Contacts of the strand formed by residues 130 - 137 (chain H) 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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91H  LEU*     4.6     8.7    -      -       +      -
     93H  VAL*     5.7     0.9    -      -       +      -
    110H  VAL      4.2     0.2    -      -       -      +
    111H  LYS*     3.4     2.6    -      -       -      -
    112H  LEU*     2.8    48.1    +      -       +      +
    128H  TYR*     3.7     5.7    -      -       -      -
    129H  ASN*     1.3    78.3    -      -       -      +
    131H  MET*     1.3    71.4    +      -       -      +
    132H  PHE*     4.6     2.2    -      -       +      +
    146H  VAL*     5.5     0.2    -      -       +      -
    147H  ILE      3.3    12.6    -      -       -      +
    148H  PHE*     3.3    28.5    -      -       +      -
    174H  LEU*     4.1    25.1    -      -       +      -
    176H  VAL*     5.7     0.9    -      -       +      -
    306H  TYR      5.1     0.7    -      -       -      +
    308H  TYR*     3.1    37.5    -      -       +      -
    311H  PHE*     4.1    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 131 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109H  TYR*     3.6    39.5    -      -       +      +
    110H  VAL      3.4    12.1    -      -       -      +
    111H  LYS*     4.1    20.0    -      -       +      -
    128H  TYR*     3.8    19.7    -      -       +      -
    130H  ILE*     1.3    75.0    -      -       -      +
    132H  PHE*     1.3    64.6    -      -       -      +
    145H  HIS*     3.5    40.2    -      -       +      +
    146H  VAL*     3.5     3.3    -      -       -      -
    147H  ILE*     2.8    57.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 132 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93H  VAL*     3.9    13.2    -      -       +      -
     95H  PHE*     3.6    17.1    -      +       -      -
    109H  TYR*     3.4     5.1    -      -       -      -
    110H  VAL*     2.9    38.7    +      -       +      +
    130H  ILE*     4.5     2.9    +      -       +      +
    131H  MET*     1.3    76.2    -      -       -      +
    133H  GLY*     1.3    63.2    +      -       -      +
    144H  VAL*     3.8    21.3    -      -       +      -
    145H  HIS      3.3    10.1    -      -       -      -
    146H  VAL*     4.0    10.3    -      -       +      -
    172H  TYR*     3.9    19.7    -      +       +      -
    173H  THR      3.5    33.0    -      -       -      -
    174H  LEU*     3.5    46.2    -      -       +      -
    184H  VAL*     4.1    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 133 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95H  PHE*     4.2     4.3    -      -       -      -
    109H  TYR*     3.6     9.5    -      -       -      +
    132H  PHE*     1.3    80.9    -      -       -      +
    134H  PRO*     1.3    76.7    -      -       -      +
    135H  ASP      3.7     0.2    +      -       -      -
    144H  VAL*     3.9    11.0    -      -       -      -
    145H  HIS*     2.9    38.0    +      -       -      +
    172H  TYR*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 134 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95H  PHE*     4.5     1.8    -      -       +      -
     97H  VAL*     4.2    10.8    -      -       +      -
     99H  HIS*     4.7     9.2    -      -       +      +
    106H  GLY      5.2     0.2    -      -       -      -
    108H  GLY*     2.8    54.1    +      -       -      +
    109H  TYR*     3.5     4.5    -      -       -      -
    133H  GLY*     1.3    85.3    -      -       -      +
    135H  ASP*     1.3    56.5    +      -       -      +
    136H  ILE*     5.2     0.9    -      -       +      -
    143H  LYS      3.4     7.6    -      -       -      +
    144H  VAL*     4.4     1.1    -      -       +      -
    163H  CYS*     3.8    15.9    -      -       +      -
    164H  LYS      5.2     0.7    -      -       -      +
    172H  TYR*     3.7    50.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 135 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106H  GLY*     3.5     4.9    -      -       -      +
    107H  GLY*     3.5    16.6    +      -       -      -
    109H  TYR*     3.9    13.5    +      -       +      -
    134H  PRO*     1.3    74.9    -      -       -      +
    136H  ILE*     1.3    74.9    +      -       -      +
    137H  CYS*     5.4     2.2    -      -       -      +
    141H  THR*     3.7    13.4    -      -       +      +
    142H  LYS*     3.7     1.7    -      -       -      -
    143H  LYS*     2.8    37.1    +      -       +      +
    145H  HIS*     3.1    37.1    +      -       +      +
    163H  CYS*     4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 136 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99H  HIS*     4.0    13.9    -      -       +      +
    103H  ILE*     3.8    35.9    -      -       +      +
    104H  ASP      3.8    13.9    -      -       -      +
    105H  CYS*     3.8     0.6    -      -       -      -
    106H  GLY      2.7    41.4    +      -       -      +
    134H  PRO      5.2     0.4    -      -       -      -
    135H  ASP*     1.3    84.8    +      -       -      +
    137H  CYS*     1.3    66.7    +      -       -      +
    138H  GLY      4.5     5.2    -      -       -      +
    141H  THR*     3.3    11.2    -      -       -      +
    142H  LYS*     4.9     6.5    -      -       +      +
    163H  CYS*     3.8    12.3    -      -       -      -
    164H  LYS      3.6    23.8    -      -       -      +
    165H  ASP*     4.0    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 137 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104H  ASP      3.7     2.2    -      -       -      -
    105H  CYS*     2.1    40.6    -      -       -      -
    135H  ASP*     5.4     3.1    -      -       -      +
    136H  ILE*     1.3    74.1    -      -       -      +
    138H  GLY*     1.3    66.9    +      -       -      +
    139H  PRO*     4.4     0.7    -      -       -      +
    140H  GLY*     4.2     1.4    +      -       -      -
    141H  THR*     3.1    37.2    +      -       +      +
----------------------------------------------------------
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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