Contacts of the strand formed by residues 168 - 175 (chain A) in PDB entry 2LBP


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 ASN 168 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  PRO      6.0     0.4    +      -       -      -
    139A  GLN      2.9    25.7    +      -       -      +
    140A  ARG*     3.5    22.2    +      -       -      +
    141A  ILE*     3.0    29.0    +      -       -      +
    163A  LYS*     4.7     3.1    -      -       -      +
    167A  ALA*     1.3    71.5    -      -       -      +
    169A  VAL*     1.3    63.4    +      -       -      +
    170A  VAL*     3.7    14.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  ILE*     3.1    16.8    -      -       +      +
    143A  ILE*     4.0    21.8    -      -       +      -
    159A  GLN*     4.9    17.5    -      -       +      +
    162A  LEU*     4.2    32.5    -      -       +      -
    163A  LYS*     5.0    10.1    -      -       +      +
    167A  ALA*     3.6    10.6    +      -       +      +
    168A  ASN*     1.3    74.7    +      -       -      +
    170A  VAL*     1.3    64.3    +      -       -      +
    171A  PHE*     3.6    17.9    -      -       -      +
    172A  PHE*     5.3     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  ARG*     3.3    50.9    -      -       +      +
    141A  ILE      2.8     9.4    +      -       -      +
    168A  ASN*     4.0    13.2    -      -       -      +
    169A  VAL*     1.3    74.5    -      -       -      +
    171A  PHE*     1.3    60.1    -      -       +      +
    192A  GLU*     3.5    40.4    -      -       +      +
    194A  ILE*     3.7    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  ILE      4.1     1.0    +      -       -      -
    142A  ALA*     3.3    25.2    -      -       +      -
    143A  ILE      3.0    26.9    +      -       -      -
    144A  ILE*     3.2    26.7    -      -       +      -
    169A  VAL*     3.6     9.4    -      -       -      +
    170A  VAL*     1.3    78.2    -      -       +      +
    172A  PHE*     1.3    55.8    +      -       -      +
    173A  ASP*     4.1    12.6    -      -       +      -
    185A  LEU*     4.5     4.9    -      -       +      -
    188A  ARG*     3.5    63.9    -      -       +      +
    189A  LEU*     3.7    15.3    -      -       +      -
    192A  GLU*     3.8    23.6    -      -       +      -
    194A  ILE*     3.9     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  ILE*     3.2    21.8    -      -       +      -
    145A  HIS*     3.3    33.9    -      +       -      -
    152A  GLU*     4.8     9.9    -      -       +      -
    155A  ALA*     3.9    25.1    -      -       +      -
    156A  ARG*     4.0    19.1    -      -       +      -
    159A  GLN*     2.9    44.2    -      -       -      +
    169A  VAL*     5.3     0.7    -      -       +      -
    171A  PHE*     1.3    74.5    -      -       -      +
    173A  ASP*     1.3    65.4    +      -       -      +
    188A  ARG*     5.7     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  ILE      2.9     7.5    +      -       -      -
    144A  ILE*     3.1    33.5    -      -       +      +
    145A  HIS*     3.2    13.3    +      -       -      -
    171A  PHE*     4.1    14.9    -      -       +      -
    172A  PHE*     1.3    79.7    -      -       -      +
    174A  GLY*     1.3    74.3    +      -       -      +
    175A  ILE*     5.1     5.9    -      -       +      +
    188A  ARG*     3.4    23.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  HIS*     3.2    26.5    +      -       -      -
    147A  LYS*     3.9    16.5    +      -       -      -
    173A  ASP*     1.3    83.9    +      -       -      +
    175A  ILE*     1.3    74.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  ILE*     3.8    14.1    -      -       +      -
    145A  HIS      2.9    13.3    +      -       -      +
    146A  ASP*     3.6    11.0    -      -       +      -
    147A  LYS*     3.3    21.8    -      -       -      +
    173A  ASP*     5.1     7.0    -      -       +      +
    174A  GLY*     1.3    87.0    -      -       -      +
    176A  THR*     1.3    73.6    +      -       -      +
    177A  ALA      4.3     1.6    -      -       -      +
    179A  GLU*     4.5     6.3    -      -       -      +
    182A  PHE*     4.0    25.6    -      -       +      -
    185A  LEU*     3.7    38.1    -      -       +      -
    199A  TYR*     4.3    21.1    -      -       +      +
    205A  GLU*     4.5     5.2    -      -       +      -
    209A  MET*     6.1     1.3    -      -       -      -
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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