5.4     2.2    -      -       -      +
    141D  THR*     3.7    14.3    -      -       +      +
    142D  LYS*     3.7     2.6    -      -       -      -
    143D  LYS*     2.8    35.9    +      -       +      +
    145D  HIS*     3.1    37.3    +      -       +      +
    163D  CYS*     4.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 136 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99D  HIS*     4.1    13.0    -      -       +      +
    103D  ILE*     3.8    34.1    -      -       +      +
    104D  ASP      3.9    14.4    -      -       -      +
    105D  CYS*     3.8     0.3    -      -       -      -
    106D  GLY*     2.7    40.6    +      -       -      +
    134D  PRO      5.2     0.4    -      -       -      -
    135D  ASP*     1.3    86.1    +      -       -      +
    137D  CYS*     1.3    66.0    +      -       -      +
    138D  GLY      4.5     5.4    -      -       -      +
    141D  THR*     3.3    10.1    -      -       -      +
    142D  LYS*     4.8     7.9    -      -       +      -
    163D  CYS*     3.8    12.3    -      -       -      -
    164D  LYS      3.6    23.8    -      -       -      +
    165D  ASP*     4.0    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 137 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104D  ASP      3.7     2.2    -      -       -      -
    105D  CYS*     2.2    40.6    -      -       -      -
    135D  ASP*     5.4     2.5    -      -       -      +
    136D  ILE*     1.3    75.6    -      -       -      +
    138D  GLY*     1.3    68.1    +      -       -      +
    139D  PRO*     4.5     0.3    -      -       -      +
    140D  GLY*     4.2     1.6    +      -       -      -
    141D  THR*     3.1    36.2    +      -       +      +
----------------------------------------------------------
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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