Contacts of the strand formed by residues 149 - 159 (chain A) in PDB entry 5ON2


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 VAL 149 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  PHE*     3.6    39.0    -      -       +      +
    143A  LEU*     3.7    13.4    +      -       +      -
    144A  TYR*     3.7    48.4    -      -       +      +
    147A  GLY*     3.4     9.6    -      -       -      +
    148A  LEU*     1.3    84.5    -      -       -      +
    150A  TYR*     1.3    68.8    +      -       -      +
    191A  TRP*     4.0    17.7    -      -       +      -
    192A  PHE      3.4    13.2    -      -       -      +
    193A  ILE*     4.4     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  TYR*     5.6     1.1    -      -       -      -
    149A  VAL*     1.3    76.4    -      -       -      +
    151A  LYS*     1.3    68.1    +      -       -      +
    152A  LYS*     2.7    45.4    +      -       +      -
    191A  TRP*     4.2     7.2    -      -       -      -
    192A  PHE*     2.9    50.2    +      -       +      +
    194A  LYS*     3.6    44.9    -      -       +      -
    419A  ASP*     2.7    26.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  TYR*     1.3    79.0    -      -       -      +
    152A  LYS*     1.3    63.3    +      -       -      +
    189A  PRO*     4.2    33.1    +      -       +      +
    190A  GLN*     3.4    20.6    -      -       -      +
    191A  TRP*     3.8    43.5    -      -       +      +
    436A  THR*     5.8     1.8    +      -       -      -
    442A  VAL*     5.6     8.0    -      -       +      +
    486A  GLU*     3.9    18.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  TYR*     2.7    44.7    +      -       +      -
    151A  LYS*     1.3    77.3    -      -       -      +
    153A  THR*     1.3    73.9    +      -       -      +
    154A  SER      3.7     0.5    +      -       -      -
    189A  PRO*     4.1     4.7    -      -       -      -
    190A  GLN*     2.9    31.7    +      -       -      +
    192A  PHE*     3.7    39.6    -      -       +      -
    329A  GLU*     4.2    14.6    -      -       -      -
    419A  ASP*     4.4     4.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  LYS*     1.3    89.7    -      -       -      +
    154A  SER*     1.3    59.0    +      -       -      +
    187A  GLU*     3.5    26.2    -      -       +      +
    188A  ILE*     3.4    32.5    -      -       -      +
    189A  PRO*     4.1     8.1    -      -       +      +
    329A  GLU*     4.9     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  THR*     1.3    76.8    -      -       -      +
    155A  ALA*     1.3    70.9    +      -       -      +
    156A  VAL*     3.7     0.7    +      -       -      +
    187A  GLU*     3.7     7.0    -      -       -      -
    188A  ILE*     3.0    33.1    +      -       -      +
    190A  GLN*     3.7    15.2    +      -       -      -
    192A  PHE*     3.6    30.3    -      -       -      -
    329A  GLU*     3.6    18.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  SER*     1.3    79.9    +      -       -      +
    156A  VAL*     1.3    65.1    +      -       -      +
    185A  ARG*     3.5    38.6    -      -       +      +
    186A  LYS      3.9     5.8    -      -       -      -
    187A  GLU*     3.8    17.8    +      -       -      +
    290A  VAL*     4.3    20.9    -      -       +      +
    329A  GLU*     5.2     3.0    +      -       -      -
     74B    C      6.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  ALA*     1.3    82.6    -      -       -      +
    157A  ASN*     1.3    70.3    +      -       -      +
    158A  TRP*     3.6     2.0    +      -       +      -
    165A  VAL*     3.3    43.5    -      -       +      -
    166A  LEU      5.0     0.2    -      -       -      +
    184A  GLU      3.5     2.4    -      -       -      +
    185A  ARG*     3.7     1.4    -      -       -      -
    186A  LYS*     3.0    37.6    +      -       +      +
    188A  ILE*     3.3    25.8    -      -       +      -
    190A  GLN*     3.4    17.0    -      -       -      +
    290A  VAL*     4.4     6.0    -      -       -      +
     74B    C      3.9    16.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  VAL*     1.3    83.6    -      -       -      +
    158A  TRP*     1.3    58.2    +      -       -      +
    159A  CYS      4.4     0.2    -      -       -      -
    165A  VAL*     3.5     1.9    -      -       -      -
    166A  LEU*     3.2    34.8    +      -       +      +
    167A  ALA      4.1     3.8    +      -       -      -
    168A  ASN*     2.9    39.8    +      -       -      +
    171A  VAL*     4.3    13.0    -      -       +      +
    183A  VAL*     3.9    14.8    -      -       +      +
    184A  GLU      3.9     5.3    -      -       -      +
    185A  ARG*     5.6     1.0    -      -       -      +
    289A  LYS*     4.3    10.5    -      -       -      +
    290A  VAL*     3.4    31.0    +      -       -      +
     74B    C      4.6     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  VAL*     4.1     1.8    -      -       +      +
    157A  ASN*     1.3    75.1    -      -       -      +
    159A  CYS*     1.3    58.2    +      -       -      +
    160A  PRO*     3.3    20.3    +      -       +      +
    163A  GLN*     3.4    40.7    -      -       +      +
    164A  THR*     3.6    15.5    -      -       -      -
    165A  VAL*     3.7    29.6    -      -       +      -
    183A  VAL*     3.5     6.1    -      -       -      +
    184A  GLU*     3.0    62.6    +      -       -      +
    186A  LYS*     3.7    53.2    -      -       +      +
    188A  ILE*     5.0     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  TRP*     1.3    70.7    -      -       -      +
    160A  PRO*     1.4    67.6    -      -       -      +
    161A  ASN*     3.4     5.2    -      -       -      -
    162A  ASP*     4.0    12.8    -      -       +      +
    163A  GLN*     3.0    27.7    +      -       -      -
    164A  THR*     3.4    10.1    +      -       -      +
    166A  LEU*     3.9    24.5    -      -       +      +
    176A  CYS*     4.0     6.5    -      -       +      -
    181A  THR*     3.2    21.1    -      -       -      -
    183A  VAL*     4.7     4.5    -      -       -      +
    900A   ZN      2.4    36.6    -      -       -      -
----------------------------------------------------------
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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