Contacts of the strand formed by residues 47 - 55 (chain B) in PDB entry 6VSB


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 VAL 47 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    568A  ASP*     4.5    19.5    -      -       -      +
    569A  ILE*     5.2    10.8    -      -       +      -
     44B  ARG*     3.6    37.7    -      -       +      -
     45B  SER      3.7    11.7    -      -       -      +
     46B  SER*     1.3    79.6    -      -       -      +
     48B  LEU*     1.3    78.3    +      -       -      +
     49B  HIS*     3.8     2.5    +      -       +      -
    277B  LEU      4.0     0.2    -      -       -      +
    279B  TYR*     3.4    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  SER      5.8     0.7    -      -       -      -
     47B  VAL*     1.3    85.6    -      -       -      +
     49B  HIS*     1.3    60.7    +      -       -      +
     50B  SER      4.1     1.0    +      -       -      -
    276B  LEU*     3.9    16.9    -      -       +      +
    277B  LEU      3.6     2.5    -      -       -      -
    278B  LYS*     3.5    38.8    -      -       +      -
    304B  LYS*     3.4    38.1    -      -       +      +
    305B  SER*     3.6    17.3    -      -       -      +
    306B  PHE*     3.7    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  PRO*     6.0     1.6    -      -       +      -
     44B  ARG*     3.5    55.6    +      -       -      +
     47B  VAL*     3.8     2.9    +      -       +      -
     48B  LEU*     1.3    73.6    -      -       -      +
     50B  SER*     1.3    65.1    +      -       -      +
     51B  THR*     3.8    30.9    +      -       +      -
    275B  PHE      3.9     0.5    -      -       -      +
    276B  LEU*     3.7     2.0    -      -       -      -
    277B  LEU*     2.7    42.7    +      -       +      +
    279B  TYR*     4.2     8.7    -      +       +      -
    964B  LYS*     5.5     9.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  LEU      4.1     0.6    +      -       -      -
     49B  HIS*     1.3    82.9    +      -       -      +
     51B  THR*     1.3    60.8    +      -       -      +
    274B  THR*     4.9     9.9    -      -       -      +
    275B  PHE      3.2    10.1    -      -       -      -
    276B  LEU*     3.6    21.0    -      -       -      +
    291B  CYS*     5.5     2.2    -      -       -      -
    301B  CYS*     5.1     6.2    +      -       -      -
    304B  LYS*     3.4    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  PRO*     4.1    20.1    -      -       +      +
     40B  ASP*     5.4     3.1    +      -       -      -
     49B  HIS*     3.8    20.7    +      -       +      -
     50B  SER*     1.3    75.1    -      -       -      +
     52B  GLN*     1.3    74.7    +      -       -      +
     53B  ASP*     5.5     0.2    -      -       -      +
     55B  PHE*     4.6     9.9    -      -       +      -
    274B  THR*     3.2     8.9    -      -       -      +
    275B  PHE      2.9    29.8    +      -       -      +
    277B  LEU*     4.1    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  THR*     1.3    86.4    +      -       -      +
     53B  ASP*     1.3    67.4    +      -       -      +
     55B  PHE*     4.4     0.7    -      -       -      -
    272B  PRO*     3.9    23.6    +      -       +      +
    273B  ARG      3.9     5.6    -      -       -      -
    274B  THR*     3.3    29.8    +      -       +      +
    754C  LEU*     5.4     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  TYR*     2.5    28.0    +      -       -      -
     39B  PRO*     4.5    13.6    -      -       +      +
     51B  THR*     5.4     0.9    -      -       +      -
     52B  GLN*     1.3    80.1    -      -       -      +
     54B  LEU*     1.3    84.0    +      -       -      +
     55B  PHE*     3.1    23.2    +      -       +      -
    204B  TYR*     5.6     0.2    +      -       -      -
    271B  GLN      3.9     0.2    -      -       -      -
    272B  PRO*     4.1     4.0    -      -       -      -
    273B  ARG      2.8    36.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  TYR*     2.9    19.3    +      -       -      +
     53B  ASP*     1.3    84.0    +      -       -      +
     55B  PHE*     1.3    58.9    +      -       -      +
     88B  ASP*     4.2    31.0    -      -       +      +
    195B  LYS*     5.4     7.9    -      -       +      -
    196B  ASN      4.8    13.2    -      -       -      +
    270B  LEU*     3.3    33.8    -      -       +      +
    271B  GLN*     3.2     7.6    -      -       -      +
    272B  PRO*     3.7    34.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  GLY      4.0     8.3    -      -       -      +
     36B  VAL*     4.5     8.1    -      -       +      -
     37B  TYR*     3.6    53.4    -      +       -      -
     39B  PRO*     4.5     9.9    -      -       +      -
     51B  THR*     4.6    12.1    -      -       +      -
     52B  GLN*     4.4     2.0    -      -       -      -
     53B  ASP*     3.1    53.3    +      -       +      +
     54B  LEU*     1.3    73.3    -      -       -      +
     56B  LEU*     1.3    62.4    +      -       -      +
     57B  PRO*     3.4     4.3    -      -       -      +
    270B  LEU*     4.1     2.9    -      -       -      -
    271B  GLN*     2.8    30.8    +      -       -      +
    273B  ARG*     3.4    12.8    -      -       +      +
    275B  PHE*     4.0    37.2    -      +       +      -
    277B  LEU*     4.7    11.0    -      -       +      -
----------------------------------------------------------
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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