Contacts of the strand formed by residues 496 - 504 (chain B) in PDB entry 2P2J


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 TYR 496 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  PHE*     3.7    19.5    -      -       +      -
    413B  TRP*     5.6     0.7    -      +       -      -
    415B  GLN*     2.7    29.6    +      -       -      -
    417B  GLU*     3.2    32.6    -      -       +      +
    418B  THR*     4.3    13.4    -      -       +      +
    465B  VAL*     3.1     6.0    -      -       -      -
    466B  ILE*     2.7    64.9    +      -       +      +
    470B  TRP*     3.9     4.9    -      +       +      -
    473B  GLN*     3.7    20.0    -      -       -      +
    484B  PHE*     5.8     1.8    -      +       -      -
    488B  TYR*     3.7    31.5    -      +       +      -
    489B  PHE*     3.7    17.3    -      +       +      -
    495B  MET*     1.3    71.0    -      -       -      +
    497B  PHE*     1.3    63.9    +      -       -      +
    498B  SER*     3.9    12.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 497 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463B  ASN*     3.8    16.2    -      -       +      -
    464B  LEU      3.5    11.4    -      -       -      -
    465B  VAL*     3.9     4.0    -      -       +      -
    487B  THR      5.2     5.7    -      -       -      +
    488B  TYR*     2.9    43.9    +      -       -      +
    491B  THR*     4.1    24.5    -      -       +      -
    492B  PHE*     3.6    44.6    -      +       +      +
    495B  MET      3.4     2.0    +      -       -      +
    496B  TYR*     1.3    75.9    -      -       -      +
    498B  SER*     1.3    69.2    +      -       -      +
    499B  GLY*     3.6    20.3    +      -       -      -
    500B  ASP      4.0     5.8    -      -       -      -
    516B  VAL*     3.6    27.1    -      -       +      -
    517B  ASP*     5.7     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 498 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413B  TRP*     3.8    19.7    -      -       -      -
    415B  GLN*     2.5    46.4    +      -       -      -
    464B  LEU*     2.9    28.7    +      -       -      +
    466B  ILE*     5.7     1.1    -      -       -      -
    488B  TYR*     5.7     3.1    -      -       -      -
    496B  TYR*     3.9     8.6    +      -       -      -
    497B  PHE*     1.3    72.8    -      -       -      +
    499B  GLY*     1.3    56.8    +      -       -      +
    500B  ASP*     2.9    24.0    +      -       -      +
    515B  ARG*     3.3     9.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 499 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497B  PHE*     3.4    25.1    +      -       -      -
    498B  SER*     1.3    79.3    +      -       -      +
    500B  ASP*     1.3    51.5    +      -       -      +
    515B  ARG*     3.3    12.5    -      -       -      -
    516B  VAL*     2.8    35.3    +      -       -      +
    517B  ASP*     3.5    23.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 500 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413B  TRP*     3.1    23.7    +      -       -      -
    415B  GLN*     3.5     3.1    +      -       -      -
    463B  ASN*     3.8     3.5    -      -       -      -
    464B  LEU*     2.9    35.5    +      -       +      +
    497B  PHE*     4.0     3.5    -      -       -      -
    498B  SER*     2.9     9.3    +      -       -      +
    499B  GLY*     1.3    80.6    -      -       -      +
    501B  GLY*     1.3    64.3    +      -       -      +
    512B  ILE*     4.4     4.0    -      -       +      -
    514B  GLY*     3.2    13.8    -      -       -      +
    515B  ARG*     3.1    10.4    -      -       -      -
    516B  VAL*     4.0     4.5    -      -       -      -
    998B  PRX      2.5    47.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 501 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462B  GLY      3.4    10.8    -      -       -      -
    464B  LEU*     4.7     0.7    -      -       -      -
    500B  ASP*     1.3    75.4    -      -       -      +
    502B  ALA*     1.3    63.5    +      -       -      +
    512B  ILE*     3.9     5.2    -      -       -      +
    513B  THR*     3.0    29.7    +      -       -      -
    514B  GLY      2.8    13.9    +      -       -      +
    516B  VAL*     3.5    18.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 502 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448B  LEU*     3.8    19.2    -      -       +      +
    461B  GLU*     3.3     4.8    -      -       -      +
    462B  GLY      3.0    30.7    +      -       -      +
    464B  LEU*     4.5     9.9    -      -       +      -
    501B  GLY*     1.3    76.9    -      -       -      +
    503B  ARG*     1.3    64.2    +      -       -      +
    510B  TYR*     4.5     8.3    -      -       +      -
    511B  TRP      3.3    16.4    -      -       -      +
    512B  ILE*     4.0    14.8    -      -       +      -
    513B  THR*     4.0     6.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 503 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448B  LEU*     4.1     2.2    -      -       -      -
    460B  THR      3.3    12.6    -      -       -      +
    461B  GLU*     3.6    23.8    -      -       +      +
    502B  ALA*     1.3    75.7    -      -       -      +
    504B  ARG*     1.3    61.8    +      -       -      +
    505B  ASP*     3.9    17.4    -      -       -      +
    509B  TYR      3.7     0.9    -      -       -      +
    510B  TYR*     3.4     3.9    -      -       -      +
    511B  TRP*     2.8    86.5    +      -       +      +
    513B  THR*     5.0     7.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 504 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    446B  PRO      5.2     0.2    +      -       -      -
    447B  ALA*     4.6     3.0    -      -       -      +
    448B  LEU*     3.7    27.2    -      -       +      +
    456B  GLN      2.7    28.3    +      -       -      -
    457B  GLU*     3.6     1.4    -      -       -      +
    458B  GLY*     3.0    37.4    +      -       -      +
    459B  ALA*     3.3     4.2    -      -       -      +
    460B  THR*     2.8    32.2    +      -       -      +
    503B  ARG*     1.3    79.5    +      -       -      +
    505B  ASP*     1.3    64.7    +      -       -      +
    508B  GLY*     3.8    29.8    -      -       -      +
    509B  TYR      3.3     4.0    -      -       -      +
    510B  TYR*     3.1    43.3    +      -       +      +
----------------------------------------------------------
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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