Contacts of the strand formed by residues 160 - 166 (chain H) 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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109H  PRO*     3.2     6.5    -      -       -      +
    110H  LEU*     3.4     0.3    -      -       -      +
    153H  MET*     3.5    19.7    -      -       -      -
    154H  ASP      3.1    11.9    -      -       -      +
    155H  SER*     2.9    20.1    +      -       -      +
    159H  VAL*     1.3    74.0    -      -       -      +
    161H  HIS*     1.3    64.4    +      -       -      +
    162H  THR*     5.3     0.9    -      -       +      -
    177H  ARG*     3.3     4.0    -      -       -      -
    178H  LEU*     2.7    43.0    +      -       +      -
    180H  LEU      2.8    22.6    +      -       -      -
    261H  LEU*     5.0     0.3    -      -       -      +
    274H  ILE*     3.4    28.1    -      -       +      +
    277H  THR*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 161 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109H  PRO*     1.6    39.9    -      -       +      +
    110H  LEU*     2.1    39.4    +      -       -      -
    136H  ILE*     4.2    20.8    -      -       +      +
    138H  ALA*     4.7     0.7    -      -       -      +
    152H  VAL      3.7     1.2    -      -       -      +
    153H  MET*     3.5     3.1    -      -       -      -
    154H  ASP*     2.9    33.4    +      -       +      +
    160H  THR*     1.3    75.1    +      -       -      +
    162H  THR*     1.3    65.9    +      -       -      +
    163H  VAL*     3.9    15.2    +      -       +      -
    175H  ILE*     3.3    23.4    -      -       +      +
    176H  LEU      3.0    16.6    -      -       -      +
    177H  ARG*     3.3    14.9    -      -       +      +
    277H  THR*     6.0     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 162 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151H  ILE*     4.3     4.9    -      -       +      -
    152H  VAL      3.4     5.8    -      -       -      +
    153H  MET*     3.6    18.8    -      -       +      -
    160H  THR*     5.3     2.0    -      -       +      -
    161H  HIS*     1.3    75.7    -      -       -      +
    163H  VAL*     1.3    59.6    +      -       -      +
    175H  ILE*     3.3     6.2    -      -       -      -
    176H  LEU*     3.0    29.6    +      -       -      +
    274H  ILE*     4.9     1.1    -      -       +      +
    277H  THR*     3.4    24.9    +      -       +      +
    278H  THR*     3.4    38.8    -      -       -      +
    281H  SER*     3.0    24.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 163 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136H  ILE*     5.4     2.5    -      -       +      -
    138H  ALA*     5.0     7.2    -      -       +      -
    139H  VAL*     3.6    33.7    -      -       +      -
    151H  ILE*     3.2    22.3    -      -       -      +
    152H  VAL*     3.2    16.6    +      -       +      +
    161H  HIS*     3.9    20.4    -      -       +      +
    162H  THR*     1.3    78.0    -      -       -      +
    164H  PRO*     1.3    60.2    -      -       -      +
    165H  ILE*     3.8    15.8    +      -       +      +
    170H  ALA*     3.8    23.8    -      -       +      -
    175H  ILE*     4.0    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 164 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150H  GLY      3.8     5.8    -      -       -      +
    151H  ILE*     4.0     7.0    -      -       +      -
    162H  THR      4.1     0.2    -      -       -      +
    163H  VAL*     1.3    83.7    -      -       -      +
    165H  ILE*     1.3    56.0    +      -       -      +
    170H  ALA*     3.5     2.3    -      -       -      -
    171H  LEU*     2.7    42.7    +      -       +      +
    174H  ALA*     3.5    31.0    -      -       +      +
    175H  ILE*     4.1     2.5    -      -       +      +
    281H  SER*     3.8    14.6    -      -       -      -
    285H  CYS*     3.2    36.1    -      -       -      -
    293H  LEU*     3.8    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 165 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43F  VAL*     2.1    21.1    -      -       -      +
     44F  MET*     1.3   112.0    -      -       +      +
     61F  LYS*     3.1     4.7    -      -       -      -
    139H  VAL*     5.3     3.6    -      -       +      -
    142H  LEU*     1.5    58.3    -      -       +      -
    148H  THR      3.4     1.3    -      -       -      +
    149H  THR*     3.2     0.5    -      -       -      +
    150H  GLY      2.9    17.1    +      -       -      +
    152H  VAL*     4.1     5.4    -      -       +      -
    163H  VAL*     3.9    21.1    -      -       +      +
    164H  PRO*     1.3    74.7    -      -       -      +
    166H  TYR*     1.3    56.2    +      -       -      +
    169H  TYR      3.2     6.1    -      -       -      +
    170H  ALA*     3.8    13.7    -      -       +      -
    171H  LEU*     4.7     0.7    -      -       -      -
    293H  LEU*     4.1     3.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 166 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53F  TYR*     3.0     2.8    -      -       -      -
     57F  GLU      2.1    27.6    -      -       -      -
     58F  ALA*     1.5    50.2    -      -       -      +
     61F  LYS*     0.8   358.7    -      -       +      +
     64F  ILE*     3.0    20.0    -      -       +      +
     65F  LEU*     2.3    45.1    -      -       +      +
    165H  ILE*     1.3    62.3    -      -       -      +
    167H  GLU*     1.3    71.2    +      -       +      +
    168H  GLY      3.4     0.4    -      -       -      -
    169H  TYR*     2.9    27.1    +      -       -      +
    289H  ILE*     3.8     2.7    -      -       +      -
----------------------------------------------------------
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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