Contacts of the strand formed by residues 496 - 504 (chain A) in PDB entry 2P2B


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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  PHE*     3.9    10.4    -      -       +      -
    413A  TRP*     5.5     0.2    -      +       -      -
    415A  GLN*     2.6    30.4    +      -       -      -
    417A  GLU*     3.2    30.5    -      -       +      +
    418A  THR*     4.3    12.3    -      -       +      -
    465A  VAL*     3.2     7.1    -      -       -      +
    466A  ILE*     2.9    62.4    +      -       +      +
    470A  TRP*     4.0     9.6    -      +       +      -
    473A  GLN*     4.0     9.0    -      -       +      +
    484A  PHE*     5.9     2.0    -      +       -      -
    488A  TYR*     3.6    41.2    -      +       +      -
    489A  PHE*     3.9    22.2    -      +       +      -
    495A  MET*     1.3    69.9    -      -       -      +
    497A  PHE*     1.3    64.0    +      -       -      +
    498A  SER*     3.8    13.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 497 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463A  ASN*     3.7    26.0    -      -       +      -
    464A  LEU      3.7     7.0    -      -       -      -
    465A  VAL*     4.1     4.3    -      -       +      -
    487A  THR      4.9     6.1    -      -       -      +
    488A  TYR*     2.9    41.6    +      -       -      +
    491A  THR*     3.8    29.8    -      -       +      +
    492A  PHE*     3.9    31.2    -      +       +      +
    495A  MET      3.6     1.5    +      -       -      +
    496A  TYR*     1.3    74.2    -      -       -      +
    498A  SER*     1.3    69.7    +      -       -      +
    499A  GLY*     3.4    27.2    +      -       -      -
    500A  ASP      4.0     8.7    -      -       -      -
    516A  VAL*     3.9    18.2    -      -       +      -
    517A  ASP*     5.7     5.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 498 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413A  TRP*     3.8    22.4    -      -       -      -
    415A  GLN*     2.7    42.0    +      -       -      -
    464A  LEU*     2.7    29.1    +      -       -      +
    465A  VAL*     5.4     0.4    -      -       -      -
    466A  ILE*     5.6     1.1    -      -       -      -
    488A  TYR*     5.8     2.5    -      -       -      -
    496A  TYR*     3.8    11.1    +      -       -      -
    497A  PHE*     1.3    73.2    -      -       -      +
    499A  GLY*     1.3    60.4    +      -       -      +
    500A  ASP*     3.1    18.7    +      -       -      +
    515A  ARG*     3.5    10.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 499 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497A  PHE*     3.3    28.3    +      -       -      -
    498A  SER*     1.3    78.2    +      -       -      +
    500A  ASP*     1.3    53.9    +      -       -      +
    515A  ARG*     3.4    14.5    +      -       -      -
    516A  VAL*     2.8    30.6    +      -       -      -
    517A  ASP*     3.4    21.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 500 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413A  TRP*     2.8    27.2    +      -       -      +
    415A  GLN*     3.8     1.3    +      -       -      -
    463A  ASN*     3.9     3.6    -      -       -      -
    464A  LEU*     3.0    30.0    +      -       +      +
    497A  PHE*     4.0     3.3    -      -       -      -
    498A  SER*     3.1     9.0    +      -       -      +
    499A  GLY*     1.3    79.7    -      -       -      +
    501A  GLY*     1.3    66.3    +      -       -      +
    512A  ILE*     4.2     7.0    -      -       +      -
    514A  GLY*     3.2    18.0    -      -       -      +
    515A  ARG*     3.2     5.3    -      -       -      -
    516A  VAL*     4.1     4.8    -      -       -      +
    999A  PRX      2.6    45.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 501 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462A  GLY      3.5    11.2    -      -       -      -
    463A  ASN*     4.7     0.2    -      -       -      -
    464A  LEU*     4.7     0.2    -      -       -      -
    500A  ASP*     1.3    76.1    -      -       -      +
    502A  ALA*     1.3    63.6    +      -       -      +
    512A  ILE*     3.7     7.1    -      -       -      +
    513A  THR*     3.1    29.5    +      -       -      -
    514A  GLY      2.8    14.9    +      -       -      -
    516A  VAL*     3.8    17.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 502 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448A  LEU*     3.6    20.2    -      -       +      +
    461A  GLU*     3.3     5.0    -      -       -      +
    462A  GLY      3.1    31.2    +      -       -      +
    464A  LEU*     4.3    10.1    -      -       +      +
    501A  GLY*     1.3    75.3    -      -       -      +
    503A  ARG*     1.3    65.9    +      -       -      +
    510A  TYR*     4.6     6.5    -      -       +      -
    511A  TRP      3.2    15.5    -      -       -      +
    512A  ILE*     4.0    15.0    -      -       +      -
    513A  THR*     3.6     5.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 503 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448A  LEU*     3.9     2.9    -      -       -      -
    460A  THR      3.3    11.2    -      -       -      +
    461A  GLU*     3.8    25.1    -      -       +      +
    502A  ALA*     1.3    75.2    -      -       -      +
    504A  ARG*     1.3    63.2    +      -       -      +
    505A  ASP      4.2     0.4    -      -       -      -
    509A  TYR      3.9     0.2    -      -       -      +
    510A  TYR*     3.4     5.7    -      -       -      +
    511A  TRP*     2.8    81.6    +      -       +      +
    513A  THR*     3.7    28.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 504 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    446A  PRO      5.1     0.4    +      -       -      -
    447A  ALA*     4.5     3.2    -      -       -      +
    448A  LEU*     3.5    26.8    -      -       +      +
    456A  GLN      2.8    27.5    +      -       -      -
    457A  GLU*     3.7     2.0    -      -       -      +
    458A  GLY*     3.2    31.3    +      -       -      +
    459A  ALA*     3.2     4.3    -      -       -      +
    460A  THR*     2.8    39.6    +      -       -      +
    503A  ARG*     1.3    76.3    -      -       -      +
    505A  ASP*     1.3    62.5    +      -       -      +
    508A  GLY*     3.7    31.4    -      -       -      +
    509A  TYR      3.5     3.8    -      -       -      +
    510A  TYR*     2.9    52.4    +      -       +      -
----------------------------------------------------------
 Back to top of page


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