Contacts of the strand formed by residues 463 - 476 (chain A) in PDB entry 4RYL


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 SER 463 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388A  SER*     3.7    15.5    -      -       -      -
    430A  ILE*     3.3    28.6    -      -       -      +
    461A  ARG*     2.9    21.0    +      -       -      -
    462A  THR*     1.3    77.3    -      -       -      +
    464A  MET*     1.3    60.6    +      -       -      +
    509A  SER*     3.6     4.4    -      -       -      -
    510A  VAL*     2.9    31.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 464 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388A  SER*     2.5    33.4    +      -       -      +
    390A  VAL*     3.8    28.0    -      -       +      -
    463A  SER*     1.3    73.2    -      -       -      +
    465A  CYS*     1.3    59.2    +      -       -      +
    466A  THR*     3.5     2.9    +      -       +      +
    507A  PRO*     3.6    25.6    -      -       +      +
    508A  PHE*     3.4    29.4    -      -       -      -
    509A  SER*     3.9    21.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 465 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    386A  ALA*     4.3    12.1    -      -       -      -
    387A  VAL      3.4     7.9    -      -       -      -
    430A  ILE*     4.0    12.0    -      -       +      +
    463A  SER      3.9     2.6    +      -       -      -
    464A  MET*     1.3    69.9    -      -       -      +
    466A  THR*     1.3    60.6    +      -       -      +
    467A  ALA      3.7    18.8    -      -       -      -
    468A  ILE*     4.2    12.3    -      -       -      -
    504A  LEU*     3.9    17.6    -      -       -      +
    507A  PRO*     3.1    24.8    -      -       -      +
    508A  PHE*     2.9    35.6    +      -       +      +
    510A  VAL*     4.4     6.5    -      -       +      -
    516A  LEU*     4.9     3.1    -      -       -      -
    538A  LEU*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 466 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387A  VAL      2.9     5.3    +      -       -      -
    389A  ASP      2.9    31.8    +      -       -      +
    390A  VAL*     4.0    14.8    -      -       +      +
    393A  HIS*     3.7    17.5    -      -       +      -
    464A  MET*     3.8    10.8    -      -       +      +
    465A  CYS*     1.3    77.5    -      -       -      +
    467A  ALA*     1.3    62.4    +      -       -      +
    504A  LEU*     3.0    27.3    +      -       -      +
    507A  PRO*     4.0    18.6    -      -       +      -
    601A  3ZG      2.6    33.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 467 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387A  VAL*     3.0    31.9    +      -       +      +
    465A  CYS*     3.7     2.7    -      -       -      -
    466A  THR*     1.3    80.8    +      -       -      +
    468A  ILE*     1.3    70.4    +      -       -      +
    501A  VAL*     3.8    16.4    -      -       +      -
    502A  PHE      3.4    14.6    -      -       -      +
    503A  LEU*     4.1     3.1    -      -       -      -
    504A  LEU*     3.9     6.4    -      -       -      +
    601A  3ZG      3.6    26.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 468 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384A  LEU*     4.1    31.0    -      -       +      -
    385A  VAL      3.6     6.1    -      -       -      +
    386A  ALA*     3.9    18.6    -      -       +      -
    387A  VAL*     4.3     0.9    -      -       -      -
    455A  PHE*     5.5     2.2    -      -       +      -
    457A  LEU*     3.9    15.5    -      -       +      -
    465A  CYS*     4.2     4.9    -      -       -      -
    467A  ALA*     1.3    84.1    -      -       -      +
    469A  ALA*     1.3    68.8    +      -       -      +
    501A  VAL*     3.7     0.6    -      -       -      -
    502A  PHE*     2.8    41.9    +      -       +      +
    504A  LEU*     4.5     3.6    -      -       +      -
    516A  LEU*     5.3     0.4    -      -       +      -
    536A  LEU*     3.9    26.5    -      -       +      -
    538A  LEU*     3.7    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 469 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384A  LEU*     3.2     8.3    -      -       -      +
    385A  VAL*     2.8    46.3    +      -       +      +
    387A  VAL*     3.8    11.3    -      -       +      +
    424A  LEU*     3.5    32.8    -      -       +      -
    468A  ILE*     1.3    76.2    -      -       -      +
    470A  GLY*     1.3    59.9    +      -       -      +
    471A  TYR*     5.8     0.4    -      -       +      -
    499A  GLN*     5.0     3.1    -      -       +      -
    500A  THR      3.2    10.1    -      -       -      +
    501A  VAL*     4.4     2.5    -      -       +      +
    502A  PHE*     4.8     0.4    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    351A  PHE*     3.8    23.5    -      -       -      -
    383A  SER      3.2    10.3    -      -       -      -
    384A  LEU*     4.0     2.2    -      -       -      -
    468A  ILE      4.3     0.2    +      -       -      -
    469A  ALA*     1.3    76.2    -      -       -      +
    471A  TYR*     1.3    66.0    +      -       -      +
    499A  GLN*     3.8     4.9    -      -       -      +
    500A  THR*     2.7    37.4    +      -       -      -
    502A  PHE*     4.4     2.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 471 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  PHE*     4.1     6.0    -      -       -      +
    382A  ILE*     3.4     8.3    -      -       -      +
    383A  SER*     2.9    51.0    +      -       -      +
    385A  VAL*     4.1    23.8    -      -       +      -
    429A  LEU*     5.9     0.2    -      -       +      -
    433A  PRO*     3.1    29.3    -      -       -      +
    469A  ALA*     5.8     0.4    -      -       +      -
    470A  GLY*     1.3    78.2    -      -       -      +
    472A  PHE*     1.3    68.9    +      -       -      +
    473A  ASP*     3.6    22.2    -      -       -      -
    487A  SER*     3.8     3.1    -      -       -      -
    488A  THR*     3.7    20.6    -      -       -      +
    489A  GLY*     3.4    23.1    -      -       -      -
    490A  PRO*     3.8    22.4    -      -       +      -
    498A  LYS      5.0     1.1    -      -       -      +
    499A  GLN*     4.3     4.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  MET*     4.0     7.9    -      -       +      -
    349A  GLY      3.4    19.7    -      -       -      -
    351A  PHE*     4.0     7.6    -      -       -      -
    352A  LEU*     3.2    45.5    -      -       +      -
    381A  THR      3.0    17.9    -      -       -      +
    382A  ILE*     4.3     2.0    -      -       +      +
    383A  SER*     4.9     0.4    -      -       -      +
    471A  TYR*     1.3    80.6    -      -       -      +
    473A  ASP*     1.3    69.2    +      -       -      +
    474A  ILE*     3.6    29.6    -      -       +      -
    486A  PHE*     4.7     0.7    -      +       -      -
    488A  THR*     2.8    44.0    +      -       +      +
    497A  TRP*     3.5    44.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with ASP 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380A  CYS*     3.3     5.2    -      -       -      -
    381A  THR*     2.9    46.3    +      -       -      +
    383A  SER*     5.1     3.1    +      -       -      -
    471A  TYR*     3.6    14.9    -      -       -      -
    472A  PHE*     1.3    82.3    -      -       -      +
    474A  ILE*     1.3    65.1    +      -       -      +
    475A  TYR*     3.8    22.3    +      -       +      +
    485A  VAL*     5.0     2.4    -      -       +      +
    486A  PHE      3.4     7.6    -      -       -      +
    487A  SER*     2.7    32.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  MET*     3.7    25.1    -      -       +      -
    352A  LEU*     4.0     1.6    -      -       +      -
    377A  PRO*     3.4    30.7    -      -       +      -
    379A  ILE      3.8     2.0    -      -       -      +
    380A  CYS*     3.9    17.0    -      -       -      -
    472A  PHE*     3.6    28.9    -      -       +      -
    473A  ASP*     1.3    78.3    -      -       -      +
    475A  TYR*     1.3    63.7    +      -       -      +
    476A  PHE*     4.0     6.8    -      -       +      -
    484A  VAL      4.0     0.3    -      -       -      +
    485A  VAL*     3.2     6.8    -      -       -      +
    486A  PHE*     2.8    74.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 475 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377A  PRO*     3.4     4.0    -      -       -      +
    378A  ASP*     3.2    23.7    +      -       -      +
    379A  ILE*     2.8    45.0    +      -       +      +
    380A  CYS      4.7     0.2    -      -       -      -
    381A  THR*     4.1    19.6    +      -       +      +
    473A  ASP*     3.8    32.3    +      -       +      -
    474A  ILE*     1.3    76.6    -      -       -      +
    476A  PHE*     1.3    66.0    +      -       -      +
    477A  GLU*     4.9    12.6    -      -       +      -
    484A  VAL      3.5     4.0    -      -       -      -
    485A  VAL*     3.6    29.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 476 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259A  SER*     4.5     9.6    -      -       -      -
    260A  TYR*     3.9    37.2    -      +       -      -
    263A  PHE*     3.3    53.2    -      +       +      -
    344A  ILE*     6.4     0.2    -      -       +      -
    376A  TYR*     3.9     3.1    -      -       +      -
    377A  PRO*     3.6    35.0    -      -       +      -
    378A  ASP*     3.3     5.2    -      -       -      -
    474A  ILE*     4.0    15.9    -      -       +      -
    475A  TYR*     1.3    74.3    -      -       -      +
    477A  GLU*     1.3    59.2    +      -       -      +
    480A  CYS*     3.9     3.7    -      -       -      -
    483A  ARG*     3.5    10.4    -      -       -      +
    484A  VAL*     2.8    54.0    +      -       +      +
    486A  PHE*     4.5    11.7    -      +       -      -
----------------------------------------------------------
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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