Contacts of the strand formed by residues 1047 - 1054 (chain C) 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 TYR1047 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    886A  TRP*     3.4    35.6    +      +       -      -
    887A  THR*     4.3    13.4    -      -       -      +
    890A  ALA*     3.8    22.2    -      -       +      -
    909C  ILE*     4.1    41.1    -      -       +      -
   1046C  GLY*     1.3    70.0    -      -       -      -
   1048C  HIS*     1.3    66.6    +      -       -      +
   1049C  LEU*     3.3     2.4    +      -       -      +
   1066C  THR*     3.2     2.7    -      -       -      -
   1067C  TYR*     2.9    56.9    +      +       -      +
   1069C  PRO*     4.3    14.8    -      -       +      -
   1108C  ASN*     4.2    19.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS1048 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    909C  ILE*     3.6     6.5    -      -       -      +
   1032C  CYS*     3.1    39.5    -      -       +      +
   1035C  GLY      4.3     2.0    -      -       -      -
   1036C  GLN*     3.5    23.7    +      -       -      +
   1037C  SER*     3.2    40.7    +      -       -      +
   1038C  LYS      6.0     0.2    -      -       -      -
   1039C  ARG      5.7     4.0    -      -       -      +
   1043C  CYS*     3.4    36.7    -      -       +      +
   1044C  GLY      5.7     0.2    -      -       -      +
   1046C  GLY      3.5     5.0    +      -       -      +
   1047C  TYR*     1.3    70.8    -      -       -      +
   1049C  LEU*     1.3    61.1    +      -       -      +
   1050C  MET*     3.5    14.2    +      -       -      -
   1051C  SER*     3.1    23.7    +      -       -      -
   1064C  HIS*     4.8     0.4    -      -       +      -
   1065C  VAL      4.4     2.5    -      -       -      -
   1066C  THR*     3.9     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1049 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    720C  ILE*     4.7     7.4    -      -       +      -
    902C  MET*     4.2    20.0    -      -       +      -
    905C  ARG*     2.8    46.3    +      -       +      +
    906C  PHE*     3.4    42.6    -      -       +      -
    909C  ILE*     3.6    33.0    -      -       +      -
   1036C  GLN*     4.0     4.0    -      -       -      +
   1047C  TYR      3.3     0.4    +      -       -      +
   1048C  HIS*     1.3    77.1    -      -       -      +
   1050C  MET*     1.3    62.4    +      -       +      +
   1065C  VAL*     3.0    15.7    +      -       +      +
   1066C  THR*     4.0     4.5    -      -       -      +
   1067C  TYR*     3.7    26.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET1050 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    881C  THR*     5.0     5.2    -      -       -      +
    898C  PHE*     3.7    28.5    -      -       +      -
    901C  GLN*     4.4    13.7    -      -       -      +
    902C  MET*     3.4    33.0    -      -       +      +
    905C  ARG*     3.8    14.8    -      -       -      +
    927C  PHE*     4.4     8.3    -      -       -      -
   1032C  CYS      4.5     0.2    -      -       -      -
   1048C  HIS*     3.5     8.4    +      -       -      -
   1049C  LEU*     1.3    81.1    -      -       -      +
   1051C  SER*     1.3    70.1    +      -       -      +
   1052C  PHE*     3.3    33.9    -      -       +      -
   1065C  VAL*     2.9    45.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER1051 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    881C  THR*     4.3     6.8    +      -       -      +
   1032C  CYS      3.6    18.8    +      -       -      -
   1033C  VAL*     3.8    28.5    +      -       -      +
   1048C  HIS*     3.1     6.0    +      -       -      -
   1050C  MET*     1.3    82.2    +      -       -      +
   1052C  PHE*     1.3    76.6    +      -       -      +
   1062C  PHE*     4.9     1.1    -      -       -      -
   1063C  LEU      3.1     9.4    -      -       -      -
   1064C  HIS*     2.4    40.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE1052 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    722C  VAL*     6.0     0.2    -      -       +      -
    802C  PHE*     3.5    16.8    -      +       -      -
    805C  ILE*     4.1    12.6    -      -       +      -
    878C  LEU*     3.2    30.3    -      -       +      -
    881C  THR*     3.8    10.3    -      -       +      -
    882C  ILE*     3.9    20.2    -      -       +      -
    927C  PHE*     4.1    12.6    -      +       -      -
   1050C  MET*     3.3    46.2    -      -       +      -
   1051C  SER*     1.3    81.2    -      -       -      +
   1053C  PRO*     1.3    69.0    -      -       -      +
   1054C  GLN*     5.4     0.9    -      -       -      +
   1062C  PHE*     3.6     4.9    -      -       -      -
   1063C  LEU*     3.0    53.8    +      -       +      +
   1065C  VAL*     4.1    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO1053 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    874C  THR*     4.1    19.6    -      -       +      +
    877C  LEU*     4.0    35.0    -      -       +      +
    878C  LEU*     4.8     3.3    -      -       -      +
    881C  THR*     5.6     0.2    -      -       +      -
   1029C  MET*     4.2    12.3    -      -       +      -
   1033C  VAL*     3.7    23.6    -      -       +      -
   1052C  PHE*     1.3    88.0    -      -       +      +
   1054C  GLN*     1.3    78.6    +      -       -      +
   1060C  VAL*     4.4     6.1    -      -       +      -
   1061C  VAL      3.7     4.3    -      -       -      +
   1062C  PHE*     4.1    19.5    -      -       +      -
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Residues in contact with GLN1054 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    805C  ILE*     3.4    26.7    +      -       -      +
    816C  SER*     3.1    19.9    +      -       -      -
    818C  ILE*     3.6    20.3    -      -       +      +
    819C  GLU*     3.1    21.9    +      -       +      +
    822C  LEU*     4.3    11.7    -      -       +      -
    874C  THR*     4.2     7.0    +      -       -      -
    878C  LEU*     3.9    11.1    -      -       -      +
   1052C  PHE*     5.4     0.4    -      -       -      +
   1053C  PRO*     1.3    91.3    +      -       -      +
   1055C  SER*     1.3    69.9    +      -       -      +
   1060C  VAL*     3.7     7.4    -      -       -      +
   1061C  VAL*     2.7    35.9    +      -       +      +
   1063C  LEU*     3.4    28.9    -      -       +      -
----------------------------------------------------------
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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