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


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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    621A  GLY*     3.3     4.9    -      -       -      -
    622A  MET*     2.8    39.1    +      -       +      +
    625A  VAL*     4.7     3.8    -      -       +      -
    638A  LYS*     1.3    79.7    -      -       -      +
    640A  VAL*     1.3    68.7    +      -       -      +
    641A  ARG*     6.4     0.2    -      -       +      -
    679A  LEU*     6.3     0.7    -      -       +      -
    680A  MET      3.5     9.0    -      -       -      +
    681A  PHE*     4.2    11.7    -      -       +      -
    682A  VAL      3.5     5.4    -      -       -      -
    684A  GLU      5.5     0.9    +      -       -      -
    990A  PHE*     4.3    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 640 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    619A  CYS*     3.7    22.7    -      -       -      -
    620A  ASP      3.3    14.8    -      -       -      +
    621A  GLY*     4.5     1.8    -      -       -      -
    622A  MET*     4.7     0.4    -      -       -      +
    639A  ALA*     1.3    82.7    -      -       -      +
    641A  ARG*     1.3    67.0    +      -       -      +
    642A  PHE*     5.0     1.3    -      -       +      +
    678A  CYS      4.1     0.6    -      -       -      +
    679A  LEU*     3.6     6.2    -      -       -      +
    680A  MET*     2.9    59.6    +      -       +      +
    682A  VAL*     4.1    14.1    -      -       +      +
    683A  ASP      4.4     3.1    -      -       -      +
    684A  GLU*     4.4    22.0    -      -       +      +
    690A  LEU*     4.2    11.2    -      -       +      -
    694A  LEU*     5.4     0.4    -      -       +      -
    733A  MET*     6.3     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 641 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    618A  SER      3.8     2.4    -      -       -      +
    619A  CYS*     3.7     2.3    -      -       -      -
    620A  ASP      3.0    30.1    +      -       -      +
    622A  MET*     3.3    20.3    -      -       +      +
    640A  VAL*     1.3    77.4    -      -       -      +
    642A  PHE*     1.3    63.8    +      -       -      +
    643A  SER*     3.8     3.1    +      -       -      -
    674A  CYS*     5.5     2.2    +      -       -      -
    676A  PRO*     4.7     4.7    -      -       +      +
    678A  CYS      3.7     2.5    -      -       -      -
    679A  LEU*     4.2    29.8    -      -       +      -
    983A  ASN*     2.5    46.0    +      -       -      +
    986A  GLY*     3.8    12.8    -      -       -      -
    987A  ASN*     2.0    55.0    +      -       -      +
    990A  PHE*     4.3     5.7    -      -       -      +
   1013A  HIS*     4.5    22.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 642 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578A  TYR*     3.9    24.7    -      +       -      -
    617A  GLU*     3.6    33.0    -      -       +      -
    618A  SER      3.8     2.0    -      -       -      -
    619A  CYS*     3.4    33.0    -      -       +      +
    640A  VAL*     4.2     1.9    -      -       +      +
    641A  ARG*     1.3    71.2    -      -       -      +
    643A  SER*     1.3    63.4    +      -       -      +
    644A  PHE*     5.3     1.3    -      -       +      -
    676A  PRO*     3.7     2.1    -      -       -      +
    677A  LEU*     2.9    43.0    +      -       +      -
    678A  CYS*     3.0    29.7    +      -       +      +
    680A  MET*     6.3     0.4    -      -       +      +
    694A  LEU*     4.5    20.0    -      -       +      -
    697A  VAL*     4.1    14.4    -      -       +      -
    701A  ARG*     5.2     1.1    -      -       -      -
    729A  TYR*     4.3    11.0    -      -       -      -
    807A  MET*     4.6    12.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 643 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    616A  LYS      4.3     0.2    -      -       -      +
    617A  GLU      3.6     0.3    -      -       -      -
    618A  SER*     2.8    38.9    +      -       -      -
    641A  ARG*     4.7     3.6    -      -       -      -
    642A  PHE*     1.3    78.5    -      -       -      +
    644A  PHE*     1.3    60.7    +      -       -      +
    674A  CYS*     3.2    21.3    -      -       -      -
    675A  ARG      3.2    19.3    -      -       -      -
    676A  PRO*     3.9     4.3    -      -       -      -
    677A  LEU*     4.4     0.7    -      -       -      +
    983A  ASN*     2.3    35.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 644 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578A  TYR*     4.1    15.7    -      +       +      +
    581A  ALA*     4.2    13.7    -      -       +      -
    582A  LEU*     3.7    33.4    -      -       +      -
    585A  ALA*     4.5     8.5    -      -       +      -
    615A  VAL*     3.8    24.2    -      -       +      -
    616A  LYS      3.5     9.6    -      -       -      +
    617A  GLU*     4.0     5.4    -      -       +      +
    642A  PHE*     5.4     1.1    -      -       +      -
    643A  SER*     1.3    73.7    -      -       -      +
    645A  THR*     1.3    68.7    +      -       -      +
    646A  ILE*     3.6    26.0    -      -       +      -
    675A  ARG*     2.9    49.9    +      -       +      +
    677A  LEU*     3.6    39.0    -      -       +      +
   1014A  TRP*     4.8     2.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 645 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    615A  VAL*     3.7     1.4    -      -       -      -
    616A  LYS*     2.9    58.5    +      -       -      +
    644A  PHE*     1.3    84.7    +      -       -      +
    646A  ILE*     1.3    74.9    +      -       -      +
    647A  MET*     3.2     2.3    +      -       +      -
    665A  GLU*     5.4     5.4    -      -       +      -
    668A  PRO*     5.0     3.4    -      -       +      +
    673A  SER*     3.2    33.3    +      -       -      +
    674A  CYS*     3.2    25.3    -      -       -      -
    675A  ARG*     4.6     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 646 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    582A  LEU*     3.6    31.0    -      -       +      -
    585A  ALA*     4.5    17.9    -      -       +      +
    586A  LEU*     4.9    11.9    -      -       +      -
    589A  LEU*     4.6    23.8    -      -       +      -
    613A  VAL*     4.1    24.7    -      -       +      -
    614A  VAL      3.9     2.7    -      -       -      +
    615A  VAL*     4.3     7.0    -      -       +      -
    644A  PHE*     3.6    15.3    -      -       +      -
    645A  THR*     1.3    80.6    -      -       -      +
    647A  MET*     1.3    63.4    +      -       -      +
    648A  SER      4.8     7.0    -      -       -      +
    649A  ILE*     5.4     2.5    -      -       +      -
    663A  PHE*     4.5     8.4    -      -       +      -
    665A  GLU*     4.0    11.1    -      -       -      +
    673A  SER*     4.9     1.4    +      -       -      -
    675A  ARG*     4.9     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 647 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    614A  VAL*     2.9    29.2    +      -       +      +
    616A  LYS*     3.8    32.1    -      -       +      -
    645A  THR*     3.2     4.4    +      -       +      +
    646A  ILE*     1.3    74.3    -      -       -      +
    648A  SER*     1.3    71.0    +      -       -      +
    663A  PHE*     4.5     1.4    -      -       -      -
    664A  GLN*     5.1    13.2    -      -       +      +
    665A  GLU*     3.2    32.8    +      -       -      +
    668A  PRO*     3.6    32.1    -      -       +      -
    977A  ALA*     4.1    12.8    -      -       +      +
    978A  TRP*     4.3    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 648 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612A  THR      3.7     1.0    -      -       -      +
    613A  VAL*     3.7     0.4    -      -       -      -
    614A  VAL*     2.9    46.9    +      -       -      +
    646A  ILE*     3.8     3.1    -      -       -      -
    647A  MET*     1.3    90.8    -      -       -      +
    649A  ILE*     1.3    59.9    +      -       -      +
    650A  SER*     4.2     1.5    +      -       -      -
    661A  THR*     5.9     1.1    -      -       -      -
    663A  PHE*     3.4    12.1    -      -       -      -
    664A  GLN*     4.4    13.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 649 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586A  LEU*     6.1     2.7    -      -       +      -
    589A  LEU*     5.2     2.7    -      -       +      -
    593A  ILE*     4.8    13.0    -      -       +      -
    611A  PHE*     3.5    28.7    -      -       +      -
    612A  THR      3.2    21.1    -      -       -      +
    613A  VAL*     3.5    25.4    -      -       +      -
    646A  ILE*     5.4     3.4    -      -       +      -
    648A  SER*     1.3    73.2    -      -       -      +
    650A  SER*     1.3    73.7    +      -       -      +
    661A  THR*     4.0     1.0    -      -       -      -
    662A  ILE*     2.9    18.7    +      -       +      +
    663A  PHE*     2.9    66.1    +      -       +      +
    720A  PHE*     4.2     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 650 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611A  PHE*     3.7     1.7    -      -       -      -
    612A  THR*     2.9    49.6    +      -       -      +
    614A  VAL*     5.8     1.6    -      -       -      +
    648A  SER*     5.3     1.6    +      -       -      -
    649A  ILE*     1.3    79.4    -      -       -      +
    651A  ILE*     1.3    64.6    +      -       -      +
    659A  GLY*     5.3     3.7    -      -       -      -
    660A  ILE      3.1    29.4    -      -       -      -
    661A  THR*     4.3     3.1    -      -       -      -
    662A  ILE*     3.9     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 651 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    597A  LEU*     4.8     4.0    -      -       +      -
    602A  LEU*     4.2    23.8    -      -       +      -
    607A  CYS*     4.9     4.3    -      -       +      -
    610A  GLY*     3.1    18.8    -      -       -      +
    611A  PHE*     3.5    44.6    -      -       +      -
    612A  THR*     5.3     1.9    -      -       -      -
    650A  SER*     1.3    79.1    +      -       -      +
    652A  ARG*     1.3    59.9    +      -       -      +
    653A  LEU*     4.2    19.7    -      -       +      +
    657A  ASP*     2.9    14.4    -      -       +      +
    659A  GLY*     5.5     0.2    -      -       -      -
    660A  ILE*     3.1    42.4    +      -       +      +
    662A  ILE*     3.7    16.6    -      -       +      -
----------------------------------------------------------
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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