Contacts of the strand formed by residues 434 - 439 (chain C) in PDB entry 1TYE


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 ASP 434 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3C  LEU*     4.9     2.7    -      -       -      -
     25C  PHE*     4.7     4.3    -      -       +      -
    363C  LEU*     4.4     3.7    -      -       -      +
    366C  LEU*     5.9     1.3    -      -       -      +
    423C  GLY*     3.2    22.7    -      -       -      -
    424C  ALA      3.5     3.6    +      -       -      -
    425C  VAL      3.1    14.0    +      -       -      +
    427C  ILE*     2.9    45.2    +      -       +      +
    428C  ASP*     3.3     1.6    -      -       -      +
    433C  PRO*     1.3    73.6    -      -       -      +
    435C  LEU*     1.3    64.2    +      -       -      +
    447C  VAL*     5.2     1.8    -      -       +      -
    448C  TYR      3.6    10.3    -      -       -      +
    449C  ARG*     3.4     9.1    -      -       -      +
    450C  ALA      3.1    22.8    +      -       -      +
   1414C   CA      2.7    28.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 435 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3C  LEU*     3.8    20.0    -      -       +      -
     25C  PHE*     4.7     1.1    -      -       -      -
    361C  ALA*     4.8     1.3    -      -       +      -
    363C  LEU*     3.6    26.7    -      -       +      -
    375C  ALA*     4.5    10.1    -      -       +      -
    389C  VAL*     4.5     9.2    -      -       +      -
    391C  VAL*     5.5     2.5    -      -       +      -
    407C  LEU*     3.9    24.0    -      -       +      -
    421C  LEU*     4.6     5.4    -      -       +      -
    422C  ARG      3.3    26.0    -      -       -      +
    434C  ASP*     1.3    81.2    -      -       -      +
    436C  ILE*     1.3    67.7    +      -       -      +
    437C  VAL*     3.9    22.0    -      -       +      -
    446C  ALA      3.8     0.3    -      -       -      +
    447C  VAL*     3.5     2.6    -      -       -      +
    448C  TYR*     2.7    39.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 436 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  LEU*     3.9    20.1    -      -       +      +
     24C  ASP      4.2    11.0    -      -       -      -
     25C  PHE*     3.6    24.9    -      -       +      -
     35C  ILE*     3.5    48.9    -      -       +      -
    420C  SER      4.1     0.2    -      -       -      +
    421C  LEU*     3.7     2.8    -      -       -      -
    422C  ARG*     2.9    56.3    +      -       +      +
    435C  LEU*     1.3    77.2    -      -       -      +
    437C  VAL*     1.3    64.6    +      -       -      +
    445C  VAL*     4.5     2.7    -      -       +      -
    446C  ALA      3.4     3.6    -      -       -      +
    447C  VAL*     4.0    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 437 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389C  VAL*     4.1     7.0    -      -       +      -
    411C  PHE*     5.6     0.2    -      -       -      -
    417C  PHE*     3.7    27.3    -      -       +      -
    418C  GLY*     3.7    24.0    -      -       -      +
    420C  SER      3.6     2.5    -      -       -      -
    421C  LEU*     3.5    23.8    -      -       +      -
    435C  LEU*     3.9    20.6    -      -       +      -
    436C  ILE*     1.3    80.2    -      -       -      +
    438C  GLY*     1.3    63.6    +      -       -      +
    439C  ALA*     5.2     0.9    -      -       -      +
    445C  VAL*     3.4     5.3    -      -       -      -
    446C  ALA*     2.7    43.1    +      -       +      +
    448C  TYR*     4.1    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 438 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20C  GLY      3.6     9.2    -      -       -      -
     23C  LEU*     3.9     8.7    -      -       -      +
    416C  ALA      3.8     1.7    -      -       -      +
    417C  PHE*     3.7     0.5    -      -       -      -
    418C  GLY      3.0    25.5    +      -       -      -
    419C  PHE*     3.9     4.5    +      -       -      -
    420C  SER*     2.9    30.2    +      -       -      -
    437C  VAL*     1.3    74.4    -      -       -      +
    439C  ALA*     1.3    60.9    +      -       -      +
    440C  TYR      4.0     1.6    -      -       -      -
    444C  GLN      4.0     4.3    -      -       -      -
    445C  VAL*     4.3     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 439 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  PHE      4.1     0.4    -      -       -      -
     20C  GLY      4.1     1.0    +      -       -      -
    411C  PHE*     4.1    22.2    -      -       +      -
    415C  SER*     3.3    20.2    -      -       -      +
    416C  ALA      4.3     0.4    -      -       -      -
    417C  PHE*     3.8    15.3    -      -       +      +
    437C  VAL      5.2     0.7    -      -       -      +
    438C  GLY*     1.3    74.3    -      -       -      +
    440C  TYR*     1.3    60.1    +      -       -      +
    441C  GLY      3.1     3.4    -      -       -      -
    442C  ALA*     2.8    22.4    +      -       +      -
    443C  ASN      3.0     8.7    +      -       -      -
    444C  GLN      2.8    20.8    +      -       -      +
----------------------------------------------------------
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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