Contacts of the strand formed by residues 396 - 411 (chain C) 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 C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374C  VAL*     3.9    11.9    -      -       +      -
    375C  GLU      3.9     2.7    -      -       -      -
    377C  THR*     5.1     0.4    -      -       -      -
    390C  LEU*     4.0    24.2    -      -       +      -
    391C  PRO*     3.4    36.6    -      -       +      +
    392C  ALA      3.6    11.4    -      -       -      +
    393C  VAL*     3.2    21.6    +      -       +      +
    394C  ASN      4.8     2.4    -      -       -      +
    395C  ASN*     1.3    76.8    -      -       -      +
    397C  TYR*     1.3    63.0    +      -       -      +
    398C  GLU*     3.8    12.3    -      -       -      +
    399C  LEU*     3.7    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 397 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375C  GLU*     2.9    35.5    +      -       -      +
    376C  THR      3.8    12.8    -      -       -      +
    377C  THR*     4.1     8.6    -      -       -      +
    379C  ARG*     3.1    49.7    +      -       +      -
    395C  ASN      3.7     2.8    +      -       -      -
    396C  ILE*     1.3    74.2    -      -       -      +
    398C  GLU*     1.3    84.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 398 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373C  GLU      4.1     0.5    -      -       -      +
    375C  GLU*     3.0    31.0    +      -       +      +
    396C  ILE*     3.5     5.4    -      -       -      +
    397C  TYR*     1.3   106.0    +      -       +      +
    399C  LEU*     1.3    62.3    +      -       -      +
    400C  ARG*     2.7    36.4    +      -       +      +
    477C  ALA*     3.5    32.5    -      -       +      +
    478C  SER      5.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 399 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372C  TYR*     4.1    25.4    -      -       +      -
    373C  GLU      4.1     0.9    -      -       -      -
    374C  VAL*     3.7    25.8    -      -       +      +
    390C  LEU*     4.2    25.8    -      -       +      -
    396C  ILE*     3.7    22.2    -      -       +      +
    398C  GLU*     1.3    72.5    -      -       -      +
    400C  ARG*     1.3    65.9    +      -       -      +
    401C  GLU*     3.9     1.2    +      -       -      +
    477C  ALA*     4.5     0.7    -      -       -      -
    478C  SER*     3.2    33.2    +      -       -      +
    480C  MET*     3.4    41.5    -      -       +      +
    498C  ILE*     4.8     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 400 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372C  TYR*     3.8     8.3    -      -       -      +
    373C  GLU*     2.7    99.1    +      -       +      +
    375C  GLU*     2.6    49.6    +      -       -      +
    381C  VAL*     4.2    10.1    -      -       -      +
    398C  GLU*     2.7    26.7    +      -       -      +
    399C  LEU*     1.3    72.9    -      -       -      +
    401C  GLU*     1.3    60.0    +      -       -      +
    475C  PHE*     4.1    13.7    -      -       +      -
    476C  GLN*     3.2     4.5    -      -       -      -
    477C  ALA*     3.4    25.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 401 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372C  TYR*     3.9     9.9    -      -       +      -
    400C  ARG*     1.3    73.9    -      -       -      +
    402C  PRO*     1.4    82.7    -      -       +      +
    403C  ILE*     3.3    15.4    +      -       -      +
    426C  ARG*     2.5    36.4    +      -       -      -
    446C  PRO*     3.3    13.8    -      -       +      +
    447C  MET      5.0     0.9    -      -       -      +
    448C  ALA*     4.3     8.0    -      -       +      +
    475C  PHE*     3.8     3.1    -      -       -      -
    476C  GLN*     2.6    33.5    +      -       -      +
    478C  SER*     3.2    20.1    +      -       -      -
    480C  MET*     3.3    28.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 402 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370C  VAL*     3.7    20.6    -      -       +      -
    371C  VAL      3.2    28.0    -      -       -      +
    372C  TYR*     3.8    13.2    -      -       +      -
    401C  GLU*     1.4    92.1    -      -       +      +
    403C  ILE*     1.3    55.5    +      -       -      +
    446C  PRO      3.7     0.5    -      -       -      -
    447C  MET*     2.7    44.7    +      -       +      +
    472C  PHE*     4.1    15.3    -      -       +      -
    474C  ARG      3.6     6.5    -      -       -      +
    475C  PHE*     3.7    12.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 403 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401C  GLU*     3.7    32.5    -      -       -      +
    402C  PRO*     1.3    75.3    -      -       -      +
    404C  ALA*     1.3    63.0    +      -       -      +
    444C  GLU*     3.8    35.9    -      -       +      +
    445C  ILE      3.8     5.8    -      -       -      +
    446C  PRO*     3.9    15.9    -      -       +      -
    447C  MET*     4.9     0.7    -      -       -      -
    472C  PHE*     4.0     2.6    -      -       -      -
    473C  LYS*     3.1    27.7    +      -       +      +
    474C  ARG*     2.8    43.2    +      -       +      +
    476C  GLN*     3.7    17.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 404 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402C  PRO      4.0     1.8    +      -       -      -
    403C  ILE*     1.3    72.6    -      -       -      +
    405C  GLU*     1.3    60.5    +      -       -      +
    406C  CYS*     3.7     7.7    +      -       -      -
    443C  TYR      3.6     0.2    -      -       -      +
    444C  GLU*     3.4     4.0    -      -       -      -
    445C  ILE      2.7    42.3    +      -       -      +
    447C  MET*     3.7    34.5    -      -       +      +
    450C  VAL*     3.9    13.7    -      -       +      -
    470C  TYR*     4.4     7.0    -      -       +      -
    471C  ASN      3.7     7.4    -      -       -      +
    473C  LYS*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 405 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    403C  ILE      3.9     1.6    +      -       -      -
    404C  ALA*     1.3    70.7    -      -       -      +
    406C  CYS*     1.3    61.2    +      -       -      +
    407C  HIS*     3.2    30.5    +      -       +      -
    430C  THR*     4.6     7.8    -      -       +      +
    442C  THR*     4.0    17.1    +      -       -      +
    443C  TYR      3.6     4.9    -      -       -      +
    444C  GLU*     4.7    10.0    -      -       +      +
    469C  ASP      3.5     2.4    -      -       -      +
    470C  TYR*     3.3     2.4    -      -       -      -
    471C  ASN*     2.9    44.3    +      -       -      +
    473C  LYS*     3.6    50.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 406 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    404C  ALA*     3.9    16.8    -      -       -      -
    405C  GLU*     1.3    75.8    -      -       -      +
    407C  HIS*     1.3    62.4    +      -       -      +
    408C  MET*     4.0    11.3    +      -       +      +
    441C  LEU      3.9     0.2    -      -       -      +
    442C  THR*     3.1     7.2    +      -       -      -
    443C  TYR      2.8    41.4    +      -       -      +
    445C  ILE*     3.7    34.5    -      -       +      -
    450C  VAL*     4.3     6.7    -      -       -      -
    454C  PHE*     5.2     1.6    -      -       -      -
    468C  LEU*     4.4    11.9    -      -       +      -
    469C  ASP      3.4     6.1    -      -       -      +
    470C  TYR*     3.8    18.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 407 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110C  ALA*     4.4     4.8    -      -       +      +
    117C  TYR*     6.5     2.5    -      +       +      -
    405C  GLU*     3.2    40.7    +      -       +      -
    406C  CYS*     1.3    70.0    -      -       -      +
    408C  MET*     1.3    64.2    +      -       -      +
    409C  LEU*     5.2     5.6    -      -       +      -
    441C  LEU      3.5     4.5    -      -       -      +
    442C  THR*     4.1    18.6    -      -       +      -
    467C  SER      3.9     0.5    -      -       -      +
    468C  LEU      3.6     1.4    -      -       -      -
    469C  ASP*     2.7    63.4    +      -       +      +
    471C  ASN*     4.5     8.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 408 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406C  CYS*     4.1    17.5    -      -       +      +
    407C  HIS*     1.3    80.4    -      -       -      +
    409C  LEU*     1.3    66.3    -      -       -      +
    410C  LEU*     4.0     7.4    -      -       +      -
    418C  VAL*     3.9     7.2    -      -       +      -
    422C  CYS*     3.6    28.7    -      -       -      -
    439C  VAL      3.4     1.6    -      -       -      +
    440C  ALA*     3.5     3.1    -      -       -      -
    441C  LEU*     2.6    72.2    +      -       +      +
    443C  TYR*     4.4    12.1    -      -       +      +
    445C  ILE*     5.4     0.2    -      -       -      -
    454C  PHE*     4.9     2.5    -      -       -      -
    458C  LEU*     3.5    28.3    -      -       +      -
    466C  ALA*     5.9     2.5    -      -       +      -
    467C  SER      3.3     9.9    -      -       -      +
    468C  LEU*     4.6    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 409 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108C  VAL*     5.9     2.5    -      -       +      +
    109C  GLU*     5.7     1.6    -      -       -      -
    110C  ALA*     4.1     9.4    -      -       +      +
    113C  LEU*     3.7    30.1    -      -       +      -
    117C  TYR*     5.7     1.3    -      -       +      +
    150C  ILE*     4.3    20.0    -      -       +      -
    407C  HIS*     5.2     4.3    -      -       +      -
    408C  MET*     1.3    82.7    -      -       -      +
    410C  LEU*     1.3    62.7    +      -       -      +
    435C  HIS*     4.6     2.2    -      -       -      +
    438C  GLN*     4.3    19.5    -      -       +      -
    439C  VAL      3.5    15.9    -      -       -      +
    440C  ALA*     3.9    20.2    -      -       +      -
    465C  TYR      3.8     2.8    -      -       -      +
    466C  ALA*     3.5     2.1    -      -       -      -
    467C  SER*     3.1    42.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 410 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    408C  MET*     3.9    17.9    -      -       +      +
    409C  LEU*     1.3    79.4    -      -       -      +
    411C  PRO*     1.4    75.2    -      -       +      +
    414C  TYR*     4.2     4.5    -      -       +      -
    415C  LEU*     3.7    31.9    -      -       +      +
    418C  VAL*     3.7    34.8    -      -       +      -
    438C  GLN*     3.2     9.6    +      -       -      +
    439C  VAL*     2.8    48.8    +      -       +      +
    441C  LEU*     4.1    21.1    -      -       +      -
    465C  TYR      4.2     0.7    -      -       -      -
    466C  ALA*     3.9    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 411 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    410C  LEU*     1.4    97.0    -      -       +      +
    412C  GLN*     1.3    64.2    +      -       -      +
    413C  ALA*     3.2     7.4    +      -       +      +
    414C  TYR*     3.4    37.8    +      -       +      -
    415C  LEU*     3.8     7.8    +      -       -      +
    437C  ASN      3.6    14.8    -      -       -      +
    438C  GLN*     3.2     9.6    -      -       -      +
    439C  VAL*     4.9     0.6    -      -       -      +
    465C  TYR*     3.7    29.2    -      -       +      +
----------------------------------------------------------
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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