Contacts of the strand formed by residues 455 - 463 (chain A) in PDB entry 6BM4


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 MET 455 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443A  LEU*     3.5    39.4    -      -       +      +
    444A  PHE      3.2     4.3    -      -       -      -
    445A  ASN*     3.2    41.3    -      -       +      +
    449A  SER*     4.3    10.1    -      -       -      +
    451A  HIS      5.7     0.7    -      -       -      +
    452A  LYS*     2.9    21.0    +      -       -      +
    454A  SER*     1.3    76.5    -      -       -      +
    456A  MET*     1.3    62.1    +      -       -      +
    490A  HIS*     4.3    14.1    -      -       +      +
    505A  CYS*     4.7     8.3    -      -       -      +
    510A  GLN*     5.7     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 456 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443A  LEU*     3.5     5.6    -      -       -      -
    444A  PHE      2.9    28.0    +      -       -      -
    452A  LYS      4.3     0.2    -      -       -      +
    453A  MET*     3.6    27.8    -      -       -      +
    455A  MET*     1.3    80.3    -      -       -      +
    457A  ALA*     1.3    61.1    +      -       -      +
    458A  HIS*     3.1    11.1    -      -       -      -
    474A  VAL*     3.6    18.2    -      -       +      -
    477A  PRO*     3.9     5.6    -      -       +      -
    478A  TYR*     3.4    35.6    +      -       +      +
    505A  CYS      3.4     7.2    -      -       -      +
    507A  VAL*     3.8    13.5    -      -       +      -
    510A  GLN*     3.6    34.3    -      -       +      -
    521A  MET*     3.6    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 457 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362A  ASP*     4.6     2.3    -      -       -      +
    441A  PRO*     5.3     2.2    -      -       +      -
    442A  VAL      3.3    11.2    -      -       -      +
    443A  LEU*     4.5     1.1    -      -       -      -
    456A  MET*     1.3    70.5    -      -       -      +
    458A  HIS*     1.3    62.0    +      -       -      +
    501A  LEU*     3.2    46.7    -      -       +      +
    502A  SER*     5.0     1.3    -      -       -      -
    505A  CYS*     2.5    19.4    +      -       +      +
    506A  ALA*     3.7     5.1    -      -       +      +
    507A  VAL*     3.2    24.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 458 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361A  LEU      4.0     4.3    -      -       -      -
    362A  ASP      3.3     8.9    -      -       -      +
    363A  GLN      2.8    22.8    +      -       -      -
    364A  VAL*     3.5    23.1    -      -       +      +
    440A  ASP      3.2     3.3    -      -       -      +
    441A  PRO*     3.6     3.6    -      -       -      +
    442A  VAL*     2.9    35.1    +      -       +      +
    444A  PHE*     3.4    20.2    -      +       +      +
    456A  MET      3.1    25.6    -      -       -      -
    457A  ALA*     1.3    73.2    -      -       -      +
    459A  ARG*     1.3    61.5    +      -       -      +
    470A  LEU*     5.3     0.9    -      -       +      -
    474A  VAL*     3.9    23.8    -      -       +      -
    478A  TYR*     2.5    25.4    +      +       -      -
    507A  VAL*     3.3    23.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 459 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  GLU*     4.2    10.3    -      -       -      +
    362A  ASP*     2.7    54.7    +      -       -      +
    363A  GLN*     3.3    38.6    -      -       +      +
    364A  VAL*     2.9    24.1    +      -       -      -
    439A  ASN*     3.4    37.3    +      -       +      +
    440A  ASP      3.6     4.7    -      -       -      +
    441A  PRO*     5.9     1.1    -      -       +      -
    458A  HIS*     1.3    71.7    -      -       -      +
    460A  VAL*     1.3    62.9    +      -       -      +
    461A  LYS      3.5     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 460 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  GLN*     4.9     1.4    +      -       -      -
    364A  VAL*     4.0     5.6    -      -       -      -
    366A  VAL*     4.1    15.5    -      -       +      -
    436A  ILE*     3.6    24.5    -      -       +      -
    437A  MET      3.3    24.9    -      -       -      +
    438A  ASP*     3.2     4.7    -      -       -      +
    439A  ASN*     2.8    27.7    +      -       -      +
    440A  ASP*     3.0    26.5    +      -       +      +
    442A  VAL*     3.6    31.2    -      -       +      -
    459A  ARG*     1.3    72.1    -      -       -      +
    461A  LYS*     1.3    63.3    +      -       -      +
    462A  VAL*     4.0    16.2    -      -       +      +
    489A  LEU*     5.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 461 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  ASN*     4.2     9.1    +      -       -      +
    359A  LEU*     3.5    33.6    -      -       +      +
    363A  GLN*     3.9    27.5    +      -       +      +
    364A  VAL      3.0    17.7    +      -       -      +
    365A  GLY*     3.5     5.1    -      -       -      -
    366A  VAL      3.0    20.8    +      -       -      -
    438A  ASP*     3.4    10.5    -      -       -      +
    459A  ARG      3.5     0.4    +      -       -      -
    460A  VAL*     1.3    75.8    -      -       -      +
    462A  VAL*     1.3    66.4    +      -       -      +
    463A  ILE*     3.3    16.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 462 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366A  VAL*     3.3    12.1    -      -       +      +
    368A  LYS*     4.0    35.2    +      -       +      +
    371A  ALA*     3.8    13.7    -      -       +      -
    399A  HIS*     3.5    37.7    -      -       +      +
    436A  ILE      3.8     7.0    -      -       -      +
    437A  MET*     4.6     1.6    -      -       -      -
    438A  ASP*     3.0    17.5    +      -       -      +
    460A  VAL*     4.0    11.0    -      -       +      -
    461A  LYS*     1.3    74.0    -      -       -      +
    463A  ILE*     1.3    65.6    +      -       -      +
    464A  PRO*     4.8     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 463 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  ASP*     5.7     1.1    -      -       -      +
    359A  LEU*     5.2     5.4    -      -       +      -
    365A  GLY*     3.6     7.4    -      -       -      -
    366A  VAL      2.8    30.6    +      -       -      +
    367A  PRO*     3.3     1.9    -      -       +      +
    368A  LYS*     3.2    23.6    +      -       -      -
    461A  LYS*     3.5    28.0    -      -       +      +
    462A  VAL*     1.3    81.0    -      -       -      +
    464A  PRO*     1.3    95.9    -      -       +      +
    465A  TYR      4.3     0.4    -      -       -      +
    467A  THR*     3.6    24.2    -      -       -      +
    469A  ARG*     3.8    21.3    -      -       +      +
----------------------------------------------------------
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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