Contacts of the strand formed by residues 233 - 241 (chain A) in PDB entry 4LG8


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 ASP 233 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  CYS*     3.1    19.1    +      -       -      +
    231A  PRO      3.4     1.0    +      -       -      -
    232A  SER*     1.3    82.7    +      -       -      +
    234A  THR*     1.3    59.3    +      -       -      +
    235A  ASN*     3.0    27.1    +      -       -      +
    236A  LYS*     3.1    47.2    +      -       +      +
    276A  GLN*     3.7    17.6    +      -       -      +
    485A  HIS*     4.0     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  LEU*     4.0    20.8    -      -       +      +
    230A  CYS      3.4    16.2    -      -       -      +
    231A  PRO*     4.7     2.2    -      -       +      +
    233A  ASP*     1.3    69.3    +      -       -      +
    235A  ASN*     1.3    60.9    +      -       -      +
    236A  LYS      3.2     7.4    -      -       -      +
    237A  ILE*     3.5    11.3    -      -       -      +
    445A  GLN*     4.2     9.4    -      -       -      +
    483A  PHE      4.2     2.2    -      -       -      +
    484A  GLY*     3.6     8.3    -      -       -      -
    485A  HIS*     2.9    59.6    +      -       +      +
    489A  PHE*     3.4    19.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  ASP*     3.0    15.6    +      -       -      +
    234A  THR*     1.3    77.9    +      -       -      +
    236A  LYS*     1.3    61.4    +      -       +      +
    237A  ILE*     3.5     3.1    -      -       -      +
    250A  ASP*     3.6     7.1    -      -       -      +
    251A  LYS*     2.9    57.8    +      -       +      +
    252A  SER*     3.1    26.9    +      -       -      +
    489A  PHE*     3.9     9.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  LEU*     3.5     3.6    -      -       -      -
    230A  CYS*     3.0    32.3    +      -       +      -
    233A  ASP*     3.1    34.9    +      -       +      +
    234A  THR      4.1     0.9    -      -       -      +
    235A  ASN*     1.3    77.4    -      -       -      +
    237A  ILE*     1.3    62.4    +      -       -      +
    248A  VAL*     5.1     1.3    -      -       +      -
    249A  PHE      3.6     2.2    -      -       -      +
    250A  ASP*     3.5    28.0    -      -       +      +
    257A  LEU*     4.1    24.6    -      -       +      +
    272A  PHE*     3.6    24.9    -      -       +      -
    276A  GLN*     3.6    24.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  LEU*     3.6    28.0    -      -       +      -
    228A  ASP      3.8     2.9    -      -       -      +
    229A  LEU*     3.7    12.1    -      -       +      -
    234A  THR      3.5    24.5    -      -       -      +
    235A  ASN      3.5     9.4    -      -       -      +
    236A  LYS*     1.3    76.5    -      -       -      +
    238A  LEU*     1.3    63.1    +      -       -      +
    239A  THR*     4.2     7.6    -      -       +      -
    247A  VAL      3.6     0.9    -      -       -      +
    248A  VAL*     3.2     7.1    -      -       -      +
    249A  PHE*     2.8    55.2    +      -       +      +
    251A  LYS*     4.1     3.6    -      -       +      -
    272A  PHE*     4.0     1.8    -      -       -      -
    499A  LEU*     4.0    17.7    -      -       +      -
    501A  PHE*     3.8    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  LEU*     3.4     2.8    -      -       -      +
    228A  ASP*     2.9    36.5    +      -       +      +
    237A  ILE*     1.3    74.4    -      -       -      +
    239A  THR*     1.3    66.1    +      -       -      +
    246A  VAL*     3.4    30.3    -      -       +      -
    247A  VAL      3.2     9.2    -      -       -      +
    248A  VAL*     4.0     9.4    -      -       +      -
    270A  VAL*     3.6    13.9    -      -       +      +
    271A  VAL      3.2    47.3    -      -       -      +
    272A  PHE*     3.5    18.8    -      -       +      +
    279A  VAL*     3.8    24.2    -      -       +      -
    280A  PHE      4.0     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  LEU*     3.8    20.3    -      -       +      +
    217A  HIS*     2.7    29.5    +      -       -      -
    224A  ILE*     3.7    16.4    -      -       +      -
    226A  ALA      3.3    11.7    -      -       -      +
    237A  ILE*     4.2    11.9    -      -       +      -
    238A  LEU*     1.3    81.0    -      -       -      +
    240A  GLY*     1.3    60.6    +      -       -      +
    246A  VAL*     3.4     8.0    -      -       -      +
    247A  VAL*     2.8    43.1    +      -       -      +
    270A  VAL*     4.0     4.9    -      -       -      -
    493A  THR*     4.1    13.5    -      -       +      -
    499A  LEU*     4.9     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  HIS*     3.8     2.0    -      -       -      -
    224A  ILE*     3.6     5.0    -      -       -      +
    225A  LEU      2.8    25.8    +      -       -      -
    226A  ALA*     3.0    12.3    +      -       -      -
    239A  THR*     1.3    74.1    -      -       -      +
    241A  GLY*     1.3    59.1    +      -       -      -
    245A  ASN      3.8     1.8    -      -       -      -
    267A  VAL*     3.7    33.0    -      -       -      -
    270A  VAL*     3.8     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  HIS*     3.3    22.4    -      -       -      -
    223A  GLY      3.6     7.2    -      -       -      -
    225A  LEU*     4.2     3.4    -      -       -      -
    240A  GLY*     1.3    74.4    -      -       -      -
    242A  ALA*     1.3    66.4    +      -       -      -
    243A  ASP*     3.0     3.8    -      -       -      -
    244A  LYS*     3.1     6.9    +      -       -      -
    245A  ASN      3.0    12.7    +      -       -      -
    267A  VAL*     3.0    24.4    +      -       -      +
----------------------------------------------------------
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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