Contacts of the strand formed by residues 528 - 535 (chain H) in PDB entry 1P8J


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 PHE 528 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263H  VAL*     3.8    31.2    -      -       +      -
    305H  CYS*     4.6     5.6    -      -       -      -
    491H  LEU      3.8    14.4    -      -       -      +
    492H  THR*     3.2     5.0    -      -       -      +
    493H  LEU*     2.9    55.3    +      -       +      +
    498H  ARG*     3.6    27.8    -      -       +      -
    501H  LEU*     4.7     5.4    -      -       +      -
    503H  ILE*     4.6     4.3    -      -       +      -
    516H  LEU*     3.5    32.5    -      -       +      -
    519H  ARG*     5.5     0.9    -      -       -      -
    526H  ASP      4.9     2.2    -      -       -      -
    527H  GLY*     1.3    77.9    -      -       -      -
    529H  ASN*     1.3    60.5    +      -       -      +
    530H  ASP      3.9     0.7    -      -       -      -
    531H  TRP*     4.0    16.8    -      +       +      -
    533H  PHE*     3.7    28.5    -      +       +      -
----------------------------------------------------------
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Residues in contact with ASN 529 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268E  ARG*     3.8    19.0    +      -       -      +
    492H  THR*     4.1    14.3    +      -       -      +
    526H  ASP      6.0     0.4    -      -       -      +
    528H  PHE*     1.3    73.5    -      -       -      +
    530H  ASP*     1.3    74.1    +      -       -      +
    531H  TRP*     3.2     6.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 530 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233E  ASP*     4.4     7.0    -      -       -      +
    267E  ALA*     5.9     0.5    -      -       -      +
    268E  ARG*     3.6    34.9    +      -       -      +
    269E  LEU*     5.5     0.5    -      -       -      +
    490H  ARG*     2.8    41.8    +      -       -      +
    491H  LEU      3.1     5.5    +      -       -      +
    492H  THR*     2.9    22.7    +      -       -      +
    529H  ASN*     1.3    77.4    -      -       -      +
    531H  TRP*     1.3    63.3    +      -       -      +
    532H  ALA*     3.5     2.4    +      -       -      +
    565H  LYS*     3.1    25.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 531 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268E  ARG*     6.1     3.8    -      -       -      -
    263H  VAL*     3.9    21.7    -      -       +      +
    264H  ASP*     3.5    31.0    -      -       -      -
    265H  GLY*     4.4     3.6    -      -       -      -
    304H  ASN      2.7    29.3    +      -       -      -
    305H  CYS*     3.7    17.3    -      -       -      +
    307H  GLY*     3.7    18.2    -      -       -      -
    310H  ASN*     4.3     9.9    -      -       -      +
    489H  ALA      3.3     0.5    -      -       -      +
    490H  ARG*     3.3     1.1    -      -       -      -
    491H  LEU      2.9    26.5    +      -       -      -
    528H  PHE*     4.0    28.4    -      +       +      -
    529H  ASN      3.2     6.0    -      -       -      +
    530H  ASP*     1.3    77.8    -      -       -      +
    532H  ALA*     1.3    60.6    +      -       -      +
    533H  PHE*     3.3    42.3    +      +       +      -
----------------------------------------------------------
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Residues in contact with ALA 532 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310H  ASN*     2.5    29.8    +      -       -      +
    488H  GLN*     3.6    33.0    +      -       +      +
    489H  ALA      3.9     4.3    -      -       -      -
    490H  ARG*     4.0    25.8    -      -       +      +
    530H  ASP      3.5     2.2    +      -       -      -
    531H  TRP*     1.3    77.3    -      -       -      +
    533H  PHE*     1.3    59.7    +      -       -      +
    534H  MET*     3.2     4.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 533 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304H  ASN*     3.9    13.7    -      -       +      +
    305H  CYS*     5.1     1.8    -      -       -      -
    310H  ASN*     3.9     4.0    -      -       -      +
    487H  VAL      3.8     0.3    -      -       -      +
    488H  GLN*     3.2     1.2    -      -       -      -
    489H  ALA*     2.7    47.8    +      -       -      +
    491H  LEU*     3.7    30.7    -      -       +      -
    503H  ILE*     4.3     6.3    -      -       +      -
    515H  LEU*     3.4    45.2    -      -       +      +
    516H  LEU*     4.0    20.6    -      -       +      -
    528H  PHE*     3.7    35.2    -      +       -      -
    531H  TRP*     3.5    36.1    -      +       +      -
    532H  ALA*     1.3    72.0    -      -       -      +
    534H  MET*     1.3    58.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 534 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304H  ASN*     3.3     6.3    +      -       -      +
    309H  THR      4.6     0.2    -      -       -      +
    310H  ASN*     3.1    41.8    +      -       -      +
    311H  SER      3.7    17.0    -      -       -      +
    312H  ILE*     4.0    16.6    -      -       +      -
    314H  THR      5.5     1.8    -      -       -      +
    334H  SER*     2.8    16.4    +      -       -      -
    335H  SER*     3.3    31.5    +      -       -      +
    486H  HIS*     4.1    17.3    -      -       +      -
    487H  VAL      3.2    14.4    -      -       -      +
    488H  GLN*     4.4     5.8    -      -       +      +
    515H  LEU*     4.8     1.1    -      -       -      -
    532H  ALA      3.2     4.0    +      -       -      +
    533H  PHE*     1.3    74.4    -      -       -      +
    535H  THR*     1.3    69.3    +      -       -      +
    536H  THR*     3.5    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 535 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334H  SER*     3.3    16.0    -      -       -      -
    485H  GLU      4.3     1.2    -      -       -      +
    486H  HIS*     4.1     1.9    -      -       -      -
    487H  VAL*     2.9    54.7    +      -       +      +
    505H  LEU*     4.5    10.5    -      -       +      -
    513H  SER*     2.8    33.8    +      -       -      +
    515H  LEU*     4.4     4.0    -      -       +      -
    534H  MET*     1.3    82.0    -      -       -      +
    536H  THR*     1.3    61.7    +      -       -      +
    537H  HIS*     3.1    12.6    +      -       -      +
    538H  SER*     4.9     7.8    +      -       -      +
    547H  TRP*     5.8     0.9    -      -       +      -
----------------------------------------------------------
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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