Contacts of the strand formed by residues 546 - 554 (chain B) in PDB entry 6TXC


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 ALA 546 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505B  MET      3.2     8.5    -      -       -      +
    506B  ASP*     4.0     6.1    -      -       +      -
    510B  GLN*     3.7    23.3    -      -       -      +
    511B  GLU*     4.0    13.7    -      -       +      +
    544B  LYS*     3.7    18.5    -      -       -      +
    545B  PHE*     1.3    81.8    -      -       -      +
    547B  GLU*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 547 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367B  ASN*     4.9     5.9    +      -       -      -
    371B  ARG*     2.8    30.4    +      -       -      +
    461B  GLN*     2.8    28.7    +      -       -      +
    504B  ASN*     3.6     5.7    -      -       -      +
    505B  MET*     2.9    49.5    +      -       +      +
    544B  LYS*     6.3     0.7    -      -       +      -
    546B  ALA*     1.3    77.5    -      -       -      +
    548B  GLN*     1.3    66.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 548 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461B  GLN*     3.2    28.8    +      -       -      +
    462B  PRO*     4.0    18.1    -      -       +      +
    466B  ILE      4.0     4.2    -      -       -      +
    467B  LYS*     3.4    13.8    -      -       -      +
    468B  ILE*     2.9    53.6    +      -       -      +
    473B  TYR*     3.9     2.6    +      -       -      -
    502B  VAL*     3.6    22.7    -      -       +      +
    503B  ILE      3.3     4.3    -      -       -      +
    504B  ASN*     3.1    27.7    +      -       -      +
    547B  GLU*     1.3    76.9    -      -       -      +
    549B  LEU*     1.3    64.5    +      -       -      +
    550B  ILE*     5.2     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 549 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371B  ARG*     3.5    40.6    -      -       +      +
    375B  GLN*     5.9     1.1    -      -       +      -
    459B  GLU*     3.5    33.2    -      -       +      +
    460B  THR      3.8     0.9    -      -       -      -
    461B  GLN*     3.7    17.9    -      -       +      +
    501B  ASP      3.5     1.7    -      -       -      +
    502B  VAL*     3.4     4.5    -      -       -      +
    503B  ILE*     2.8    45.2    +      -       +      +
    505B  MET*     3.8    27.4    -      -       +      -
    547B  GLU*     5.1     0.7    -      -       +      -
    548B  GLN*     1.3    80.9    -      -       -      +
    550B  ILE*     1.3    63.1    +      -       -      +
    551B  ARG*     4.0    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 550 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458B  GLY      3.9     0.5    -      -       -      +
    459B  GLU*     3.4     2.6    -      -       -      -
    460B  THR*     2.8    44.7    +      -       +      +
    462B  PRO*     3.8    22.9    -      -       +      -
    468B  ILE*     3.5    28.0    -      -       +      -
    476B  LEU*     5.2     0.4    -      -       +      -
    500B  VAL*     3.6    29.8    -      -       +      -
    501B  ASP      3.5     3.8    -      -       -      +
    502B  VAL*     4.2    16.8    -      -       +      -
    548B  GLN*     5.2     0.7    -      -       +      -
    549B  LEU*     1.3    77.8    -      -       -      +
    551B  ARG*     1.3    62.3    +      -       -      +
    552B  VAL*     4.2     1.1    +      -       +      +
    572B  TRP*     3.8    20.6    -      -       +      -
    578B  PHE*     3.9    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 551 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371B  ARG*     5.2     5.7    +      -       -      +
    375B  GLN*     2.8    33.5    +      -       -      +
    376B  HIS*     4.8     0.8    -      -       -      +
    377B  LYS*     3.9    22.5    -      -       +      +
    380B  ASN*     3.6     5.7    +      -       -      -
    456B  TYR*     3.9    20.4    -      -       +      -
    458B  GLY      3.5     3.8    -      -       -      +
    459B  GLU*     3.0    33.5    +      -       -      -
    499B  ILE      3.8     0.5    -      -       -      +
    500B  VAL*     3.4     4.0    -      -       -      +
    501B  ASP*     2.9    37.0    +      -       +      +
    503B  ILE*     3.2    31.3    -      -       -      +
    549B  LEU*     4.4    12.2    -      -       -      +
    550B  ILE*     1.3    76.0    -      -       -      +
    552B  VAL*     1.3    62.9    +      -       -      +
    553B  TYR*     3.6    29.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 552 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    456B  TYR*     4.0     2.3    -      -       -      -
    457B  VAL*     2.8    33.7    +      -       +      +
    458B  GLY      3.1     9.7    +      -       -      +
    480B  VAL*     4.8     4.5    -      -       +      -
    498B  PHE*     4.0    20.9    -      -       +      -
    499B  ILE      3.3     7.0    -      -       -      +
    500B  VAL*     4.2    15.9    -      -       +      -
    550B  ILE*     4.6     2.5    -      -       +      -
    551B  ARG*     1.3    77.7    -      -       -      +
    553B  TYR*     1.3    73.9    +      -       -      +
    569B  PHE*     3.5    42.0    -      -       +      -
    572B  TRP*     4.1    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 553 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377B  LYS*     2.8    39.6    +      -       -      -
    378B  VAL*     6.2     0.4    -      -       +      -
    380B  ASN*     4.0     8.8    -      -       +      +
    381B  ILE*     3.3    41.7    -      -       +      -
    384B  THR*     6.2     0.2    -      -       +      -
    454B  PHE*     4.4     8.1    -      -       +      -
    455B  LYS      3.0    10.5    -      -       -      +
    456B  TYR*     3.8    30.3    -      +       +      -
    457B  VAL*     4.0     4.0    -      -       -      -
    498B  PHE*     3.6     4.9    -      -       -      -
    499B  ILE*     2.9    45.5    +      -       +      +
    501B  ASP*     4.1    15.5    +      -       +      -
    551B  ARG*     3.6    36.1    +      -       +      +
    552B  VAL*     1.3    81.4    -      -       -      +
    554B  CYS*     1.3    60.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 554 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454B  PHE*     3.8     2.6    -      -       -      -
    455B  LYS*     2.7    33.1    +      -       -      +
    457B  VAL*     4.0     6.1    -      -       +      -
    493B  LEU*     4.4    13.5    -      -       -      -
    497B  ASP*     3.5    11.2    -      -       -      -
    498B  PHE*     4.8     3.6    -      -       +      +
    553B  TYR*     1.3    73.7    -      -       -      +
    555B  LYS*     1.3    63.7    +      -       -      +
    556B  LYS*     3.4    36.9    +      -       -      +
    557B  VAL*     5.4     0.2    -      -       -      +
    561B  SER      4.6     4.0    -      -       -      -
    562B  LEU*     4.8     5.2    -      -       +      -
    565B  ALA*     3.9    31.0    -      -       +      -
----------------------------------------------------------
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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