Contacts of the strand formed by residues 639 - 651 (chain C) in PDB entry 6DBT


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 639 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    621C  GLY*     3.6     1.4    -      -       -      -
    622C  MET*     2.8    41.8    +      -       +      +
    625C  VAL*     5.8     2.5    -      -       +      -
    637C  GLU      5.0     1.3    -      -       -      +
    638C  LYS*     1.3    79.3    -      -       -      +
    640C  VAL*     1.3    74.3    +      -       -      +
    679C  LEU*     6.3     1.1    -      -       +      -
    680C  MET      3.5    10.5    -      -       -      +
    681C  PHE*     4.5    10.3    -      -       +      -
    682C  VAL      3.2     4.6    +      -       -      +
    684C  GLU      5.5     0.5    +      -       -      -
    990C  PHE*     4.8    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 640 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    619C  CYS*     3.8    25.8    -      -       -      -
    620C  ASP      3.3    15.9    -      -       -      +
    621C  GLY*     4.5     3.1    -      -       -      -
    622C  MET*     4.7     1.1    -      -       -      +
    639C  ALA*     1.3    82.1    -      -       -      +
    641C  ARG*     1.3    66.1    +      -       -      +
    642C  PHE*     4.2     0.4    -      -       +      -
    678C  CYS      4.2     0.2    -      -       -      +
    679C  LEU*     3.8     9.0    -      -       -      +
    680C  MET*     3.3    51.0    +      -       +      +
    682C  VAL*     3.8    15.3    -      -       +      +
    683C  ASP      4.2     3.8    -      -       -      +
    684C  GLU*     4.2    21.8    -      -       +      +
    690C  LEU*     4.5    10.3    -      -       +      -
    694C  LEU*     6.3     0.2    -      -       +      -
    733C  MET*     5.9     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 641 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    618C  SER      3.6     2.8    -      -       -      +
    619C  CYS*     3.5     2.5    -      -       -      -
    620C  ASP*     3.0    33.2    +      -       -      +
    622C  MET*     3.0    23.2    -      -       +      +
    640C  VAL*     1.3    75.2    -      -       -      +
    642C  PHE*     1.3    67.5    +      -       -      +
    643C  SER*     4.6     2.5    -      -       -      -
    674C  CYS*     4.6     4.4    -      -       -      -
    676C  PRO*     4.2    20.0    -      -       +      -
    678C  CYS      3.9     4.5    -      -       -      +
    679C  LEU*     4.9    13.5    -      -       +      -
    983C  ASN*     2.4    47.0    +      -       -      +
    986C  GLY*     3.3     9.9    +      -       -      -
    987C  ASN*     2.6    48.3    +      -       -      +
    990C  PHE*     4.7     7.4    -      -       -      +
   1013C  HIS*     4.3    15.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 642 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578C  TYR*     4.2    12.6    -      +       -      -
    617C  GLU*     3.6    31.4    -      -       +      -
    618C  SER      3.5     5.2    -      -       -      -
    619C  CYS*     3.5    26.2    -      -       +      +
    640C  VAL*     4.2     1.5    -      -       +      +
    641C  ARG*     1.3    70.7    -      -       -      +
    643C  SER*     1.3    69.9    +      -       -      +
    644C  PHE*     5.4     0.9    -      -       +      -
    676C  PRO*     3.7     1.4    -      -       -      +
    677C  LEU*     2.9    39.1    +      -       +      -
    678C  CYS*     3.3    29.8    +      -       +      +
    680C  MET*     6.0     1.3    -      -       +      +
    694C  LEU*     4.3    29.6    -      -       +      -
    697C  VAL*     4.2    22.9    -      -       +      -
    701C  ARG*     5.1     4.5    -      -       +      -
    729C  TYR*     4.3    12.8    -      -       -      -
    807C  MET*     4.8     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 643 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    617C  GLU*     3.6     0.9    -      -       -      -
    618C  SER*     2.9    38.0    +      -       -      +
    641C  ARG*     4.6     3.8    -      -       -      -
    642C  PHE*     1.3    78.7    -      -       -      +
    644C  PHE*     1.3    61.5    +      -       -      +
    674C  CYS*     2.8    34.9    -      -       -      -
    675C  ARG      2.7    24.6    +      -       -      -
    676C  PRO*     3.6    10.5    -      -       -      -
    677C  LEU      4.3     0.7    -      -       -      +
    983C  ASN*     3.9    10.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 644 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578C  TYR*     4.8    11.2    -      +       -      +
    581C  ALA*     4.3    10.1    -      -       +      -
    582C  LEU*     4.2    31.4    -      -       +      -
    585C  ALA*     4.7     4.5    -      -       +      -
    615C  VAL*     4.2    12.8    -      -       +      -
    616C  LYS*     3.1    15.0    -      -       -      +
    617C  GLU*     4.0    14.6    -      -       -      +
    642C  PHE*     5.5     1.8    -      +       +      -
    643C  SER*     1.3    76.2    +      -       -      +
    645C  THR*     1.3    75.0    +      -       -      +
    646C  ILE*     4.1    25.1    -      -       +      -
    675C  ARG*     2.9    55.8    +      -       +      +
    677C  LEU*     3.5    37.7    -      -       +      -
   1014C  TRP*     5.0     2.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 645 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    615C  VAL*     3.7     1.6    -      -       -      -
    616C  LYS*     2.9    56.7    +      -       -      +
    644C  PHE*     1.3    85.4    +      -       -      +
    646C  ILE*     1.3    75.7    +      -       -      +
    647C  MET*     3.2     6.6    +      -       -      -
    665C  GLU*     5.4     1.1    -      -       +      -
    668C  PRO*     5.0     5.4    -      -       +      +
    673C  SER*     2.9    50.8    +      -       -      +
    674C  CYS*     3.2     8.8    -      -       -      +
    675C  ARG*     4.7     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 646 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    582C  LEU*     4.5    11.2    -      -       +      -
    585C  ALA*     4.5     9.2    -      -       +      -
    586C  LEU*     5.0     6.7    -      -       +      -
    589C  LEU*     4.4    24.7    -      -       +      -
    613C  VAL*     3.8    28.9    -      -       +      -
    614C  VAL      4.0     2.0    -      -       -      +
    615C  VAL*     3.7    22.7    -      -       +      -
    644C  PHE*     4.1    18.6    -      -       +      -
    645C  THR*     1.3    79.3    -      -       -      +
    647C  MET*     1.3    64.5    +      -       -      +
    648C  SER      4.5     5.4    -      -       -      +
    649C  ILE*     5.6     0.4    -      -       +      -
    663C  PHE*     4.5    12.5    -      -       +      -
    665C  GLU*     3.9    11.3    -      -       -      +
    673C  SER*     5.0     1.4    +      -       -      -
    675C  ARG*     4.4    20.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 647 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    614C  VAL*     3.0    19.1    +      -       +      +
    616C  LYS*     3.7    24.2    -      -       +      +
    645C  THR*     3.2     5.4    +      -       -      +
    646C  ILE*     1.3    74.5    -      -       -      +
    648C  SER*     1.3    66.5    +      -       -      +
    663C  PHE*     4.6     1.0    -      -       -      -
    664C  GLN*     4.0     5.3    -      -       +      +
    665C  GLU*     3.0    36.2    +      -       -      +
    668C  PRO*     3.6    32.8    -      -       +      -
    977C  ALA*     3.5    31.2    -      -       +      +
    978C  TRP*     3.6    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 648 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612C  THR      3.8     0.9    -      -       -      +
    613C  VAL*     3.4     2.9    -      -       -      +
    614C  VAL*     2.9    45.3    +      -       -      +
    646C  ILE*     3.7     5.1    -      -       -      -
    647C  MET*     1.3    84.8    -      -       -      +
    649C  ILE*     1.3    61.4    +      -       -      +
    650C  SER*     5.4     1.8    +      -       -      -
    661C  THR*     5.4     2.5    -      -       -      -
    663C  PHE*     3.2    13.9    -      -       -      -
    664C  GLN*     4.1    16.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 649 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586C  LEU*     5.9     1.1    -      -       +      -
    589C  LEU*     6.0     1.1    -      -       +      -
    593C  ILE*     4.3    17.0    -      -       +      -
    611C  PHE*     3.8    24.7    -      -       +      -
    612C  THR      3.3    32.8    -      -       -      +
    613C  VAL*     3.5    21.5    -      -       +      -
    646C  ILE*     5.6     1.1    -      -       +      -
    648C  SER*     1.3    75.2    -      -       -      +
    650C  SER*     1.3    73.7    +      -       -      +
    661C  THR*     4.0     1.1    -      -       -      -
    662C  ILE*     2.9    31.2    +      -       +      +
    663C  PHE*     2.9    50.7    +      -       +      +
    720C  PHE*     4.7     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 650 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611C  PHE*     4.0     1.2    -      -       -      -
    612C  THR*     3.3    28.2    +      -       -      -
    648C  SER*     4.3     2.2    -      -       -      -
    649C  ILE*     1.3    90.8    -      -       -      +
    651C  ILE*     1.3    74.9    +      -       -      +
    659C  GLY*     5.5     2.1    -      -       -      -
    660C  ILE      3.2    25.8    -      -       -      -
    661C  THR*     4.2     4.0    -      -       -      -
    662C  ILE*     3.8     5.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 651 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    597C  LEU*     4.7     5.8    -      -       +      -
    602C  LEU*     4.0    24.9    -      -       +      -
    606C  MET      6.1     0.2    -      -       -      +
    607C  CYS*     5.0     5.2    -      -       +      -
    610C  GLY      3.6     9.4    -      -       -      +
    611C  PHE*     3.6    37.9    -      -       +      -
    612C  THR*     5.7     0.7    -      -       -      -
    650C  SER*     1.3    86.9    +      -       -      +
    652C  ARG*     1.3    69.1    -      -       -      +
    653C  LEU*     4.4    15.7    -      -       +      +
    657C  ASP*     3.1    17.1    -      -       +      +
    659C  GLY*     5.5     0.2    -      -       -      -
    660C  ILE*     3.0    38.5    +      -       +      +
    662C  ILE*     3.6    19.1    -      -       +      -
----------------------------------------------------------
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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