Contacts of the strand formed by residues 394 - 403 (chain F) 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 THR 394 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69F  LEU*     3.7    22.4    -      -       +      -
    103F  GLN*     4.4    14.4    -      -       +      +
    104F  VAL      3.2    13.9    -      -       -      +
    105F  ARG*     2.7    33.2    +      -       -      +
    374F  CYS      5.2     3.5    -      -       -      +
    375F  LEU*     5.5     2.9    -      -       -      +
    377F  ASN*     5.7     2.9    +      -       -      -
    392F  GLY      3.5     3.0    +      -       -      -
    393F  ASP*     1.3    74.5    -      -       -      +
    395F  VAL*     1.3    70.8    +      -       -      +
    396F  SER*     6.1     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 395 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103F  GLN*     3.4     2.1    -      -       -      +
    104F  VAL*     2.6    45.0    +      -       +      +
    355F  VAL*     4.9     8.3    -      -       +      -
    373F  THR      3.5     8.5    -      -       -      +
    374F  CYS*     4.2    15.0    -      -       -      -
    375F  LEU*     4.3     4.0    -      -       +      +
    386F  CYS*     3.4    39.5    -      -       +      -
    389F  LEU*     3.7    26.5    -      -       +      -
    393F  ASP      4.4     0.2    +      -       -      -
    394F  THR*     1.3    80.0    -      -       -      +
    396F  SER*     1.3    61.7    +      -       -      +
    397F  PHE*     3.8    20.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 396 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101F  SER*     5.6     1.3    -      -       -      -
    102F  ILE      3.3    10.8    -      -       -      -
    103F  GLN*     3.7    17.3    -      -       -      -
    372F  ALA*     3.8     0.2    -      -       -      -
    373F  THR*     2.8    54.0    +      -       -      +
    377F  ASN*     5.9     0.2    +      -       -      -
    394F  THR*     6.1     0.4    -      -       -      -
    395F  VAL*     1.3    77.3    -      -       -      +
    397F  PHE*     1.3    68.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 397 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101F  SER*     3.8     5.4    +      -       -      -
    102F  ILE*     2.8    49.1    +      -       +      +
    104F  VAL*     4.3    10.3    -      -       +      -
    355F  VAL*     3.8    37.0    -      -       +      -
    357F  LEU*     3.4    35.2    -      -       +      -
    370F  PHE*     5.1     3.8    -      +       +      -
    371F  ASN      3.4     6.7    -      -       -      -
    372F  ALA*     3.6    29.6    -      -       +      -
    373F  THR*     6.1     0.2    -      -       -      -
    383F  LEU      4.8     0.2    -      -       -      -
    384F  LYS*     3.7    24.0    -      -       +      -
    385F  SER      4.0     0.7    -      -       -      -
    386F  CYS*     4.4     4.3    -      -       -      -
    395F  VAL*     3.8    22.0    -      -       +      -
    396F  SER*     1.3    78.9    -      -       -      +
    398F  SER*     1.3    62.6    +      -       -      +
    399F  ILE*     4.5     2.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 398 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99F  ASN*     5.0     3.1    +      -       -      +
    100F  PHE      3.5     9.5    +      -       -      -
    101F  SER*     5.5     0.7    -      -       -      -
    369F  SER      3.6     0.5    -      -       -      +
    370F  PHE*     3.5     4.9    -      -       -      +
    371F  ASN*     2.7    43.7    +      -       -      -
    397F  PHE*     1.3    77.3    -      -       -      +
    399F  ILE*     1.3    62.0    +      -       -      +
   1015F  NAG      4.7     9.5    -      -       -      +
   1020F  NAG      2.7    25.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 399 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99F  ASN*     3.1     4.4    -      -       -      +
    100F  PHE*     2.8    71.4    +      -       +      +
    102F  ILE*     3.5    32.8    -      -       +      -
    357F  LEU*     5.3     2.0    -      -       +      -
    368F  LEU*     3.6    31.9    -      -       +      -
    369F  SER      3.2    12.1    -      -       -      +
    370F  PHE*     3.5    31.2    -      -       +      -
    397F  PHE*     4.5     2.2    -      -       +      -
    398F  SER*     1.3    79.1    -      -       -      +
    400F  GLU*     1.3    64.0    +      -       -      +
    401F  ALA      4.3     0.2    -      -       -      -
    416F  ILE*     4.9     6.3    -      -       +      -
    425F  LEU*     5.2     3.8    -      -       +      -
   1020F  NAG      4.6     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 400 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97F  SER*     3.7    27.6    +      -       -      -
     98F  LYS      3.4    17.5    -      -       -      +
     99F  ASN*     4.2     8.8    -      -       +      +
    367F  SER      3.7     0.3    -      -       -      +
    368F  LEU*     3.3     9.3    -      -       -      -
    369F  SER*     3.0    39.9    +      -       -      -
    399F  ILE*     1.3    76.0    -      -       -      +
    401F  ALA*     1.3    61.5    +      -       -      +
    402F  LYS*     4.1     3.9    +      -       +      +
   1020F  NAG      3.3    37.6    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 401 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90F  LEU*     3.9    23.8    -      -       +      -
     92F  LEU*     4.1     8.2    -      -       +      +
     96F  ASP      4.0     0.2    -      -       -      +
     97F  SER*     3.1     7.4    -      -       -      -
     98F  LYS      2.9    34.4    +      -       -      +
    100F  PHE*     4.5     5.8    -      -       +      -
    366F  LEU*     3.8    14.1    -      -       +      -
    367F  SER      3.5     5.4    -      -       -      -
    368F  LEU*     3.6    14.8    -      -       +      -
    399F  ILE      4.3     0.6    -      -       -      -
    400F  GLU*     1.3    72.9    -      -       -      +
    402F  LYS*     1.3    61.3    +      -       -      +
    414F  PHE*     5.6     1.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 402 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92F  LEU*     4.9     0.2    -      -       -      -
     95F  ASP*     4.2    16.6    +      -       -      +
     96F  ASP      3.5     9.2    -      -       -      +
     97F  SER*     3.3    21.1    -      -       -      +
    366F  LEU*     3.3     2.8    -      -       -      +
    367F  SER*     3.0    46.2    +      -       -      +
    400F  GLU*     5.2     4.3    -      -       -      +
    401F  ALA*     1.3    75.2    -      -       -      +
    403F  VAL*     1.3    81.5    +      -       -      +
    404F  ARG*     4.2     7.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 403 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92F  LEU*     3.4    36.1    -      -       +      +
     93F  ARG      3.8     4.9    -      -       -      +
     94F  PRO*     4.3     1.3    -      -       +      -
     95F  ASP*     3.3    39.8    -      -       -      +
     96F  ASP      3.6     3.7    +      -       -      +
    365F  GLU      3.6     6.1    -      -       -      +
    366F  LEU*     3.7    21.5    -      -       +      -
    402F  LYS*     1.3    85.2    +      -       -      +
    404F  ARG*     1.3    60.6    +      -       -      +
    405F  GLY      3.4    11.8    +      -       -      +
    406F  CYS*     5.8     1.1    -      -       -      -
    407F  PRO*     5.9     0.4    -      -       +      -
    431F  PHE*     3.6    26.2    -      -       +      -
----------------------------------------------------------
 Back to top of page


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