Contacts of the strand formed by residues 150 - 155 (chain G) 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 G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44E  MET*     1.3    89.7    -      -       -      +
    149G  THR*     1.3    61.4    -      -       -      +
    151G  ILE*     1.3    56.4    +      -       -      -
    165G  ILE      2.9    16.7    +      -       -      -
    292G  ASP      4.5     0.4    +      -       -      -
    293G  LEU*     3.0    21.8    -      -       -      +
    296G  ASN*     3.4    11.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 151 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44E  MET*     2.9     1.1    -      -       -      +
    150G  GLY*     1.3    74.8    -      -       -      +
    152G  VAL*     1.3    73.3    +      -       -      +
    162G  THR*     4.3     7.4    -      -       +      -
    163G  VAL      3.2    19.7    -      -       -      +
    164G  PRO*     4.0    14.6    -      -       +      -
    278G  THR*     4.0    20.9    -      -       +      +
    281G  SER*     3.7    30.3    -      -       -      -
    282G  ILE*     4.3    11.7    -      -       +      -
    293G  LEU*     3.4    31.4    -      -       +      +
    296G  ASN      2.9     6.2    +      -       -      +
    297G  THR*     3.4    13.0    -      -       +      +
    298G  VAL*     2.9    24.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 152 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45E  VAL*     3.0    15.5    -      -       +      +
    138G  ALA*     3.5    23.3    -      -       +      +
    142G  LEU*     2.1    52.3    -      -       +      -
    151G  ILE*     1.3    78.2    -      -       -      +
    153G  MET*     1.3    63.4    +      -       -      +
    154G  ASP*     3.9     0.7    -      -       -      -
    161G  HIS      3.7     0.9    -      -       -      +
    162G  THR*     3.4     4.9    -      -       -      -
    163G  VAL*     3.2    31.9    +      -       +      +
    165G  ILE*     4.7     1.3    -      -       +      -
    297G  THR*     6.3     0.2    -      -       -      -
    298G  VAL*     3.2    10.8    -      -       +      +
    300G  SER*     3.5    26.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 153 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151G  ILE*     5.9     0.2    -      -       +      -
    152G  VAL*     1.3    74.5    -      -       -      +
    154G  ASP*     1.3    61.3    +      -       -      +
    155G  SER*     3.9     4.9    +      -       -      -
    160G  THR*     3.5    28.9    -      -       +      -
    161G  HIS      3.5     2.7    -      -       -      -
    162G  THR*     3.6     8.7    -      -       +      -
    261G  LEU*     6.5     0.4    -      -       +      -
    274G  ILE*     3.5    25.6    -      -       +      -
    278G  THR*     3.5    25.1    -      -       +      +
    297G  THR*     5.5     4.0    -      -       +      -
    298G  VAL      2.8    13.0    +      -       -      +
    299G  LEU*     3.5    17.3    -      -       +      -
    300G  SER      2.9    23.1    +      -       -      +
    304G  THR*     4.0    17.6    -      -       +      +
    309G  ILE*     5.3     6.1    -      -       +      -
    313G  MET*     3.8    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 154 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109G  PRO*     3.7    11.7    -      -       +      +
    137G  GLN*     2.9    18.3    -      -       -      +
    138G  ALA*     1.5    71.0    +      -       +      -
    141G  SER*     3.4     1.4    +      -       -      -
    153G  MET*     1.3    73.0    -      -       -      +
    155G  SER*     1.3    60.4    +      -       -      +
    156G  GLY      4.5     1.9    +      -       -      -
    159G  VAL      3.6     1.4    -      -       -      +
    160G  THR*     3.1    24.9    -      -       -      +
    161G  HIS      2.9    11.7    +      -       -      +
    300G  SER*     2.6    20.9    +      -       -      +
    301G  GLY*     4.9     2.5    -      -       -      -
    339G  VAL*     4.4     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 155 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153G  MET*     3.9     6.8    +      -       -      -
    154G  ASP*     1.3    73.0    +      -       -      +
    156G  GLY*     1.3    60.6    +      -       -      +
    159G  VAL      3.7     2.7    -      -       -      -
    160G  THR*     2.9    24.4    +      -       -      +
    181G  ALA*     4.2     3.8    -      -       -      -
    261G  LEU*     4.4     6.3    -      -       -      +
    300G  SER      3.0    10.5    +      -       -      -
    301G  GLY*     3.3    12.9    -      -       -      -
    303G  THR*     3.0    50.0    +      -       -      +
    304G  THR*     4.2    13.7    -      -       -      -
----------------------------------------------------------
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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