Contacts of the strand formed by residues 414 - 431 (chain A) in PDB entry 4ED3


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 GLU 414 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332A  ALA      3.7     9.9    -      -       -      +
    333A  THR*     4.6     9.1    -      -       -      +
    334A  ARG*     4.6     1.1    -      -       -      -
    407A  ASN*     2.7    28.2    +      -       -      -
    409A  SER*     3.3    18.1    +      -       -      +
    411A  ILE*     3.3    40.0    +      -       +      +
    412A  GLN      3.3     1.0    -      -       -      +
    413A  THR*     1.3   101.9    -      -       -      +
    415A  TRP*     1.3    54.9    +      -       -      +
    416A  SER*     6.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 415 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331A  LEU      4.2     4.9    -      -       -      +
    332A  ALA*     2.8    40.2    +      -       -      +
    333A  THR      4.1     8.3    -      -       -      +
    334A  ARG*     4.7     8.5    -      -       +      -
    337A  VAL*     4.0    19.7    -      -       +      -
    370A  ILE*     5.0     0.2    -      -       +      -
    372A  VAL*     5.6     0.4    -      -       -      +
    400A  PHE*     3.5    28.0    -      +       -      -
    403A  ILE*     3.7    39.7    -      -       +      -
    404A  LYS*     3.8    13.2    -      -       -      -
    406A  CYS*     4.3     8.2    +      -       +      +
    407A  ASN*     3.4    35.6    -      -       +      +
    413A  THR      4.0     0.4    +      -       -      -
    414A  GLU*     1.3    75.1    -      -       -      +
    416A  SER*     1.3    65.9    +      -       -      +
    417A  PRO*     3.1    24.6    +      -       -      +
    418A  PRO*     3.9     6.6    -      -       -      +
    419A  LEU*     3.2    38.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 416 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406A  CYS      3.8     0.3    -      -       -      +
    407A  ASN*     2.9     8.9    +      -       -      +
    408A  THR*     2.6    41.1    +      -       -      +
    409A  SER*     2.9    32.8    +      -       -      -
    414A  GLU*     6.0     0.7    -      -       -      -
    415A  TRP*     1.3    78.6    -      -       -      +
    417A  PRO*     1.3    68.4    -      -       -      +
    418A  PRO*     4.7     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 417 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372A  VAL*     3.8    29.8    -      -       +      -
    373A  GLN*     4.3    14.6    -      -       +      +
    406A  CYS      4.7     6.1    -      -       -      +
    408A  THR*     4.0    15.5    -      -       -      +
    415A  TRP*     3.1    15.8    +      -       -      +
    416A  SER*     1.3    90.1    -      -       -      +
    418A  PRO*     1.3    77.8    -      -       +      +
    419A  LEU*     4.0     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 418 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330A  ALA*     3.5    25.4    -      -       +      +
    331A  LEU      3.2    16.6    -      -       -      +
    332A  ALA*     4.4    13.9    -      -       +      -
    372A  VAL*     3.7     1.7    -      -       -      -
    373A  GLN*     3.0    44.3    +      -       +      +
    415A  TRP*     4.0     4.5    -      -       +      +
    416A  SER*     3.8     4.9    -      -       -      -
    417A  PRO*     1.3    91.1    -      -       +      +
    419A  LEU*     1.3    60.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 419 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325A  PHE*     3.7     5.1    -      -       -      +
    330A  ALA*     3.3     4.9    -      -       -      -
    331A  LEU*     3.0    37.3    +      -       +      +
    337A  VAL*     3.8    24.9    -      -       +      -
    370A  ILE*     3.9    20.4    -      -       +      -
    371A  ARG      3.5    14.4    -      -       -      +
    372A  VAL*     3.9    12.6    -      -       +      -
    403A  ILE*     4.3     5.4    -      -       +      -
    415A  TRP*     3.2    41.3    -      -       +      +
    417A  PRO      4.0     1.3    -      -       -      +
    418A  PRO*     1.3    70.8    -      -       -      +
    420A  THR*     1.3    61.8    +      -       -      +
    421A  MET      4.5     7.2    -      -       -      +
    422A  LEU*     3.9    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 420 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    324A  ASN*     3.3     6.2    -      -       -      +
    325A  PHE*     2.7    46.0    +      -       -      +
    326A  PRO*     5.0     5.1    -      -       +      +
    327A  GLY      5.2     0.7    -      -       -      +
    330A  ALA*     3.9     4.3    -      -       +      -
    371A  ARG*     3.0    39.8    +      -       -      +
    372A  VAL      3.8     4.3    +      -       -      -
    373A  GLN*     3.7    39.9    -      -       +      +
    418A  PRO      3.9     0.2    +      -       -      -
    419A  LEU*     1.3    76.1    -      -       -      +
    421A  MET*     1.3    60.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 421 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322A  SER*     5.2     4.0    -      -       -      -
    323A  LYS      3.4    10.1    -      -       -      +
    324A  ASN*     3.4    20.4    -      -       -      +
    325A  PHE*     4.1     2.0    -      -       -      -
    369A  SER*     3.6    16.4    -      -       -      +
    370A  ILE*     3.3    33.7    -      -       -      +
    371A  ARG*     3.3    30.8    +      -       +      +
    378A  LEU      3.6    19.7    -      -       -      +
    379A  SER*     4.3     2.9    -      -       -      -
    419A  LEU*     3.5     2.8    -      -       -      +
    420A  THR*     1.3    83.0    +      -       -      +
    422A  LEU*     1.3    89.0    +      -       -      +
    423A  PHE*     3.6    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 422 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322A  SER*     3.4     2.1    -      -       -      -
    323A  LYS      3.0    31.9    +      -       -      +
    325A  PHE*     3.8    13.2    -      -       +      -
    331A  LEU*     4.0    11.0    -      -       +      -
    337A  VAL*     4.2     3.6    -      -       +      +
    340A  TRP*     3.7    32.1    -      -       +      -
    341A  LEU*     3.9    33.2    -      -       +      +
    344A  LEU*     3.6    15.4    -      -       +      +
    368A  VAL*     6.3     0.2    -      -       +      -
    369A  SER      3.6     2.0    -      -       -      -
    370A  ILE*     3.8    19.3    -      -       +      -
    403A  ILE*     4.8     2.7    -      -       +      -
    419A  LEU*     3.9    20.9    -      -       +      -
    421A  MET*     1.3    85.9    -      -       -      +
    423A  PHE*     1.3    62.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 423 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320A  GLY*     4.1     5.6    -      -       -      -
    321A  CYS      3.1    26.9    -      -       -      -
    322A  SER*     3.3    16.8    -      -       -      -
    341A  LEU*     5.9     0.4    -      -       -      +
    344A  LEU*     4.5     0.2    -      -       -      -
    367A  VAL*     5.7     4.5    -      -       +      -
    368A  VAL*     3.5     7.0    -      -       -      +
    369A  SER*     2.9    50.6    +      -       -      +
    421A  MET*     3.6    16.6    -      -       +      -
    422A  LEU*     1.3    77.4    -      -       -      +
    424A  LEU*     1.3    77.6    +      -       -      +
    425A  CYS*     4.0    24.9    -      -       +      -
      6T    T      5.0    17.5    -      +       +      -
      7T    G      5.6    12.1    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 424 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320A  GLY*     3.3     1.4    -      -       -      -
    321A  CYS*     2.8    36.6    +      -       +      +
    341A  LEU*     3.9    16.2    -      -       +      +
    344A  LEU*     3.8    17.0    -      -       +      +
    345A  ALA*     3.6    38.8    -      -       +      +
    348A  LEU*     3.9    18.9    -      -       +      +
    366A  LEU*     4.5     9.2    -      -       +      -
    367A  VAL      3.5     2.2    -      -       -      +
    368A  VAL*     3.8    15.9    -      -       +      -
    395A  MET*     5.3     3.6    -      -       +      +
    396A  SER*     5.4     0.2    -      -       -      -
    399A  ALA*     3.7    29.4    -      -       +      -
    423A  PHE*     1.3    82.8    -      -       -      +
    425A  CYS*     1.3    61.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 425 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  THR*     3.6    32.3    -      -       -      -
    319A  ILE      3.6    10.3    -      -       -      -
    320A  GLY*     4.2     3.1    -      -       -      -
    365A  GLN      3.7     0.5    -      -       -      +
    366A  LEU*     3.5     7.5    -      -       -      +
    367A  VAL*     2.7    53.5    +      -       +      +
    423A  PHE*     4.0    24.5    -      -       +      -
    424A  LEU*     1.3    75.9    -      -       -      +
    426A  ALA*     1.3    61.9    +      -       -      +
    427A  THR*     3.7    10.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 426 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  THR*     3.4     3.8    -      -       -      -
    319A  ILE*     2.9    36.2    +      -       +      +
    348A  LEU*     4.3     5.2    -      -       +      +
    352A  LEU*     3.6    35.7    -      -       +      -
    363A  ALA*     3.7     6.5    -      -       +      -
    365A  GLN      3.4     5.4    -      -       -      -
    387A  LEU*     3.7    20.2    -      -       +      -
    425A  CYS*     1.3    69.6    -      -       -      +
    427A  THR*     1.3    66.7    +      -       -      +
    429A  PHE*     3.8     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 427 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  LYS      4.4     2.7    -      -       -      -
    318A  THR*     3.5    22.4    -      -       +      -
    363A  ALA*     3.7     2.1    -      -       -      +
    364A  THR      3.0    18.7    +      -       -      -
    365A  GLN*     2.9    44.5    +      -       -      +
    367A  VAL*     4.1    11.1    -      -       +      +
    425A  CYS*     3.7    17.7    -      -       -      +
    426A  ALA*     1.3    80.4    -      -       -      +
    428A  LYS*     1.3    69.9    +      -       -      +
    429A  PHE*     3.6     9.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 428 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  LYS      4.6     2.6    +      -       -      -
    364A  THR*     2.6    43.0    +      -       -      +
    365A  GLN*     3.2    38.3    +      -       +      +
    427A  THR*     1.3    87.1    -      -       -      +
    429A  PHE*     1.3    66.7    +      -       -      +
    430A  SER*     4.3     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 429 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  LYS*     3.3    33.2    -      -       -      -
    318A  THR*     4.1     2.2    -      -       -      -
    319A  ILE*     3.8    26.0    -      -       +      -
    352A  LEU*     4.3     6.3    -      -       +      -
    355A  ASP*     3.4    18.4    -      -       -      -
    361A  ARG*     3.6    39.0    -      -       +      +
    362A  VAL*     3.3     8.7    -      -       -      -
    363A  ALA*     3.5    33.7    -      -       +      -
    390A  TYR*     4.4     1.3    -      -       -      -
    426A  ALA      3.8    15.7    -      -       -      -
    427A  THR*     4.3     2.2    -      -       -      -
    428A  LYS*     1.3    79.8    -      -       -      +
    430A  SER*     1.3    61.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 430 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361A  ARG*     3.2     4.6    -      -       -      -
    362A  VAL*     2.8    39.2    +      -       -      +
    364A  THR*     3.9    18.3    +      -       -      +
    428A  LYS      4.3     0.5    +      -       -      -
    429A  PHE*     1.3    76.7    +      -       -      +
    431A  ALA*     1.3    69.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 431 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  ASP      3.7     9.0    -      -       -      +
    361A  ARG*     4.3     1.8    -      -       -      +
    362A  VAL*     4.6     1.7    -      -       -      +
    430A  SER*     1.3    81.6    -      -       -      +
    432A  SER*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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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