Contacts of the strand formed by residues 457 - 465 (chain S) in PDB entry 1O19


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 TYR 457 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166S  MET*     3.6    42.8    -      -       +      -
    167S  LEU*     4.9    15.6    +      -       +      +
    170S  ARG*     3.9    52.4    +      -       +      +
    171S  GLU      4.5     3.8    -      -       -      +
    172S  ASN*     2.9    18.4    -      -       -      +
    253S  HIS*     3.5     7.0    -      -       -      +
    254S  PHE*     2.7    35.0    +      -       -      +
    255S  GLY      3.8    19.5    -      -       -      -
    256S  ALA      4.4    10.2    +      -       -      -
    455S  ARG*     3.8     0.6    -      -       -      +
    456S  GLN*     1.3   117.7    +      -       +      +
    458S  PHE*     1.3    58.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 458 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166S  MET*     3.7     4.0    -      -       -      +
    172S  ASN*     3.0    35.4    +      -       +      +
    173S  GLN      3.2    28.3    +      -       -      -
    249S  PHE*     4.7     6.1    -      +       -      -
    251S  ARG*     3.7    40.8    -      -       +      -
    252S  ILE      3.0    13.9    -      -       -      +
    253S  HIS*     3.6    32.1    -      +       +      +
    457S  TYR*     1.3    78.7    -      -       -      +
    459S  ILE*     1.3    68.8    +      -       -      +
    460S  GLY*     3.6    19.1    -      -       -      -
    663S  ASN*     4.3    15.5    -      -       -      -
    666S  SER*     5.0     4.0    -      -       -      -
    667S  THR*     4.0    16.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 459 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162S  ALA*     4.6     0.9    -      -       +      -
    163S  TYR*     4.3    14.1    -      -       +      +
    166S  MET*     3.7    16.6    -      -       +      -
    173S  GLN*     3.6    22.0    -      -       +      -
    175S  ILE*     4.2    16.2    -      -       +      -
    196S  PHE*     3.7    42.4    -      -       +      -
    250S  ILE      3.5     2.3    -      -       -      +
    252S  ILE*     2.7    29.6    +      -       +      +
    254S  PHE*     3.3    29.6    -      -       +      -
    458S  PHE*     1.3    81.4    -      -       -      +
    460S  GLY*     1.3    61.6    +      -       -      +
    461S  VAL*     3.7     8.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 460 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173S  GLN      3.0    14.8    +      -       -      -
    174S  SER*     3.0     5.7    -      -       -      -
    175S  ILE*     2.7    32.6    +      -       -      +
    249S  PHE*     3.9    18.4    -      -       -      -
    250S  ILE      3.3     8.7    -      -       -      -
    458S  PHE*     3.6    11.1    -      -       -      -
    459S  ILE*     1.3    73.5    -      -       -      +
    461S  VAL*     1.3    59.1    +      -       -      +
    462S  LEU      3.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 461 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175S  ILE*     3.7    14.4    -      -       +      +
    177S  ILE*     4.0    17.9    -      -       +      -
    189S  THR*     3.7    30.5    -      -       +      +
    192S  VAL*     4.8    11.4    -      -       +      -
    193S  ILE*     4.7    14.6    -      -       +      -
    196S  PHE*     4.9     1.3    -      -       +      -
    248S  MLY      3.7     2.3    -      -       -      +
    249S  PHE*     3.5     5.0    -      -       -      -
    250S  ILE*     3.1    34.8    +      -       +      +
    252S  ILE*     4.6    12.1    -      -       +      -
    459S  ILE*     4.1    19.5    -      -       +      +
    460S  GLY*     1.3    77.4    -      -       -      +
    462S  LEU*     1.3    59.8    +      -       -      +
    463S  ASP*     3.9     0.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 462 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174S  SER*     6.3     0.2    -      -       -      -
    175S  ILE      3.0    11.7    +      -       -      +
    176S  LEU*     3.6    37.5    -      -       +      -
    177S  ILE*     2.9    34.8    +      -       -      +
    178S  THR*     5.7     2.5    -      -       -      +
    248S  MLY      3.5     7.2    -      -       -      +
    249S  PHE*     3.6    22.9    -      -       +      -
    268S  TYR*     5.1     0.4    -      -       +      -
    460S  GLY      3.9     0.2    -      -       -      -
    461S  VAL*     1.3    74.6    -      -       -      +
    463S  ASP*     1.3    60.3    +      -       -      +
    464S  ILE*     3.3    40.8    -      -       +      +
    487S  LEU*     4.6    19.5    -      -       +      -
    660S  LEU*     4.3    15.7    -      -       +      -
    664S  LEU*     4.7     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 463 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177S  ILE*     4.0     5.8    -      -       +      -
    185S  LYS*     4.4    19.8    +      -       -      +
    186S  THR*     3.8    15.6    +      -       -      +
    189S  THR*     3.1    37.8    +      -       +      +
    244S  SER*     4.7     8.1    +      -       -      -
    246S  PHE      4.5     7.8    -      -       -      +
    247S  GLY*     3.3     0.7    -      -       -      -
    248S  MLY      2.4    62.4    +      -       +      +
    461S  VAL      3.9     0.4    +      -       -      +
    462S  LEU*     1.3    74.4    -      -       -      +
    464S  ILE*     1.3    68.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 464 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177S  ILE      3.7     7.9    +      -       -      +
    178S  THR*     3.5    15.8    +      -       -      +
    185S  LYS*     3.8    15.4    -      -       -      +
    247S  GLY*     4.2    12.1    -      -       -      -
    248S  MLY      4.2     5.8    -      -       -      +
    268S  TYR*     4.3    18.6    -      -       +      -
    269S  LEU*     6.1     2.0    -      -       +      -
    462S  LEU*     3.3    32.0    -      -       +      +
    463S  ASP*     1.3    86.0    +      -       -      +
    465S  ALA*     1.3    84.8    +      -       +      +
    480S  ILE*     4.6    14.6    -      -       +      -
    483S  THR*     4.4    25.1    -      -       +      -
    487S  LEU*     5.2     5.2    -      -       +      -
    660S  LEU*     4.5     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 465 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178S  THR*     4.2     2.0    +      -       -      -
    179S  GLY      4.2     9.2    -      -       -      +
    181S  SER      6.3     0.4    -      -       -      +
    185S  LYS*     4.6     8.2    -      -       -      +
    247S  GLY*     5.7     0.2    -      -       -      -
    464S  ILE*     1.3    92.1    -      -       +      +
    466S  GLY*     1.3    60.2    +      -       -      +
    468S  GLU*     5.3     6.3    -      -       -      +
    480S  ILE*     4.4    21.0    -      -       +      +
    484S  ASN*     2.5    27.9    +      -       -      +
    487S  LEU*     5.6     0.2    -      -       -      +
----------------------------------------------------------
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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