Contacts of the strand formed by residues 150 - 155 (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 GLY 150 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44F  MET*     1.3    91.8    -      -       -      +
    149H  THR*     1.3    62.2    -      -       -      +
    151H  ILE*     1.3    57.2    +      -       -      -
    165H  ILE      2.9    15.9    +      -       -      -
    293H  LEU*     3.0    22.5    -      -       -      +
    296H  ASN*     3.4    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 151 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44F  MET*     2.9     1.1    -      -       -      +
    150H  GLY*     1.3    74.6    -      -       -      +
    152H  VAL*     1.3    71.8    +      -       -      +
    162H  THR*     4.3     7.2    -      -       +      -
    163H  VAL      3.2    20.4    -      -       -      +
    164H  PRO*     4.0    14.8    -      -       +      -
    278H  THR*     4.0    20.4    -      -       +      +
    281H  SER*     3.7    29.4    -      -       -      -
    282H  ILE*     4.3    11.9    -      -       +      -
    293H  LEU*     3.4    31.6    -      -       +      +
    296H  ASN      2.9     6.0    +      -       -      +
    297H  THR*     3.4    13.7    -      -       +      +
    298H  VAL*     2.9    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 152 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45F  VAL*     3.0    15.5    -      -       +      +
    138H  ALA*     3.5    23.3    -      -       +      +
    142H  LEU*     2.1    52.3    -      -       +      -
    151H  ILE*     1.3    78.9    -      -       -      +
    153H  MET*     1.3    64.7    +      -       -      +
    154H  ASP*     3.9     0.7    -      -       -      -
    161H  HIS      3.7     0.9    -      -       -      +
    162H  THR*     3.4     4.7    -      -       -      -
    163H  VAL*     3.2    30.7    +      -       +      +
    165H  ILE*     4.7     1.1    -      -       +      -
    298H  VAL*     3.2    10.8    -      -       +      +
    300H  SER*     3.5    26.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 153 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151H  ILE*     5.9     0.2    -      -       +      -
    152H  VAL*     1.3    75.2    -      -       -      +
    154H  ASP*     1.3    61.0    +      -       -      +
    155H  SER*     3.9     4.7    +      -       -      -
    160H  THR*     3.5    29.2    -      -       +      -
    161H  HIS      3.5     2.5    -      -       -      -
    162H  THR*     3.6     8.5    -      -       +      -
    261H  LEU*     6.6     0.2    -      -       +      -
    274H  ILE*     3.5    26.0    -      -       +      -
    278H  THR*     3.5    25.1    -      -       +      +
    297H  THR*     5.5     3.8    -      -       +      -
    298H  VAL      2.8    14.1    +      -       -      +
    299H  LEU*     3.5    16.1    -      -       +      -
    300H  SER      2.9    22.7    +      -       -      +
    304H  THR*     4.0    17.8    -      -       +      +
    309H  ILE*     5.3     6.3    -      -       +      -
    313H  MET*     3.8    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 154 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109H  PRO*     3.7    10.6    -      -       +      +
    137H  GLN*     2.9    18.6    -      -       -      +
    138H  ALA*     1.5    72.3    +      -       +      +
    141H  SER*     3.4     1.2    +      -       -      -
    153H  MET*     1.3    73.0    -      -       -      +
    155H  SER*     1.3    60.7    +      -       -      +
    156H  GLY      4.5     2.1    +      -       -      -
    159H  VAL      3.6     1.4    -      -       -      +
    160H  THR*     3.1    25.1    -      -       -      +
    161H  HIS      2.9    11.9    +      -       -      +
    300H  SER*     2.6    19.5    +      -       -      +
    301H  GLY*     4.9     2.8    -      -       -      -
    339H  VAL*     4.4     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 155 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153H  MET*     3.9     6.7    +      -       -      -
    154H  ASP*     1.3    73.0    +      -       -      +
    156H  GLY*     1.3    59.9    +      -       -      +
    159H  VAL      3.7     2.7    -      -       -      -
    160H  THR*     2.9    24.7    +      -       -      +
    181H  ALA*     4.2     3.5    -      -       -      -
    261H  LEU*     4.4     6.2    -      -       -      +
    300H  SER      3.0    10.5    +      -       -      -
    301H  GLY*     3.3    13.3    -      -       -      -
    303H  THR*     3.0    49.0    +      -       -      +
    304H  THR*     4.2    13.9    -      -       -      -
----------------------------------------------------------
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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