Contacts of the strand formed by residues 457 - 465 (chain A) in PDB entry 1O1F


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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  MET*     3.6    43.5    -      -       +      -
    167A  LEU*     4.9    13.9    +      -       +      +
    170A  ARG*     3.9    52.0    +      -       +      +
    171A  GLU      4.5     3.6    -      -       -      +
    172A  ASN*     2.9    18.6    -      -       -      +
    253A  HIS*     3.5     7.2    -      -       -      +
    254A  PHE*     2.7    35.2    +      -       -      +
    255A  GLY      3.8    19.5    -      -       -      -
    256A  ALA      4.4    10.6    +      -       -      -
    455A  ARG      3.8     0.2    -      -       -      -
    456A  GLN*     1.3   118.9    +      -       +      +
    458A  PHE*     1.3    60.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 458 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  MET*     3.7     3.2    -      -       -      +
    172A  ASN*     3.0    35.3    +      -       +      +
    173A  GLN      3.2    28.5    +      -       -      -
    249A  PHE*     4.7     5.8    -      +       -      -
    251A  ARG*     3.7    40.8    -      -       +      -
    252A  ILE      3.0    14.4    -      -       -      +
    253A  HIS*     3.6    31.6    -      +       +      +
    457A  TYR*     1.3    77.7    -      -       -      +
    459A  ILE*     1.3    70.0    +      -       -      +
    460A  GLY*     3.6    18.4    -      -       -      -
    663A  ASN*     4.3    16.2    -      -       -      -
    666A  SER*     5.0     3.8    -      -       -      -
    667A  THR*     4.0    16.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 459 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  ALA*     4.6     0.9    -      -       +      -
    163A  TYR*     4.3    14.4    -      -       +      +
    166A  MET*     3.7    15.9    -      -       +      -
    173A  GLN*     3.6    23.3    -      -       +      +
    175A  ILE*     4.2    15.9    -      -       +      -
    196A  PHE*     3.7    42.6    -      -       +      -
    250A  ILE      3.5     2.1    -      -       -      +
    252A  ILE*     2.7    29.6    +      -       +      +
    254A  PHE*     3.3    30.1    -      -       +      -
    458A  PHE*     1.3    82.0    -      -       -      +
    460A  GLY*     1.3    62.1    +      -       -      +
    461A  VAL*     3.7     8.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 460 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  GLN      3.0    14.2    +      -       -      -
    174A  SER*     3.0     6.4    -      -       -      -
    175A  ILE*     2.7    32.2    +      -       -      +
    249A  PHE*     3.9    18.2    -      -       -      -
    250A  ILE      3.3     8.3    -      -       -      -
    458A  PHE*     3.6    12.1    -      -       -      -
    459A  ILE*     1.3    72.6    -      -       -      +
    461A  VAL*     1.3    59.1    +      -       -      +
    462A  LEU      3.9     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 461 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  ILE*     3.7    15.3    -      -       +      +
    177A  ILE*     4.0    16.8    -      -       +      -
    189A  THR*     3.7    30.0    -      -       +      +
    192A  VAL*     4.8    11.9    -      -       +      -
    193A  ILE*     4.7    15.7    -      -       +      -
    196A  PHE*     4.9     0.7    -      -       +      -
    248A  MLY      3.7     1.9    -      -       -      +
    249A  PHE*     3.5     4.9    -      -       -      -
    250A  ILE*     3.1    33.3    +      -       +      +
    252A  ILE*     4.6    12.1    -      -       +      -
    459A  ILE*     4.1    19.3    -      -       +      +
    460A  GLY*     1.3    77.3    -      -       -      +
    462A  LEU*     1.3    61.8    +      -       -      +
    463A  ASP*     3.9     0.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 462 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  SER*     6.3     0.2    -      -       -      -
    175A  ILE      3.0    11.0    +      -       -      +
    176A  LEU*     3.6    37.5    -      -       +      -
    177A  ILE*     2.9    34.3    +      -       -      +
    178A  THR*     5.7     2.9    -      -       -      +
    248A  MLY      3.5     6.5    -      -       -      +
    249A  PHE*     3.6    21.8    -      -       +      -
    268A  TYR*     5.1     0.4    -      -       +      -
    460A  GLY      3.9     0.6    -      -       -      +
    461A  VAL*     1.3    75.3    -      -       -      +
    463A  ASP*     1.3    59.7    +      -       -      +
    464A  ILE*     3.3    39.5    -      -       +      +
    487A  LEU*     4.6    20.0    -      -       +      -
    660A  LEU*     4.3    16.4    -      -       +      -
    664A  LEU*     4.7     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 463 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  ILE*     4.0     5.6    -      -       +      -
    185A  LYS*     4.4    19.3    +      -       -      +
    186A  THR*     3.8    15.6    +      -       -      +
    189A  THR*     3.1    37.9    +      -       +      +
    244A  SER*     4.7     6.6    +      -       -      -
    246A  PHE      4.5     8.3    -      -       -      +
    247A  GLY*     3.3     0.7    -      -       -      -
    248A  MLY      2.4    62.6    +      -       +      +
    461A  VAL      3.9     0.2    +      -       -      -
    462A  LEU*     1.3    73.2    -      -       -      +
    464A  ILE*     1.3    67.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 464 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  ILE      3.7     7.3    +      -       -      +
    178A  THR*     3.5    14.7    +      -       -      +
    185A  LYS*     3.8    15.1    -      -       -      +
    247A  GLY*     4.2    11.4    -      -       -      -
    248A  MLY      4.2     6.5    -      -       -      +
    268A  TYR*     4.3    19.3    -      -       +      -
    269A  LEU*     6.1     2.5    -      -       +      -
    462A  LEU*     3.3    31.6    -      -       +      +
    463A  ASP*     1.3    86.8    +      -       -      +
    465A  ALA*     1.3    84.6    +      -       +      +
    480A  ILE*     4.6    14.8    -      -       +      -
    483A  THR*     4.4    24.9    -      -       +      -
    487A  LEU*     5.2     4.9    -      -       +      -
    660A  LEU*     4.5     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 465 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  THR*     4.2     2.6    +      -       -      -
    179A  GLY      4.2     9.2    -      -       -      +
    181A  SER      6.3     0.4    -      -       -      +
    185A  LYS*     4.6     7.6    -      -       -      +
    464A  ILE*     1.3    92.3    -      -       -      +
    466A  GLY*     1.3    59.9    +      -       -      +
    468A  GLU*     5.3     6.3    -      -       -      +
    480A  ILE*     4.4    20.6    -      -       +      +
    484A  ASN*     2.5    27.4    +      -       -      +
    487A  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