Contacts of the strand formed by residues 130 - 137 (chain G) 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 G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91G  LEU*     3.9    17.7    -      -       +      -
     93G  VAL*     5.8     1.1    -      -       +      -
    111G  LYS*     3.4     2.8    -      -       -      -
    112G  LEU*     2.8    46.5    +      -       +      +
    128G  TYR*     3.6     6.2    -      -       -      -
    129G  ASN*     1.3    86.8    -      -       +      +
    131G  MET*     1.3    72.8    +      -       -      +
    132G  PHE*     4.6     2.0    -      -       +      +
    146G  VAL*     5.5     0.4    -      -       +      -
    147G  ILE      3.3    10.8    -      -       -      +
    148G  PHE*     3.9    26.7    -      -       +      -
    174G  LEU*     4.1    22.0    -      -       +      -
    176G  VAL*     5.1     4.3    -      -       +      -
    306G  TYR      5.3     1.6    -      -       -      +
    308G  TYR*     3.9    12.6    -      -       +      -
    311G  PHE*     3.9    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 131 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109G  TYR*     3.6    39.3    -      -       +      -
    110G  VAL      3.4    13.0    -      -       -      +
    111G  LYS*     4.1    20.4    -      -       +      +
    128G  TYR*     3.8    19.7    -      -       +      -
    130G  ILE*     1.3    77.6    -      -       -      +
    132G  PHE*     1.3    65.6    +      -       -      +
    145G  HIS*     3.5    40.6    -      -       +      +
    146G  VAL*     3.5     4.2    -      -       -      -
    147G  ILE*     2.9    54.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 132 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93G  VAL*     4.0    12.8    -      -       +      -
     95G  PHE*     3.6    15.8    -      +       -      -
    109G  TYR*     3.4     4.9    -      -       -      -
    110G  VAL*     2.9    38.5    +      -       +      +
    112G  LEU*     6.5     0.4    -      -       +      -
    130G  ILE*     4.7     3.1    -      -       +      -
    131G  MET*     1.3    77.3    -      -       -      +
    133G  GLY*     1.3    61.3    +      -       -      +
    144G  VAL*     3.8    20.9    -      -       +      -
    145G  HIS      3.3    10.3    -      -       -      -
    146G  VAL*     4.0    11.0    -      -       +      -
    172G  TYR*     3.9    20.4    -      +       +      -
    173G  THR      3.5    33.4    -      -       -      -
    174G  LEU*     3.5    45.1    -      -       +      -
    184G  VAL*     4.0    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 133 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95G  PHE*     4.2     3.8    -      -       -      -
    109G  TYR*     3.6     9.4    -      -       -      +
    132G  PHE*     1.3    82.9    -      -       -      +
    134G  PRO*     1.3    76.7    -      -       -      +
    135G  ASP      3.7     0.2    +      -       -      -
    144G  VAL*     4.0     9.4    -      -       -      -
    145G  HIS*     2.9    37.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 134 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95G  PHE*     4.4     1.8    -      -       +      -
     97G  VAL*     4.2     9.6    -      -       +      -
     99G  HIS*     4.7    10.1    -      -       -      +
    108G  GLY*     2.8    55.4    +      -       -      +
    109G  TYR*     3.5     4.7    -      -       -      -
    133G  GLY*     1.3    87.0    -      -       -      +
    135G  ASP*     1.3    54.9    +      -       -      +
    136G  ILE*     5.2     1.1    -      -       +      -
    143G  LYS      3.4     7.2    -      -       -      +
    144G  VAL*     4.4     1.8    -      -       +      -
    163G  CYS*     3.8    15.3    -      -       +      -
    164G  LYS      5.2     0.7    -      -       -      +
    172G  TYR*     3.7    50.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 135 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106G  GLY      3.6     5.5    -      -       -      +
    107G  GLY*     3.5    16.3    +      -       -      -
    109G  TYR*     3.9    12.9    +      -       +      -
    134G  PRO*     1.3    76.1    -      -       -      +
    136G  ILE*     1.3    74.9    +      -       -      +
    137G  CYS*     5.4     2.3    -      -       -      +
    141G  THR*     3.7    13.6    -      -       +      +
    143G  LYS*     2.8    36.6    +      -       +      +
    145G  HIS*     3.1    37.3    +      -       +      +
    163G  CYS*     4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 136 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99G  HIS*     4.0    15.0    -      -       +      +
    103G  ILE*     3.8    33.9    -      -       +      +
    104G  ASP      3.8    14.8    -      -       -      +
    105G  CYS*     3.8     0.3    -      -       -      -
    106G  GLY*     2.7    41.0    +      -       -      +
    134G  PRO      5.2     0.4    -      -       -      -
    135G  ASP*     1.3    86.8    +      -       -      +
    137G  CYS*     1.3    65.1    +      -       -      +
    138G  GLY      4.4     3.4    -      -       -      +
    141G  THR*     3.3    10.3    -      -       -      +
    142G  LYS*     4.2    11.4    -      -       +      -
    163G  CYS*     3.8    12.3    -      -       -      -
    164G  LYS      3.6    24.2    -      -       -      +
    165G  ASP*     4.1    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 137 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104G  ASP      3.7     2.5    -      -       -      -
    105G  CYS*     2.2    40.4    -      -       -      -
    135G  ASP*     5.4     2.5    -      -       -      +
    136G  ILE*     1.3    75.5    -      -       -      +
    138G  GLY*     1.3    65.8    +      -       -      +
    140G  GLY*     4.2     1.2    +      -       -      -
    141G  THR*     3.0    35.6    +      -       +      +
----------------------------------------------------------
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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