Contacts of the strand formed by residues 336 - 344 (chain B) in PDB entry 5TXN


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 GLN 336 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331B  LYS      4.0     0.2    -      -       -      -
    332B  GLN*     2.9    36.6    +      -       +      +
    333B  GLY      3.1    16.1    +      -       -      +
    334B  GLN*     3.3    10.6    +      -       -      +
    335B  GLY*     1.3    74.6    -      -       -      +
    337B  TRP*     1.3    66.4    +      -       -      +
    353B  LYS*     3.4    35.0    -      -       +      +
    354B  TYR      3.3     7.6    -      -       -      +
    355B  ALA*     3.7    15.9    -      -       +      +
    427B  TYR*     2.5    33.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 337 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    408A  ALA*     4.2    15.0    -      -       +      -
    329B  ILE*     4.1    19.7    -      -       +      -
    330B  GLN      3.4     8.1    -      -       -      +
    331B  LYS*     3.6    36.3    -      -       +      -
    335B  GLY*     3.5    15.7    -      -       -      -
    336B  GLN*     1.3    81.1    -      -       -      +
    338B  THR*     1.3    62.8    +      -       -      +
    339B  TYR*     4.8     1.0    -      -       -      -
    353B  LYS*     3.2     3.3    -      -       -      +
    354B  TYR*     2.6    43.7    +      -       +      +
    357B  MET*     3.5    22.9    -      -       +      -
    364B  ASP*     3.4    36.6    -      -       -      -
    367B  GLN*     3.0    39.6    +      -       +      +
    368B  LEU*     4.1    22.2    -      -       +      -
    371B  ALA*     5.0     5.4    -      -       +      -
    392B  PRO*     4.7     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 338 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242B  GLN*     5.0     2.5    -      -       +      -
    329B  ILE*     3.3     6.7    -      -       -      +
    330B  GLN*     2.5    54.8    +      -       -      +
    332B  GLN*     3.0    30.9    +      -       +      +
    337B  TRP*     1.3    75.0    -      -       -      +
    339B  TYR*     1.3    62.7    +      -       -      +
    340B  GLN*     4.3     0.9    -      -       -      -
    352B  GLY      3.3     6.5    -      -       -      +
    353B  LYS*     3.6    30.5    -      -       +      -
    426B  TRP*     3.9    17.1    -      -       +      +
    427B  TYR*     4.0    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 339 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  THR      4.9     0.3    +      -       -      -
    327B  ALA*     5.8     0.9    -      -       +      -
    328B  GLU      3.1    14.1    -      -       -      +
    329B  ILE*     4.3     2.2    -      -       +      -
    337B  TRP      4.8     0.9    -      -       -      -
    338B  THR*     1.3    76.3    -      -       -      +
    340B  GLN*     1.3    73.0    +      -       -      +
    341B  ILE*     4.2    22.2    -      -       +      -
    350B  LYS*     3.3    22.0    +      -       +      -
    351B  THR*     3.3     4.0    -      -       -      -
    352B  GLY*     2.9    62.8    +      -       -      +
    353B  LYS*     3.7     1.8    -      -       -      -
    354B  TYR*     3.3    40.7    +      +       -      -
    375B  ILE*     3.6    34.8    -      -       +      -
    378B  GLU*     2.8    27.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 340 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326B  ILE      3.6     1.6    -      -       -      +
    327B  ALA*     3.3     3.6    -      -       -      -
    328B  GLU*     3.0    40.4    +      -       +      +
    330B  GLN*     2.7    42.8    +      -       -      -
    338B  THR*     4.3     0.8    -      -       -      -
    339B  TYR*     1.3    88.9    +      -       -      +
    341B  ILE*     1.3    63.8    +      -       -      +
    342B  TYR*     4.2     6.9    -      -       +      -
    348B  ASN*     4.0    16.8    -      -       -      +
    350B  LYS      3.4     8.3    -      -       -      +
    351B  THR*     3.8     7.9    -      -       +      -
    352B  GLY      5.1     0.2    +      -       -      -
    426B  TRP*     3.1    56.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 341 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325B  LEU*     4.0    23.6    -      -       +      -
    326B  ILE      3.3     9.2    -      -       -      +
    327B  ALA*     4.4     4.7    -      -       +      -
    339B  TYR*     4.2    15.3    -      -       +      -
    340B  GLN*     1.3    76.8    -      -       -      +
    342B  TYR*     1.3    65.2    +      -       -      +
    348B  ASN*     3.5     2.3    -      -       -      -
    349B  LEU*     2.8    24.4    +      -       +      -
    350B  LYS*     2.8    23.9    +      -       +      +
    375B  ILE*     3.8    24.9    -      -       +      +
    378B  GLU*     5.1     2.9    -      -       +      +
    379B  SER*     3.5    23.1    -      -       -      +
    383B  TRP*     3.8    35.4    -      -       +      -
    387B  PRO*     4.9     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 342 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325B  LEU*     3.6     4.3    -      -       -      -
    326B  ILE*     2.7    77.5    +      -       +      +
    328B  GLU*     2.7    44.1    +      -       +      -
    340B  GLN*     4.2     9.0    -      -       +      -
    341B  ILE*     1.3    74.8    -      -       -      +
    343B  GLN*     1.3    65.4    +      -       -      +
    344B  GLU      3.4    19.1    -      -       -      +
    345B  PRO*     4.0    19.7    -      -       +      -
    346B  PHE      5.7     0.7    -      -       -      -
    347B  LYS      3.2    17.0    -      -       -      +
    348B  ASN*     3.2    24.9    -      -       -      +
    349B  LEU*     4.2     6.1    -      -       -      +
    390B  LYS*     3.8     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 343 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318B  TYR      3.9     4.3    -      -       -      +
    319B  TYR*     3.3    27.5    -      -       -      -
    320B  ASP*     2.7    51.5    +      -       -      +
    323B  LYS*     3.0    35.7    +      -       +      +
    324B  ASP      3.4    18.9    -      -       -      +
    325B  LEU*     3.8    11.2    -      -       +      +
    326B  ILE*     4.9     4.8    -      -       -      +
    342B  TYR*     1.3    82.2    -      -       -      +
    344B  GLU*     1.3    70.8    +      -       +      +
    345B  PRO*     4.5     1.9    -      -       -      +
    347B  LYS      4.1     2.6    +      -       -      -
    349B  LEU*     3.9     8.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 344 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323B  LYS*     2.9    41.6    +      -       +      +
    342B  TYR*     3.4     7.4    -      -       -      -
    343B  GLN*     1.3    81.7    -      -       +      +
    345B  PRO*     1.3    84.6    -      -       +      +
    346B  PHE      3.4     0.5    +      -       -      -
    347B  LYS*     3.2    34.2    +      -       +      +
----------------------------------------------------------
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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