Contacts of the strand formed by residues 91 - 99 (chain E) 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 LEU 91 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22E  TYR*     5.0     0.2    -      -       +      -
     84E  PHE*     3.6    34.1    -      -       +      -
     86E  ASN*     4.0    19.7    -      -       +      +
     89E  GLN      3.7     0.8    +      -       -      -
     90E  THR*     1.3    75.0    -      -       -      +
     92E  VAL*     1.3    66.5    +      -       -      +
     93E  VAL*     4.3     9.4    -      -       +      +
    112E  LEU*     4.3     9.6    -      -       +      -
    130E  ILE*     3.9    28.0    -      -       +      -
    174E  LEU*     3.7     1.3    -      -       +      +
    175E  ILE*     3.5     2.1    -      -       -      -
    176E  VAL*     2.8    49.2    +      -       +      +
    311E  PHE*     3.9    18.8    -      -       +      -
    332E  ILE*     3.8    17.5    -      -       +      -
    333E  THR      3.8     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 92 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90E  THR*     4.0    17.0    -      -       +      -
     91E  LEU*     1.3    78.2    -      -       -      +
     93E  VAL*     1.3    66.5    +      -       -      +
     94E  GLN*     4.2     2.2    -      -       +      -
    173E  THR*     3.8    17.9    -      -       +      -
    174E  LEU      3.3     9.4    -      -       -      +
    175E  ILE*     4.2    10.3    -      -       +      -
    331E  LEU      3.6     0.9    -      -       -      +
    332E  ILE*     3.3     9.4    -      -       -      +
    333E  THR*     2.8    48.0    +      -       +      +
    335E  ASP      4.1     5.2    -      -       -      +
    336E  GLU*     4.0    24.0    -      -       -      +
    339E  ALA*     3.6    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 93 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91E  LEU*     4.3    13.7    -      -       +      -
     92E  VAL*     1.3    76.3    -      -       -      +
     94E  GLN*     1.3    63.9    +      -       -      +
     95E  PHE*     4.7     3.4    -      -       +      -
    110E  VAL*     4.1    25.8    -      -       +      -
    112E  LEU*     3.3    34.5    -      -       +      -
    130E  ILE*     5.8     1.6    -      -       +      -
    132E  PHE*     4.0    11.9    -      -       +      -
    172E  TYR      3.8     0.7    -      -       -      +
    173E  THR*     3.4     1.9    -      -       -      -
    174E  LEU*     2.8    55.2    +      -       +      +
    314E  LEU*     4.9     2.9    -      -       +      -
    331E  LEU      3.7     4.7    -      -       -      +
    332E  ILE*     4.8    10.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 94 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92E  VAL*     4.7     4.7    -      -       +      -
     93E  VAL*     1.3    77.5    -      -       -      +
     95E  PHE*     1.3    70.3    +      -       -      +
    171E  LEU*     3.6    21.0    -      -       +      +
    172E  TYR      3.2    12.8    -      -       -      +
    173E  THR*     2.8    31.2    +      -       +      +
    188E  ASN*     4.5     2.3    -      -       -      +
    329E  ASN      5.0     1.7    +      -       -      +
    330E  PHE*     3.4     1.4    -      -       -      +
    331E  LEU*     2.8    46.9    +      -       +      +
    339E  ALA*     3.0    35.9    +      -       -      +
    342E  PHE*     4.1    14.6    -      -       -      -
    343E  GLY*     3.5    18.0    -      -       -      +
    346E  THR*     5.2     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 95 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93E  VAL*     4.7     2.2    -      -       +      -
     94E  GLN*     1.3    83.1    -      -       -      +
     96E  THR*     1.3    65.3    +      -       -      +
     97E  VAL*     3.3    31.9    -      -       +      -
    108E  GLY      3.4    15.0    -      -       -      -
    110E  VAL*     3.7    39.7    -      -       +      -
    132E  PHE*     3.7    36.3    -      +       -      -
    133E  GLY*     4.3     4.3    -      -       -      -
    134E  PRO*     4.5     0.4    -      -       +      -
    171E  LEU*     3.7     4.5    -      -       -      +
    172E  TYR*     2.9    40.8    +      -       +      +
    314E  LEU*     6.0     0.4    -      -       +      -
    327E  PHE*     4.5     7.2    -      +       -      -
    328E  ASP      3.8     4.5    -      -       -      +
    329E  ASN      3.5    10.1    -      -       -      -
    330E  PHE*     3.6    21.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with THR 96 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95E  PHE*     1.3    76.4    -      -       -      +
     97E  VAL*     1.3    65.4    +      -       -      +
    169E  THR*     3.6    27.3    -      -       +      +
    170E  HIS      3.3     5.6    -      -       -      +
    171E  LEU*     3.8    23.6    -      -       +      -
    326E  ILE      4.4     1.0    +      -       -      -
    327E  PHE*     3.4     6.1    -      -       -      -
    328E  ASP*     2.9    56.3    +      -       -      +
    329E  ASN*     3.5    18.3    +      -       +      +
    347E  TRP*     4.0    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 97 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95E  PHE*     3.3    34.3    -      -       +      -
     96E  THR*     1.3    73.2    -      -       -      +
     98E  LYS*     1.3    61.4    +      -       -      +
     99E  HIS*     3.8    28.3    -      -       +      +
    108E  GLY      3.6    11.2    -      -       -      +
    134E  PRO*     4.3     4.9    -      -       +      -
    168E  PHE      3.6     2.1    -      -       -      +
    169E  THR*     3.6     1.5    -      -       -      -
    170E  HIS*     2.8    40.3    +      -       -      +
    172E  TYR*     4.1    20.4    -      -       +      -
    325E  THR*     3.9    17.5    -      -       +      -
    326E  ILE      3.6     3.1    -      -       -      -
    327E  PHE*     4.0     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 98 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53E  SER      3.5     9.9    +      -       -      -
     56E  PHE*     2.7    45.4    +      -       -      -
     57E  TYR*     4.4     3.2    -      -       -      +
     63E  ASP*     5.6     4.4    +      -       -      +
     97E  VAL*     1.3    75.1    -      -       -      +
     99E  HIS*     1.3    60.0    +      -       -      +
    100E  GLU*     3.1    34.2    +      -       +      +
    167E  GLU      3.5    14.8    -      -       -      +
    168E  PHE      3.7     5.8    -      -       -      +
    169E  THR*     3.3    26.0    -      -       +      +
    324E  GLY      4.0     0.5    -      -       -      +
    325E  THR*     3.3     2.5    -      -       -      -
    326E  ILE*     2.9    50.4    +      -       +      +
    354E  GLU*     3.5    13.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 99 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97E  VAL*     3.8    18.7    +      -       +      +
     98E  LYS*     1.3    69.6    -      -       -      +
    100E  GLU*     1.3    58.7    +      -       -      +
    101E  GLN*     3.0    16.0    +      -       -      +
    102E  ASN*     3.1     9.5    +      -       -      -
    103E  ILE*     3.7    40.1    -      -       +      +
    106E  GLY      4.8     1.3    -      -       -      -
    107E  GLY      4.3    13.2    -      -       -      -
    108E  GLY*     4.4     3.5    +      -       -      -
    134E  PRO*     4.7    10.9    -      -       +      +
    136E  ILE*     4.0    20.4    -      -       +      +
    164E  LYS      4.6     7.0    -      -       -      -
    165E  ASP*     5.3     1.8    -      -       -      +
    166E  ASP      3.6    13.4    +      -       -      +
    167E  GLU*     3.4    16.6    -      -       -      -
    168E  PHE      4.3     4.6    +      -       -      -
    325E  THR*     2.7    37.6    +      -       +      +
----------------------------------------------------------
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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