Contacts of the strand formed by residues 160 - 166 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  PRO*     3.2     6.6    -      -       -      +
    110A  LEU*     3.4     0.3    -      -       -      +
    153A  MET*     3.5    20.0    -      -       -      -
    154A  ASP      3.1    11.9    -      -       -      +
    155A  SER*     2.9    19.6    +      -       -      +
    159A  VAL*     1.3    73.5    -      -       -      +
    161A  HIS*     1.3    63.8    +      -       -      +
    162A  THR*     5.3     1.1    -      -       +      -
    177A  ARG*     3.3     4.2    -      -       -      -
    178A  LEU*     2.7    43.6    +      -       +      -
    180A  LEU      2.8    22.3    +      -       -      -
    181A  ALA*     4.1     0.2    -      -       -      +
    261A  LEU*     5.0     0.3    -      -       -      +
    274A  ILE*     3.4    27.6    -      -       +      +
    277A  THR*     6.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  PRO*     1.6    41.0    -      -       +      +
    110A  LEU*     2.1    39.0    +      -       -      -
    136A  ILE*     4.2    22.3    -      -       +      +
    138A  ALA*     4.7     0.3    -      -       -      +
    152A  VAL      3.7     1.2    -      -       -      +
    153A  MET*     3.5     2.4    -      -       -      -
    154A  ASP*     2.9    34.7    +      -       +      +
    160A  THR*     1.3    74.5    -      -       -      +
    162A  THR*     1.3    65.6    -      -       -      +
    163A  VAL*     3.9    15.4    +      -       +      -
    175A  ILE*     3.3    22.7    -      -       +      +
    176A  LEU      3.0    18.8    -      -       -      -
    177A  ARG*     3.3    14.4    -      -       +      +
    277A  THR*     6.0     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  ILE*     4.3     4.7    -      -       +      -
    152A  VAL      3.4     4.7    -      -       -      +
    153A  MET*     3.6    19.7    -      -       +      -
    160A  THR*     5.3     1.3    -      -       +      -
    161A  HIS*     1.3    76.4    -      -       -      +
    163A  VAL*     1.3    60.7    +      -       -      +
    175A  ILE*     3.3     6.4    -      -       -      -
    176A  LEU*     3.0    29.0    +      -       -      +
    274A  ILE*     4.9     0.9    -      -       +      +
    277A  THR*     3.4    25.5    +      -       +      +
    278A  THR*     3.4    38.8    -      -       -      +
    281A  SER*     3.0    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  ILE*     5.4     2.5    -      -       +      -
    138A  ALA*     5.0     7.0    -      -       +      -
    139A  VAL*     3.6    33.4    -      -       +      -
    151A  ILE*     3.2    22.3    -      -       -      +
    152A  VAL*     3.2    15.7    +      -       +      +
    161A  HIS*     3.9    20.0    -      -       +      +
    162A  THR*     1.3    77.0    -      -       -      +
    164A  PRO*     1.3    61.2    -      -       -      +
    165A  ILE*     3.8    16.9    +      -       +      +
    170A  ALA*     3.8    24.0    -      -       +      -
    175A  ILE*     4.0    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  GLY      3.8     5.2    -      -       -      +
    151A  ILE*     4.0     7.0    -      -       +      -
    162A  THR      4.1     0.2    -      -       -      +
    163A  VAL*     1.3    83.7    -      -       -      +
    165A  ILE*     1.3    55.8    +      -       -      +
    170A  ALA*     3.5     1.7    -      -       -      -
    171A  LEU*     2.7    42.3    +      -       +      +
    174A  ALA*     3.5    31.2    -      -       +      +
    175A  ILE*     4.1     2.7    -      -       +      +
    281A  SER*     3.8    14.6    -      -       -      -
    285A  CYS*     3.2    36.8    -      -       -      -
    293A  LEU*     3.8    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  VAL*     5.3     5.6    -      -       +      +
    142A  LEU*     1.5    67.8    -      -       +      -
    148A  THR*     3.4    21.5    -      -       -      +
    149A  THR*     3.2     6.1    -      -       -      +
    150A  GLY      2.9    37.2    +      -       -      +
    152A  VAL*     4.1     4.7    -      -       +      -
    163A  VAL*     3.9    22.2    -      -       +      +
    164A  PRO*     1.3    76.6    -      -       -      +
    166A  TYR*     1.3    57.0    +      -       -      +
    168A  GLY*     3.6     7.0    -      -       -      +
    169A  TYR      3.2    22.4    -      -       -      +
    170A  ALA*     3.8    15.0    -      -       +      +
    171A  LEU*     4.7     0.7    -      -       -      -
    293A  LEU*     4.1     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  THR*     3.8    14.6    -      -       +      -
    165A  ILE*     1.3    71.4    -      -       -      +
    167A  GLU*     1.3    99.9    +      -       +      +
    168A  GLY      3.4     0.2    -      -       -      -
    169A  TYR*     2.9    27.9    +      -       -      +
    171A  LEU*     4.0    18.2    -      -       +      +
    289A  ILE*     3.8    41.7    -      -       +      -
----------------------------------------------------------
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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