Contacts of the strand formed by residues 160 - 166 (chain J) in PDB entry 3LUE


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 THR 160 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109J  PRO*     3.2     6.5    -      -       -      +
    110J  LEU*     3.4     0.2    -      -       -      +
    153J  MET*     3.5    18.8    -      -       -      -
    154J  ASP      3.1    12.6    -      -       -      +
    155J  SER*     2.9    19.2    +      -       -      +
    159J  VAL*     1.3    73.3    -      -       -      +
    161J  HIS*     1.3    64.0    +      -       -      +
    162J  THR*     5.3     0.9    -      -       +      -
    177J  ARG*     3.3     3.8    -      -       -      -
    178J  LEU*     2.7    43.9    +      -       +      -
    180J  LEU      2.8    22.6    +      -       -      -
    261J  LEU*     5.0     0.5    -      -       -      +
    274J  ILE*     3.4    28.7    -      -       +      +
    277J  THR*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 161 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109J  PRO*     1.6    39.9    -      -       +      +
    110J  LEU*     2.1    40.1    +      -       -      -
    136J  ILE*     4.2    22.2    -      -       +      +
    138J  ALA*     4.7     0.3    -      -       -      +
    152J  VAL      3.7     1.4    -      -       -      +
    153J  MET*     3.5     2.8    -      -       -      -
    154J  ASP*     2.9    33.9    +      -       +      +
    160J  THR*     1.3    75.4    -      -       -      +
    162J  THR*     1.3    64.2    +      -       -      +
    163J  VAL*     3.9    15.4    -      -       +      +
    175J  ILE*     3.3    23.2    -      -       +      +
    176J  LEU      3.0    18.6    -      -       -      +
    177J  ARG*     3.3    14.6    -      -       +      +
    277J  THR*     6.0     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 162 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151J  ILE*     4.3     4.5    -      -       +      -
    152J  VAL      3.4     5.2    -      -       -      +
    153J  MET*     3.6    19.7    -      -       +      -
    160J  THR*     5.3     1.8    -      -       +      -
    161J  HIS*     1.3    76.7    -      -       -      +
    163J  VAL*     1.3    59.2    +      -       -      +
    164J  PRO*     4.3     0.2    -      -       -      -
    175J  ILE*     3.3     6.4    -      -       -      -
    176J  LEU*     3.0    28.6    +      -       -      +
    274J  ILE*     4.9     1.6    -      -       +      +
    277J  THR*     3.4    25.5    +      -       +      +
    278J  THR*     3.4    38.1    -      -       -      +
    281J  SER*     3.0    25.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 163 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136J  ILE*     5.4     1.8    -      -       +      -
    138J  ALA*     5.0     7.0    -      -       +      -
    139J  VAL*     3.6    33.2    -      -       +      -
    151J  ILE*     3.2    23.3    -      -       -      +
    152J  VAL*     3.2    15.4    +      -       +      +
    161J  HIS*     3.9    20.4    -      -       +      +
    162J  THR*     1.3    77.6    -      -       -      +
    164J  PRO*     1.3    61.1    -      -       -      +
    165J  ILE*     3.8    16.4    +      -       +      +
    170J  ALA*     3.8    22.9    -      -       +      -
    175J  ILE*     4.0    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 164 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150J  GLY      3.8     6.1    -      -       -      +
    151J  ILE*     4.0     7.2    -      -       +      -
    162J  THR      4.1     0.2    -      -       -      +
    163J  VAL*     1.3    82.2    -      -       -      +
    165J  ILE*     1.3    54.5    +      -       -      +
    170J  ALA*     3.5     2.1    -      -       -      -
    171J  LEU*     2.7    42.7    +      -       +      +
    174J  ALA*     3.5    31.4    -      -       +      +
    175J  ILE*     4.1     2.5    -      -       +      +
    281J  SER*     3.8    14.4    -      -       -      -
    285J  CYS*     3.2    37.2    -      -       -      -
    293J  LEU*     3.8    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 165 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43H  VAL*     2.1    19.5    -      -       -      +
     44H  MET*     1.3   112.5    -      -       +      +
     61H  LYS*     3.1     5.6    -      -       -      -
    139J  VAL*     5.3     4.3    -      -       +      -
    142J  LEU*     1.5    59.0    -      -       +      -
    148J  THR      3.4     0.7    -      -       -      +
    149J  THR*     3.5     0.2    -      -       -      +
    150J  GLY      2.9    16.4    +      -       -      +
    152J  VAL*     4.1     4.9    -      -       +      -
    163J  VAL*     3.9    20.2    -      -       +      +
    164J  PRO*     1.3    75.3    -      -       -      +
    166J  TYR*     1.3    56.0    +      -       -      +
    169J  TYR      3.2     5.8    -      -       -      +
    170J  ALA*     3.8    13.2    -      -       +      -
    171J  LEU*     4.7     1.1    -      -       -      -
    293J  LEU*     4.1     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 166 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53H  TYR*     3.0     3.1    -      -       -      -
     57H  GLU      2.1    28.3    -      -       -      -
     58H  ALA*     1.5    49.2    -      -       -      +
     61H  LYS*     0.8   350.6    -      -       +      +
     64H  ILE*     3.0    19.5    -      -       +      +
     65H  LEU*     2.3    45.1    -      -       +      +
    165J  ILE*     1.3    61.8    -      -       -      +
    167J  GLU*     1.3    71.1    +      -       +      +
    168J  GLY      3.4     0.4    -      -       -      -
    169J  TYR*     2.9    27.0    +      -       -      +
    289J  ILE*     3.8     2.2    -      -       +      -
----------------------------------------------------------
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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