Contacts of the strand formed by residues 483 - 496 (chain B) in PDB entry 2PY5


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 TRP 483 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  PHE*     3.7    32.8    -      -       +      -
    249B  ASP      3.7     3.4    -      -       -      -
    250B  VAL*     3.5    34.0    -      -       +      +
    440B  THR*     3.5    22.3    +      -       +      +
    441B  THR*     3.8    15.7    -      -       -      -
    444B  ALA*     3.5    29.8    -      -       +      +
    458B  ASP      3.4    19.3    -      -       -      -
    460B  ILE*     3.8    31.9    -      -       +      -
    471B  ILE*     5.4     5.2    -      -       +      -
    474B  ILE*     2.8    43.4    +      -       +      +
    475B  VAL*     3.1    21.9    -      -       +      +
    476B  ASP      2.9    23.8    +      -       -      -
    481B  GLY      4.9     3.0    +      -       -      -
    482B  TYR*     1.3    73.4    -      -       -      +
    484B  ALA*     1.3    59.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 484 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  PHE*     3.1     6.5    -      -       -      -
    249B  ASP*     2.8    38.8    +      -       +      +
    251B  ASN*     3.4    21.5    -      -       -      +
    476B  ASP      3.4    13.4    +      -       -      +
    477B  PRO*     3.9    12.6    -      -       +      +
    482B  TYR      3.7     1.4    +      -       -      -
    483B  TRP*     1.3    73.7    -      -       -      +
    485B  HIS*     1.3    63.6    +      -       -      +
    486B  GLU*     3.1     5.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 485 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  MET*     3.3    31.5    -      -       +      +
    247B  VAL      3.6     5.8    -      -       -      -
    248B  PHE*     3.8    18.5    -      +       +      -
    465B  THR      4.9     2.5    -      -       -      -
    467B  ILE*     4.7    12.5    -      -       +      +
    475B  VAL*     4.4     8.8    -      -       +      +
    477B  PRO*     5.4     1.6    -      -       -      +
    483B  TRP      3.8     3.2    +      -       -      -
    484B  ALA*     1.3    71.0    -      -       -      +
    486B  GLU*     1.3    59.7    +      -       -      +
    487B  SER      3.1    18.9    +      -       -      -
    488B  THR*     2.9    21.0    +      -       -      -
    517B  SER*     6.1     0.7    -      -       -      -
   9003B  EDO      3.2    43.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 486 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247B  VAL*     2.9    23.9    +      -       +      +
    249B  ASP*     2.9    47.1    -      -       +      +
    484B  ALA*     3.1    10.1    +      -       +      +
    485B  HIS*     1.3    73.7    -      -       -      +
    487B  SER*     1.3    68.1    +      -       -      +
    515B  GLU*     3.5    21.8    -      -       -      +
   9003B  EDO      3.7     6.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 487 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  MET*     3.4     0.7    -      -       -      -
    247B  VAL*     2.9    45.4    +      -       -      +
    485B  HIS*     3.1    12.5    +      -       -      -
    486B  GLU*     1.3    86.6    +      -       -      +
    488B  THR*     1.3    63.6    +      -       -      +
    489B  PHE*     5.5     0.9    -      -       -      -
    502B  GLN*     4.7     1.6    +      -       -      -
    504B  ILE*     4.0    31.3    -      -       -      +
    515B  GLU*     4.2     7.9    -      -       -      -
   9003B  EDO      3.8     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 488 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  GLY      3.2    17.3    -      -       -      +
    246B  MET*     4.2     1.7    -      -       +      +
    465B  THR*     3.5    31.0    +      -       +      +
    485B  HIS*     2.9    17.5    +      -       -      -
    487B  SER*     1.3    72.1    -      -       -      +
    489B  PHE*     1.3    61.2    +      -       -      +
    504B  ILE*     3.5     7.9    -      -       -      +
    505B  TYR*     3.0    39.9    +      -       +      +
    515B  GLU*     5.6     0.2    -      -       -      +
    516B  GLY      4.0     8.7    +      -       -      -
    517B  SER*     4.8     1.4    -      -       -      -
    518B  PRO*     3.8     9.1    -      -       +      +
   9003B  EDO      2.7    26.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 489 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242B  ILE*     4.1     5.2    -      -       +      -
    243B  GLY      3.3    22.0    -      -       -      -
    244B  GLU*     3.2     7.2    -      -       -      +
    245B  GLY*     2.8    52.9    +      -       -      +
    246B  MET*     3.7    19.3    -      -       -      -
    247B  VAL*     4.3     7.6    -      -       +      -
    453B  ILE*     3.9    22.4    -      -       +      -
    461B  HIS*     5.1     0.2    -      -       +      -
    487B  SER*     5.5     0.9    -      -       -      -
    488B  THR*     1.3    76.4    -      -       -      +
    490B  LYS*     1.3    59.0    +      -       -      +
    491B  ARG      3.7    13.9    -      -       -      +
    492B  ALA*     3.6    13.5    -      -       +      -
    494B  TYR*     3.7     8.3    -      -       -      -
    502B  GLN*     3.5    37.9    -      -       +      -
    503B  ASP      3.2    18.6    -      -       -      +
    504B  ILE*     4.1     4.7    -      -       +      +
    505B  TYR*     3.7     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 490 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243B  GLY*     3.1    19.5    -      -       -      -
    244B  GLU*     3.2     6.9    +      -       +      +
    489B  PHE*     1.3    72.8    -      -       -      +
    491B  ARG*     1.3    66.6    +      -       +      +
    503B  ASP*     2.7    23.0    +      -       +      +
    505B  TYR*     3.6    35.2    -      -       +      +
    521B  TYR*     4.5     9.8    +      -       -      +
    524B  ILE*     3.6    32.2    -      -       +      +
   8007B  EDO      4.7     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 491 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  GLU*     5.5     0.4    -      -       -      -
    242B  ILE      3.1    15.7    -      -       -      +
    243B  GLY      3.3     3.8    -      -       -      -
    489B  PHE*     3.6     6.5    -      -       -      -
    490B  LYS*     1.3    86.8    -      -       +      +
    492B  ALA*     1.3    65.5    +      -       -      +
    502B  GLN*     3.6     0.9    -      -       -      -
    503B  ASP*     2.9    54.4    +      -       +      +
    543B  PHE*     3.6    46.7    -      -       +      +
    544B  GLU*     5.4     2.2    +      -       -      -
   8007B  EDO      3.3    35.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 492 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  GLU*     3.8     4.9    -      -       -      +
    242B  ILE*     2.9    34.6    +      -       +      +
    489B  PHE*     3.6    23.3    -      -       +      -
    491B  ARG*     1.3    77.4    -      -       -      +
    493B  LYS*     1.3    64.8    +      -       -      +
    494B  TYR*     3.6    19.3    -      -       +      -
    501B  ILE      3.2    15.5    -      -       -      +
    502B  GLN*     4.0     5.8    -      -       +      -
    543B  PHE*     3.8     7.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 493 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239B  GLU      4.5     8.1    -      -       -      +
    240B  LYS      3.6    22.2    -      -       -      +
    241B  GLU*     3.4    29.9    +      -       -      +
    492B  ALA*     1.3    75.3    -      -       -      +
    494B  TYR*     1.3    62.4    +      -       -      +
    495B  LEU*     3.8    18.6    -      -       +      -
    500B  TYR*     3.2     3.8    -      -       -      -
    501B  ILE*     2.9    43.9    +      -       +      +
    543B  PHE*     2.7    27.8    +      -       -      -
    544B  GLU      4.8     2.6    +      -       -      -
    546B  PHE*     2.6    38.1    +      -       +      +
    547B  LYS*     4.9     5.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 494 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233B  LEU*     3.5    23.6    -      -       +      -
    237B  PHE      3.6     6.3    +      -       -      +
    238B  LYS*     3.9     1.2    -      -       -      -
    239B  GLU*     2.7    32.1    +      -       -      -
    240B  LYS      4.3     3.4    +      -       -      -
    242B  ILE*     3.7    20.2    -      -       +      -
    453B  ILE*     3.8    17.9    -      -       +      -
    454B  TYR*     3.8    30.1    -      +       +      -
    461B  HIS*     2.7    38.4    +      -       +      +
    489B  PHE*     3.7     5.7    -      -       -      -
    492B  ALA*     3.6    21.1    -      -       +      -
    493B  LYS*     1.3    76.0    -      -       -      +
    495B  LEU*     1.3    56.5    +      -       -      +
    496B  ARG      5.1     1.6    -      -       -      +
    499B  THR      3.8     3.8    -      -       -      +
    500B  TYR*     3.4    29.8    -      +       +      -
    502B  GLN*     2.9    16.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 495 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233B  LEU*     3.8     2.5    -      -       -      -
    238B  LYS*     3.4    11.4    -      -       -      +
    239B  GLU*     4.0    21.3    -      -       +      +
    493B  LYS*     3.8    27.1    -      -       +      -
    494B  TYR*     1.3    75.9    -      -       -      +
    496B  ARG*     1.3    90.9    +      -       +      +
    499B  THR*     2.9    15.1    +      -       +      +
    546B  PHE*     3.5    35.0    -      -       +      -
    547B  LYS*     3.6    37.9    -      -       -      +
    548B  VAL*     3.9     8.7    -      -       +      +
    574B  ILE*     3.9    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 496 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233B  LEU*     3.7    15.7    -      -       -      +
    238B  LYS*     3.5    22.6    -      -       -      +
    239B  GLU*     2.9    25.7    +      -       -      -
    454B  TYR*     4.6     3.1    -      -       -      -
    494B  TYR*     5.0     2.1    -      -       -      +
    495B  LEU*     1.3    97.5    +      -       +      +
    497B  GLN*     1.3    73.5    +      -       -      +
    498B  LYS      3.3     0.9    +      -       -      -
    499B  THR*     3.0    27.2    +      -       -      +
    500B  TYR*     5.3     0.5    -      -       -      +
    548B  VAL*     3.4    21.2    -      -       -      +
    574B  ILE*     4.9     6.1    -      -       +      -
    575B  LYS*     3.0    40.4    +      -       -      +
   8002B  EDO      3.9    21.3    -      -       -      -
----------------------------------------------------------
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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