Contacts of the strand formed by residues 398 - 409 (chain A) in PDB entry 4TVJ


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 398 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387A  GLN*     5.7     2.7    -      -       -      -
    390A  HIS*     3.8     9.2    -      -       +      +
    395A  SER      6.2     0.2    -      -       -      +
    397A  TYR*     1.3    79.6    -      -       -      +
    399A  MET*     1.3    63.7    +      -       -      +
    577A  PHE*     3.5     4.2    -      -       -      -
    578A  ASN*     2.7    55.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 399 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    386A  LEU*     3.7    25.8    -      -       +      +
    387A  GLN*     2.9    29.4    +      -       -      +
    390A  HIS*     3.5    24.8    +      -       +      +
    397A  TYR*     3.6    15.9    -      -       +      -
    398A  THR*     1.3    83.3    -      -       -      +
    400A  THR*     1.3    63.6    +      -       -      +
    467A  SER*     3.5    27.8    -      -       -      +
    468A  SER*     4.2     8.5    -      -       -      -
    471A  ALA*     3.6    24.0    -      -       +      -
    485A  LEU*     4.1     2.5    -      -       -      -
    575A  VAL*     3.7    24.7    -      -       +      -
    576A  GLN      3.3     3.4    -      -       -      -
    577A  PHE*     4.2     5.6    -      -       +      -
    578A  ASN*     3.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 400 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387A  GLN*     4.8     0.9    -      -       -      +
    399A  MET*     1.3    72.6    +      -       -      +
    401A  LEU*     1.3    71.3    +      -       -      +
    402A  LEU*     3.3    14.4    +      -       +      -
    575A  VAL*     3.4     4.4    -      -       -      -
    576A  GLN*     2.7    50.1    +      -       -      +
    578A  ASN*     2.8    26.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 401 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A  HIS*     5.2     1.2    -      -       -      -
    379A  PHE*     3.5    35.6    -      -       +      -
    382A  ILE*     4.8     5.2    -      -       +      -
    383A  SER*     3.3    36.6    -      -       -      +
    386A  LEU*     3.9    16.0    -      -       +      +
    387A  GLN*     5.0     2.1    -      -       -      +
    399A  MET      4.2     1.0    +      -       -      -
    400A  THR*     1.3    77.5    -      -       -      +
    402A  LEU*     1.3    61.1    +      -       -      +
    403A  ASP      3.5    22.7    -      -       -      +
    404A  LEU*     4.8     2.5    -      -       +      -
    573A  LEU*     3.6    38.8    -      -       +      -
    574A  LYS      3.7     6.1    -      -       -      +
    575A  VAL*     4.4     2.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 402 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A  HIS*     3.3    17.4    -      -       -      -
    400A  THR*     3.3    13.9    +      -       +      -
    401A  LEU*     1.3    74.3    -      -       -      +
    403A  ASP*     1.3    61.6    +      -       -      +
    482A  THR*     4.5    10.5    -      -       -      +
    574A  LYS*     2.7    41.3    +      -       +      +
    575A  VAL      4.5     2.0    -      -       -      -
    576A  GLN*     3.8    50.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 403 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  ARG*     2.8    58.7    +      -       -      +
    374A  HIS*     2.9    16.2    +      -       -      -
    379A  PHE*     4.8     0.9    -      -       -      -
    401A  LEU*     3.5    10.5    -      -       -      +
    402A  LEU*     1.3    80.4    -      -       -      +
    404A  LEU*     1.3    69.7    +      -       -      +
    405A  PHE*     4.0    20.3    -      -       +      -
    573A  LEU*     3.6     0.2    -      -       -      -
    574A  LYS*     2.9    37.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 404 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371A  PRO*     3.5     4.2    -      -       -      +
    372A  LEU*     2.9    50.7    +      -       +      +
    374A  HIS*     4.5     0.4    +      -       -      -
    379A  PHE*     3.8    47.8    -      -       +      +
    382A  ILE*     3.9    19.5    -      -       +      -
    401A  LEU*     4.8     3.1    -      -       +      -
    403A  ASP*     1.3    86.0    +      -       -      +
    405A  PHE*     1.3    67.5    +      -       -      +
    571A  TYR*     4.0    13.7    -      -       +      -
    572A  LEU      3.6     5.6    -      -       -      +
    573A  LEU*     3.8    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 405 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  ARG*     3.8    29.8    -      -       +      -
    238A  VAL*     4.1     8.5    -      -       +      -
    241A  LEU*     4.0    36.3    -      -       +      -
    369A  LEU*     4.7     6.5    -      -       +      -
    370A  ARG      3.3     8.3    -      -       -      +
    371A  PRO*     3.7    33.2    -      -       +      -
    372A  LEU*     4.6     0.7    -      -       -      -
    403A  ASP*     4.0    33.2    -      -       +      -
    404A  LEU*     1.3    75.8    -      -       -      +
    406A  GLU*     1.3    67.6    +      -       -      +
    571A  TYR*     3.2    10.8    -      -       -      +
    572A  LEU*     2.9    52.5    +      -       +      +
    574A  LYS*     4.7    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 406 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368A  ALA      3.6     0.9    -      -       -      +
    369A  LEU*     3.3     8.0    -      -       -      -
    370A  ARG*     2.7    77.0    +      -       +      +
    372A  LEU*     4.1    25.3    -      -       +      +
    405A  PHE*     1.3    75.1    -      -       -      +
    407A  VAL*     1.3    66.5    +      -       -      +
    408A  GLU*     4.4     2.3    -      -       +      +
    570A  ARG*     3.5    28.7    +      -       -      +
    571A  TYR*     4.3     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 407 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367A  CYS*     3.6    25.1    -      -       -      -
    368A  ALA      3.5     3.4    -      -       -      +
    369A  LEU*     4.2     8.7    -      -       +      -
    406A  GLU*     1.3    81.9    -      -       -      +
    408A  GLU*     1.3    64.1    +      -       -      +
    409A  LYS      4.4     1.3    -      -       -      +
    439A  LEU*     4.6     4.9    -      -       +      -
    486A  LEU*     4.5     5.8    -      -       +      -
    568A  ARG*     5.5     1.4    +      -       -      -
    569A  MET*     3.1    38.7    -      -       +      +
    570A  ARG*     2.8    28.6    +      -       -      +
    571A  TYR      3.7     7.6    -      -       -      +
    572A  LEU*     3.7    36.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 408 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367A  CYS*     3.5     1.1    -      -       -      -
    368A  ALA*     2.8    40.3    +      -       +      +
    370A  ARG*     3.0    39.4    +      -       -      +
    406A  GLU*     4.4     2.3    -      -       +      +
    407A  VAL*     1.3    74.4    -      -       -      +
    409A  LYS*     1.3    66.0    +      -       -      +
    410A  ASP*     3.6     4.6    +      -       -      +
    413A  LYS*     4.8    16.9    -      -       +      +
    568A  ARG*     4.7    17.3    -      -       -      +
    569A  MET      4.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 409 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365A  LEU      3.0    11.3    +      -       -      -
    366A  HIS*     2.9    26.8    +      -       -      +
    367A  CYS*     3.7     8.5    -      -       +      +
    407A  VAL*     4.0     2.4    -      -       +      +
    408A  GLU*     1.3    77.9    -      -       -      +
    410A  ASP*     1.3    78.5    +      -       -      +
    411A  GLY      3.2     0.5    +      -       -      -
    412A  GLU*     3.1    51.5    +      -       +      +
    413A  LYS      4.5     1.7    +      -       -      -
    439A  LEU      3.1    19.6    +      -       -      +
    440A  SER      2.7    29.8    +      -       -      -
    441A  HIS*     4.6     2.7    -      -       -      +
    442A  GLY*     4.4     8.3    -      -       -      +
    569A  MET*     3.7    18.5    +      -       +      -
----------------------------------------------------------
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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