Contacts of the strand formed by residues 157 - 165 (chain A) in PDB entry 5LXM


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 PHE 157 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  ARG*     3.5     2.8    -      -       -      -
    152A  GLU*     3.0    26.3    +      -       +      +
    155A  SER*     3.1    21.2    +      -       -      +
    156A  LYS*     1.3    76.1    -      -       -      +
    158A  ILE*     1.3    70.5    +      -       -      +
    159A  LEU*     3.5    35.7    +      -       +      +
    197A  TYR*     4.6    13.7    -      +       -      -
    212A  TYR      6.3     0.2    -      -       -      -
     19D  PHE*     3.6    44.0    -      +       +      -
----------------------------------------------------------
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Residues in contact with ILE 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  LEU*     3.7    24.0    -      -       +      -
    150A  ALA      3.4     7.2    -      -       -      +
    151A  ARG*     3.3    45.1    -      -       +      +
    156A  LYS      3.6     2.2    +      -       -      +
    157A  PHE*     1.3    86.4    -      -       -      +
    159A  LEU*     1.3    67.7    +      -       -      +
    212A  TYR*     3.4    45.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  PHE*     3.7    25.6    -      -       +      -
    149A  LEU*     3.5     9.9    -      -       -      +
    150A  ALA*     2.7    49.1    +      -       +      +
    152A  GLU*     4.6     1.6    -      -       +      -
    157A  PHE*     3.5    33.4    +      -       +      +
    158A  ILE*     1.3    76.2    -      -       -      +
    160A  ALA*     1.3    61.2    +      -       -      +
    197A  TYR*     3.6    31.2    -      -       +      -
    209A  ILE*     3.7    11.9    -      -       +      -
    210A  LEU      3.6     7.4    -      -       -      +
    211A  GLU*     4.8     1.1    -      -       -      -
    212A  TYR*     4.1     8.5    -      -       -      -
     19D  PHE*     3.6    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  LEU*     3.7    20.6    -      -       +      -
    147A  VAL*     4.2     7.0    -      -       +      -
    148A  TYR      3.3     4.0    -      -       -      -
    159A  LEU*     1.3    77.5    -      -       -      +
    161A  LEU*     1.3    61.6    +      -       -      +
    162A  LYS      4.0     0.4    -      -       -      -
    208A  LEU      3.5     1.0    -      -       -      +
    209A  ILE*     3.7     2.3    -      -       -      -
    210A  LEU*     2.8    43.0    +      -       +      +
    211A  GLU      4.2     1.1    -      -       -      +
    212A  TYR*     4.4     2.2    -      -       -      +
    501A  ADP      3.5    30.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  LEU*     4.3     9.4    -      -       +      -
    133A  PHE*     4.7    16.6    -      -       +      -
    135A  ILE*     3.6    27.6    -      -       +      -
    146A  ASN      3.8     0.7    -      -       -      +
    147A  VAL*     3.4     3.0    -      -       -      -
    148A  TYR*     2.7    45.8    +      -       +      +
    150A  ALA*     4.0    13.6    -      -       +      +
    160A  ALA*     1.3    72.7    -      -       -      +
    162A  LYS*     1.3    59.7    +      -       -      +
    163A  VAL*     3.6    12.7    +      -       +      -
    200A  PHE*     4.3     4.5    -      -       +      -
    207A  TYR*     4.0    31.0    -      -       +      -
    208A  LEU      3.3    21.1    -      -       -      +
    209A  ILE*     4.2    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  GLY      6.1     0.4    -      -       -      +
    146A  ASN      4.8     0.7    -      -       -      +
    147A  VAL*     3.6    20.2    -      -       +      +
    160A  ALA      3.9     1.4    +      -       -      -
    161A  LEU*     1.3    69.2    -      -       -      +
    163A  VAL*     1.3    59.9    +      -       -      +
    164A  LEU*     4.0    29.2    +      -       +      +
    181A  GLU*     2.7    31.5    +      -       -      +
    206A  VAL      3.3     5.9    -      -       -      +
    207A  TYR*     3.4     1.8    -      -       -      -
    208A  LEU*     2.8    56.2    +      -       +      +
    210A  LEU*     3.8    19.1    -      -       +      -
    274A  ASP*     3.5     5.7    +      -       -      +
    501A  ADP      2.4    53.4    +      -       -      +
    505A  PEG      4.0     2.9    -      -       -      -
    510A   MG      3.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  ILE*     6.3     0.4    -      -       +      -
    145A  GLY*     3.2    26.9    -      -       -      -
    146A  ASN      2.9    12.8    +      -       -      +
    148A  TYR*     3.9    28.3    -      -       +      -
    161A  LEU*     4.0    11.2    -      -       +      +
    162A  LYS*     1.3    74.1    -      -       -      +
    164A  LEU*     1.3    68.9    +      -       -      +
    165A  PHE*     4.3     9.9    -      -       +      -
    205A  ARG*     3.6    33.7    -      -       +      +
    206A  VAL      3.5     2.5    -      -       -      -
    207A  TYR*     3.7    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  PHE*     3.5    22.4    -      -       +      +
    145A  GLY*     4.4     3.6    -      -       -      +
    162A  LYS*     4.0    32.3    -      -       +      +
    163A  VAL*     1.3    85.6    -      -       -      +
    165A  PHE*     1.3    63.7    +      -       -      +
    166A  LYS      3.5     0.5    +      -       -      -
    169A  LEU*     3.8    18.6    -      -       +      -
    178A  LEU*     3.6    37.5    -      -       +      -
    205A  ARG*     3.2     4.3    -      -       -      -
    206A  VAL*     2.6    48.5    +      -       +      +
    208A  LEU*     4.8     6.5    -      -       +      -
    501A  ADP      4.9     2.5    -      -       -      +
    505A  PEG      4.3    17.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  PHE      3.1    20.7    +      -       -      +
    145A  GLY*     4.1    16.4    -      -       -      -
    146A  ASN*     5.2     1.3    -      -       -      -
    148A  TYR*     6.2     0.2    -      -       -      -
    163A  VAL*     4.9     7.4    -      -       +      -
    164A  LEU*     1.3    70.8    -      -       -      +
    166A  LYS*     1.3    65.5    +      -       -      +
    167A  ALA*     3.3     6.7    +      -       +      +
    168A  GLN*     3.3    19.8    +      -       +      +
    169A  LEU*     3.3    24.5    +      -       -      +
    204A  THR      3.8     5.8    -      -       -      +
    205A  ARG*     3.2    44.4    -      -       +      +
----------------------------------------------------------
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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