Contacts of the strand formed by residues 510 - 515 (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 510 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    423B  ILE*     4.0    30.5    -      -       +      -
    436B  SER*     2.8    21.7    +      -       -      -
    437B  ALA      3.3    13.7    +      -       -      -
    438B  THR      2.7    23.3    +      -       -      +
    440B  PRO*     4.4    10.3    -      -       +      -
    446B  PRO*     3.7    44.1    +      -       +      +
    447B  ALA      5.2     0.2    -      -       -      -
    448B  LEU*     4.0    30.3    -      -       +      -
    464B  LEU*     4.6     2.7    -      -       +      -
    502B  ALA*     4.5    10.1    -      -       +      -
    503B  ARG      3.4    11.0    -      -       -      -
    504B  ARG*     3.1    32.4    +      -       +      -
    508B  GLY      3.7    13.9    -      -       -      -
    509B  TYR*     1.3    73.3    -      -       -      +
    511B  TRP*     1.3    59.5    +      -       -      +
    512B  ILE*     4.0     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 511 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    392B  PRO*     5.3     4.7    -      -       +      -
    433B  LYS*     3.8    31.6    -      -       +      -
    434B  ALA      3.3    26.5    -      -       -      -
    435B  GLY*     3.6    21.1    -      -       -      +
    436B  SER*     3.6    22.0    +      -       -      -
    502B  ALA*     3.3     2.8    -      -       -      -
    503B  ARG*     2.8    82.3    +      -       +      +
    505B  ASP*     3.1    23.0    +      -       +      -
    509B  TYR      3.6    10.5    +      -       -      -
    510B  TYR*     1.3    76.9    -      -       -      +
    512B  ILE*     1.3    63.5    +      -       -      +
    513B  THR*     3.5     7.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 512 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389B  PRO*     4.0    16.6    -      -       -      +
    413B  TRP*     3.6    38.6    -      -       +      +
    423B  ILE*     4.6     5.4    -      -       +      -
    435B  GLY      5.1     5.1    +      -       -      +
    437B  ALA*     3.6    30.9    -      -       +      +
    464B  LEU*     4.3    11.4    -      -       +      -
    500B  ASP*     4.4     9.0    -      -       +      -
    501B  GLY      3.9     8.3    -      -       -      +
    502B  ALA*     4.0     2.9    -      -       +      -
    510B  TYR*     4.3    16.4    -      -       +      +
    511B  TRP*     1.3    72.1    -      -       -      +
    513B  THR*     1.3    62.6    +      -       -      +
    514B  GLY*     3.9    10.1    -      -       -      +
    998B  PRX      3.6    29.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 513 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389B  PRO*     4.0    11.8    -      -       -      +
    461B  GLU*     6.6     0.4    -      -       -      -
    501B  GLY*     3.0    22.5    +      -       -      -
    502B  ALA*     4.0     3.8    +      -       -      -
    503B  ARG*     5.0     7.6    -      -       +      +
    511B  TRP*     3.5    14.6    +      -       +      +
    512B  ILE*     1.3    76.2    -      -       -      +
    514B  GLY*     1.3    58.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 514 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389B  PRO*     4.6     9.2    -      -       -      -
    500B  ASP*     3.2    11.6    -      -       -      +
    501B  GLY*     2.8    30.5    +      -       -      -
    512B  ILE*     3.6     7.5    -      -       -      +
    513B  THR*     1.3    81.0    +      -       -      +
    515B  ARG*     1.3    62.8    +      -       -      -
    516B  VAL*     4.3     0.7    -      -       -      +
    998B  PRX      4.5     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 515 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  GLY*     5.6     1.2    -      -       -      -
    415B  GLN*     3.2    13.7    -      -       -      +
    488B  TYR*     6.0     2.2    -      -       -      -
    498B  SER      3.5    14.1    +      -       -      -
    499B  GLY*     3.3     6.7    +      -       -      -
    500B  ASP*     3.1    15.0    -      -       -      -
    514B  GLY*     1.3    73.6    -      -       -      -
    516B  VAL*     1.3    60.1    +      -       -      +
    517B  ASP*     2.8    45.8    +      -       -      +
    519B  VAL*     3.6    45.7    -      -       +      +
    520B  LEU      5.4     4.0    -      -       -      -
    521B  ASN*     5.7     3.1    -      -       +      +
    526B  ARG*     3.8    31.0    -      -       +      +
    998B  PRX      2.9    32.5    +      -       -      +
----------------------------------------------------------
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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