Contacts of the strand formed by residues 396 - 411 (chain F) in PDB entry 3CB4


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 ILE 396 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374F  VAL*     4.0     7.4    -      -       +      -
    375F  GLU      4.0     2.2    -      -       -      -
    376F  THR*     4.8     0.2    -      -       -      +
    377F  THR*     4.5     0.7    -      -       -      -
    390F  LEU*     3.9    22.7    -      -       +      -
    391F  PRO*     3.3    38.8    -      -       +      +
    392F  ALA      3.7     8.5    -      -       -      +
    393F  VAL*     3.3    25.7    +      -       +      +
    394F  ASN      4.6     3.4    -      -       -      +
    395F  ASN*     1.3    77.0    -      -       -      +
    397F  TYR*     1.3    63.1    +      -       -      +
    398F  GLU      3.7    26.5    -      -       -      +
    399F  LEU*     3.8    19.3    -      -       +      +
    480F  MET      6.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 397 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375F  GLU*     2.9    20.6    +      -       +      +
    376F  THR      3.4    15.5    -      -       -      +
    377F  THR*     3.8     9.8    -      -       -      +
    379F  ARG*     3.1    47.6    +      -       +      -
    395F  ASN      3.5     3.6    +      -       -      -
    396F  ILE*     1.3    75.5    -      -       -      +
    398F  GLU*     1.3    85.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 398 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373F  GLU      4.3     0.2    -      -       -      +
    374F  VAL*     3.8     1.6    -      -       -      -
    375F  GLU*     2.9    36.5    +      -       +      +
    396F  ILE*     3.7     4.5    -      -       -      +
    397F  TYR*     1.3   104.6    +      -       +      +
    399F  LEU*     1.3    62.3    +      -       -      +
    400F  ARG*     2.8    35.1    +      -       -      +
    477F  ALA*     3.6    29.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 399 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372F  TYR*     4.0    24.7    -      -       +      -
    373F  GLU      4.2     0.4    -      -       -      -
    374F  VAL*     3.6    26.2    -      -       +      -
    390F  LEU*     4.1    27.8    -      -       +      -
    396F  ILE*     3.8    19.3    -      -       +      +
    398F  GLU*     1.3    73.1    -      -       -      +
    400F  ARG*     1.3    63.3    +      -       -      +
    401F  GLU      4.0     0.9    +      -       -      -
    477F  ALA*     3.6     2.3    -      -       -      -
    478F  SER*     3.1    33.7    +      -       -      +
    480F  MET*     3.6    42.3    -      -       +      +
    498F  ILE*     4.8     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 400 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372F  TYR*     3.8     5.7    -      -       -      -
    373F  GLU*     2.7    93.4    +      -       +      +
    374F  VAL      5.2     0.2    -      -       -      -
    375F  GLU*     2.7    45.7    +      -       -      +
    381F  VAL*     4.7     7.3    -      -       -      +
    398F  GLU*     2.8    25.1    +      -       +      +
    399F  LEU*     1.3    72.8    -      -       -      +
    401F  GLU*     1.3    62.4    +      -       -      +
    475F  PHE*     3.6    17.0    -      -       +      -
    476F  GLN*     3.4    10.1    -      -       -      +
    477F  ALA*     3.3    28.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 401 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372F  TYR*     3.6    15.5    -      -       +      -
    399F  LEU      4.0     1.6    +      -       -      -
    400F  ARG*     1.3    72.7    -      -       -      +
    402F  PRO*     1.3    83.3    -      -       +      +
    403F  ILE*     3.5     9.8    +      -       +      +
    426F  ARG*     2.9    39.6    +      -       -      -
    446F  PRO*     3.3    14.8    -      -       +      +
    448F  ALA*     4.3     9.2    -      -       +      +
    475F  PHE*     4.0     1.3    -      -       -      -
    476F  GLN*     2.9    29.4    +      -       -      +
    478F  SER*     3.2    22.3    -      -       -      -
    480F  MET*     3.4    26.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 402 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370F  VAL*     3.7    26.9    -      -       +      -
    371F  VAL      3.4    24.5    -      -       -      +
    372F  TYR*     4.0     3.1    -      -       +      -
    401F  GLU*     1.3    89.2    -      -       +      +
    403F  ILE*     1.3    56.9    +      -       -      +
    446F  PRO*     3.6     4.3    -      -       -      +
    447F  MET*     2.8    43.4    +      -       +      -
    448F  ALA      5.3     0.2    -      -       -      +
    472F  PHE*     3.7    23.6    -      -       +      -
    474F  ARG      3.4     6.5    -      -       -      +
    475F  PHE*     3.7     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 403 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401F  GLU*     4.0    15.5    -      -       -      +
    402F  PRO*     1.3    79.9    -      -       -      +
    404F  ALA*     1.3    61.9    +      -       -      +
    444F  GLU*     3.7    43.7    -      -       +      +
    445F  ILE      3.9     2.0    -      -       -      +
    446F  PRO*     4.2    21.3    -      -       +      -
    447F  MET*     5.1     0.7    -      -       -      -
    472F  PHE*     3.9     3.4    -      -       -      -
    473F  LYS*     3.0    28.9    +      -       +      +
    474F  ARG*     2.7    36.2    +      -       +      +
    476F  GLN*     3.7    32.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 404 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402F  PRO      4.1     0.8    +      -       -      -
    403F  ILE*     1.3    74.1    -      -       -      +
    405F  GLU*     1.3    62.6    +      -       -      +
    406F  CYS*     3.6     6.7    +      -       -      -
    443F  TYR      3.5     0.9    -      -       -      +
    444F  GLU*     3.3     4.0    -      -       -      -
    445F  ILE      2.7    42.2    +      -       -      +
    447F  MET*     3.7    33.9    -      -       +      -
    450F  VAL*     4.1    12.1    -      -       +      -
    470F  TYR*     4.5     6.5    -      -       +      -
    471F  ASN      3.4     7.0    -      -       -      +
    473F  LYS*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 405 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    404F  ALA*     1.3    68.7    -      -       -      +
    406F  CYS*     1.3    61.6    +      -       -      +
    407F  HIS*     2.8    34.4    +      -       -      +
    430F  THR*     4.6     9.8    -      -       +      +
    442F  THR*     4.4    12.8    -      -       -      +
    443F  TYR      3.6     5.2    -      -       -      +
    444F  GLU*     4.2    11.8    -      -       +      +
    469F  ASP      3.5     2.9    -      -       -      +
    470F  TYR*     3.2     3.8    -      -       -      -
    471F  ASN*     2.9    43.5    +      -       -      +
    473F  LYS*     3.0    48.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 406 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    404F  ALA      3.8    13.7    -      -       -      -
    405F  GLU*     1.3    71.8    -      -       -      +
    407F  HIS*     1.3    62.9    +      -       -      +
    408F  MET*     3.8     9.6    +      -       +      +
    441F  LEU      3.5     2.4    -      -       -      +
    442F  THR*     3.3     3.3    -      -       -      -
    443F  TYR*     2.7    39.7    +      -       +      +
    445F  ILE*     3.8    32.5    -      -       +      -
    450F  VAL*     4.2    13.2    -      -       -      -
    454F  PHE*     5.1     1.1    -      -       +      -
    468F  LEU*     3.9    17.0    -      -       +      -
    469F  ASP      3.6     4.3    -      -       -      -
    470F  TYR*     3.8    16.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 407 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110F  ALA*     4.8     2.5    -      -       +      +
    114F  ALA*     5.8     1.4    -      -       +      +
    117F  TYR*     6.1    10.5    -      +       +      -
    405F  GLU*     2.8    37.6    +      -       +      -
    406F  CYS*     1.3    70.7    -      -       -      +
    408F  MET*     1.3    59.7    +      -       -      +
    409F  LEU*     5.2     5.8    -      -       +      -
    441F  LEU      3.6     3.6    -      -       -      -
    442F  THR*     4.0    22.4    -      -       +      -
    467F  SER      3.4     4.0    -      -       -      +
    468F  LEU*     3.8     0.3    -      -       -      -
    469F  ASP*     2.8    64.0    +      -       +      +
    471F  ASN*     3.7    16.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 408 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406F  CYS*     4.2    14.1    -      -       +      +
    407F  HIS*     1.3    79.6    -      -       -      +
    409F  LEU*     1.3    69.3    +      -       -      +
    410F  LEU*     3.9    11.7    -      -       +      -
    418F  VAL*     4.4     3.8    -      -       +      -
    422F  CYS*     3.6    31.2    -      -       -      -
    439F  VAL      3.7     0.2    -      -       -      +
    440F  ALA*     3.6     0.3    -      -       -      +
    441F  LEU*     2.7    66.5    +      -       +      +
    443F  TYR*     3.9    19.1    -      -       +      -
    454F  PHE*     4.8     6.7    -      -       -      -
    458F  LEU*     3.5    31.6    -      -       +      -
    466F  ALA*     5.6     0.2    -      -       +      -
    467F  SER      3.4     7.0    -      -       -      +
    468F  LEU*     4.5    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 409 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109F  GLU*     5.7     1.8    -      -       -      -
    110F  ALA*     4.1    10.3    -      -       +      +
    113F  LEU*     3.8    28.7    -      -       +      -
    117F  TYR*     5.8     0.2    -      -       -      +
    150F  ILE*     4.8    12.8    -      -       +      -
    407F  HIS*     5.2     3.8    -      -       +      -
    408F  MET*     1.3    82.1    -      -       -      +
    410F  LEU*     1.3    60.2    +      -       -      +
    435F  HIS*     4.7     7.6    -      -       -      +
    438F  GLN*     3.9    34.3    -      -       +      +
    439F  VAL      3.7     9.0    -      -       -      +
    440F  ALA*     4.2    18.2    -      -       +      -
    465F  TYR      3.2     4.6    -      -       -      +
    466F  ALA*     3.1     4.7    -      -       -      -
    467F  SER*     2.9    48.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 410 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    408F  MET*     3.9    20.4    -      -       +      +
    409F  LEU*     1.3    79.0    -      -       -      +
    411F  PRO*     1.4    74.2    -      -       +      +
    414F  TYR*     4.2     2.9    -      -       +      -
    415F  LEU*     3.5    43.7    -      -       +      +
    418F  VAL*     3.5    22.0    -      -       +      -
    438F  GLN*     3.6     8.3    +      -       -      -
    439F  VAL*     2.7    47.7    +      -       +      +
    441F  LEU*     3.7    22.7    -      -       +      -
    465F  TYR      3.8     0.7    -      -       -      -
    466F  ALA*     4.0    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 411 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    410F  LEU*     1.4    91.5    -      -       +      +
    412F  GLN*     1.3    66.7    +      -       -      +
    413F  ALA*     4.6     3.6    -      -       +      +
    414F  TYR*     3.1    43.8    +      -       +      +
    415F  LEU      3.9     3.8    +      -       -      -
    437F  ASN*     3.6    15.7    -      -       -      +
    438F  GLN*     4.3     6.9    -      -       +      +
    462F  SER*     6.0     0.2    -      -       -      -
    465F  TYR*     3.6    33.0    -      -       +      +
----------------------------------------------------------
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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