Contacts of the strand formed by residues 468 - 479 (chain A) in PDB entry 6PAU


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 GLY 468 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  TRP*     3.3     4.5    -      -       -      -
    298A  HIS*     2.8    37.6    +      -       -      +
    327A  TYR*     5.7     2.9    +      -       -      -
    466A  LYS      3.7     1.0    +      -       -      -
    467A  PHE*     1.3    75.2    -      -       -      +
    469A  ILE*     1.3    67.6    +      -       -      -
      8C  ILE*     4.7    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 469 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  ARG*     3.6    38.4    -      -       +      +
    297A  TRP*     3.4    37.5    -      -       +      -
    468A  GLY*     1.3    72.9    -      -       -      +
    470A  GLY*     1.3    65.1    +      -       -      +
      8C  ILE*     4.0     2.4    -      -       -      +
      9C  PHE*     3.1    39.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 470 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  ARG*     3.2    20.3    +      -       -      -
    296A  TYR      2.6    24.1    +      -       -      -
    298A  HIS*     3.4     7.9    -      -       -      -
    468A  GLY      3.5     1.4    +      -       -      -
    469A  ILE*     1.3    79.9    -      -       -      +
    471A  ASP*     1.3    60.8    +      -       -      -
    472A  GLY      3.4     2.5    -      -       -      -
      6C  SER*     3.3     7.9    -      -       -      -
      7C  LYS      3.1    11.9    -      -       -      -
      9C  PHE*     4.1     6.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 471 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  ASP*     4.1    16.9    +      -       -      +
    185A  ASP*     4.6     0.5    -      -       -      +
    295A  ARG*     3.7     9.1    +      -       -      +
    470A  GLY*     1.3    70.8    -      -       -      -
    472A  GLY*     1.3    59.3    +      -       -      +
    473A  ASN      4.3     0.2    +      -       -      -
      5C  LEU      4.6     1.9    -      -       -      +
      6C  SER*     3.4     4.0    +      -       -      -
      7C  LYS*     2.8    72.3    +      -       -      +
      9C  PHE*     4.2    26.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  ARG*     3.6     3.7    -      -       -      -
    296A  TYR*     3.2    26.8    +      -       -      +
    470A  GLY      3.4     0.8    -      -       -      -
    471A  ASP*     1.3    81.6    -      -       -      +
    473A  ASN*     1.3    67.5    +      -       -      +
      4C  VAL*     3.9    13.9    -      -       -      -
      6C  SER*     3.0    19.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284A  GLY*     3.9    10.1    -      -       -      +
    293A  THR*     4.2    12.1    -      -       +      +
    294A  CYS      3.4    10.7    -      -       -      +
    295A  ARG*     2.9    52.3    +      -       -      +
    471A  ASP      4.3     0.6    +      -       -      -
    472A  GLY*     1.3    73.0    -      -       -      -
    474A  LEU*     1.3    59.9    +      -       -      +
    475A  GLN*     3.7    18.9    +      -       -      +
      4C  VAL*     3.4    19.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  THR*     3.7    31.4    -      -       +      +
    283A  ALA      3.8     5.2    -      -       -      +
    292A  ALA      4.1     0.2    -      -       -      +
    293A  THR*     3.7     0.5    -      -       -      -
    294A  CYS*     2.9    38.1    +      -       +      +
    296A  TYR*     4.3    12.9    -      -       +      +
    453A  LEU*     4.1    21.3    -      -       +      -
    473A  ASN*     1.3    71.9    -      -       -      +
    475A  GLN*     1.3    62.9    +      -       -      +
    476A  TYR*     4.0    16.6    -      -       +      +
    495A  LEU*     5.8     2.7    -      -       +      +
    503A  GOL      3.4    34.1    -      -       -      +
      3C  LYS*     3.7    14.8    -      -       +      -
      4C  VAL*     3.6    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 475 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  THR*     3.1     8.5    -      -       -      -
    283A  ALA      2.9    40.8    +      -       -      +
    284A  GLY      3.1    26.3    +      -       -      -
    285A  VAL      3.4     9.7    +      -       -      -
    286A  VAL*     4.0    17.5    -      -       +      +
    290A  PRO*     4.0    12.8    -      -       +      -
    292A  ALA      3.4     2.9    -      -       -      -
    293A  THR*     3.4    35.8    +      -       -      +
    473A  ASN*     3.7    16.3    +      -       -      +
    474A  LEU*     1.3    73.0    -      -       -      +
    476A  TYR*     1.3    62.3    +      -       -      +
    477A  TYR*     3.3    29.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 476 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  VAL*     5.0     2.2    -      -       +      -
    281A  TYR      3.6     5.8    -      -       -      -
    282A  THR*     3.6    20.8    -      -       +      +
    290A  PRO*     3.3     7.4    -      -       -      +
    291A  ILE*     2.8    47.6    +      -       +      -
    292A  ALA*     2.9    13.7    +      -       +      +
    294A  CYS*     3.7    29.6    -      -       +      -
    362A  LEU*     4.0    17.5    -      -       +      -
    453A  LEU*     3.8     9.2    -      -       -      +
    455A  LEU*     3.5    10.2    -      -       -      +
    474A  LEU*     4.0    20.4    -      -       +      +
    475A  GLN*     1.3    77.9    -      -       -      +
    477A  TYR*     1.3    57.9    +      -       -      +
    491A  VAL*     4.0    11.4    -      -       +      -
    493A  LEU*     2.7    44.7    +      -       +      -
    494A  VAL*     4.1     5.2    -      -       -      -
    495A  LEU*     4.5     4.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 477 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  VAL*     3.3     8.6    -      -       -      +
    281A  TYR*     2.8    76.4    +      +       +      +
    283A  ALA*     3.8    18.4    -      -       +      -
    285A  VAL      2.8    10.0    +      -       -      -
    286A  VAL*     3.4     2.6    -      -       -      -
    287A  LEU*     2.7    52.2    +      -       +      -
    288A  PRO      3.9     5.8    -      -       -      -
    290A  PRO*     3.5    30.2    -      -       +      +
    291A  ILE*     4.5     2.2    -      -       -      -
    475A  GLN*     3.3    35.9    -      -       +      +
    476A  TYR*     1.3    73.7    -      -       -      +
    478A  LEU*     1.3    65.2    +      -       -      +
    504A  GOL      3.4     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 478 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  ILE*     3.6    39.3    -      -       +      -
    242A  MET*     4.3    13.5    -      -       +      -
    279A  ALA      3.3     8.7    -      -       -      +
    280A  VAL*     3.5    30.5    -      -       +      -
    281A  TYR*     4.9     1.8    +      -       -      -
    291A  ILE*     4.0    17.5    -      -       +      +
    362A  LEU*     4.3    11.4    -      -       +      -
    477A  TYR*     1.3    76.4    -      -       -      +
    479A  TYR*     1.3    60.3    +      -       -      +
    480A  ASN      4.0     1.6    +      -       -      -
    481A  TRP*     3.9    30.2    -      -       +      +
    483A  CYS*     4.1     4.3    -      -       -      -
    504A  GOL      3.0    30.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 479 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  ILE*     6.2     1.1    -      -       +      -
    268A  THR*     3.9    20.4    +      -       +      +
    272A  ASN*     5.7     0.4    -      -       -      -
    277A  PHE      4.4     1.3    -      -       -      -
    278A  GLN*     3.2     6.4    -      -       -      +
    279A  ALA*     2.8    41.1    +      -       +      +
    281A  TYR*     4.3    10.9    -      +       +      -
    477A  TYR      4.2     0.4    -      -       -      -
    478A  LEU*     1.3    70.5    -      -       -      +
    480A  ASN*     1.3    84.9    +      -       +      +
    481A  TRP*     3.3     2.2    +      -       -      +
   1000C  MYR      3.8    60.8    -      -       +      -
----------------------------------------------------------
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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