Contacts of the strand formed by residues 496 - 503 (chain A) in PDB entry 1Y24


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 PRO 496 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  THR*     3.6    24.0    -      -       +      -
    318A  TYR*     3.8     6.1    -      -       +      +
    368A  ARG*     3.0    28.9    -      -       -      +
    372A  ASN*     4.1     1.3    -      -       -      +
    375A  ARG*     3.3    29.8    +      -       -      +
    404A  GLU      3.1     9.0    -      -       -      +
    405A  VAL*     3.6    17.7    -      -       +      -
    436A  ALA*     3.8     0.9    -      -       -      -
    437A  ALA*     2.9    34.2    +      -       +      +
    494A  VAL      3.1     4.9    -      -       -      +
    495A  PHE*     1.3    82.7    -      -       -      +
    497A  THR*     1.3    62.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 497 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375A  ARG*     3.2     9.5    +      -       -      +
    402A  TRP*     3.7    14.8    -      -       +      -
    403A  ALA*     3.0    25.1    -      -       -      -
    404A  GLU*     3.0    24.8    +      -       +      +
    434A  TRP*     3.1    24.6    +      -       -      -
    435A  ARG      3.3    10.3    +      -       -      -
    436A  ALA*     4.4     0.2    -      -       -      +
    489A  ARG*     3.5    17.1    +      -       -      +
    495A  PHE*     3.4    28.0    -      -       +      -
    496A  PRO*     1.3    75.1    -      -       -      +
    498A  ALA*     1.3    64.6    +      -       -      +
    499A  GLU*     4.4     0.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 498 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375A  ARG*     3.7    18.3    -      -       +      +
    378A  HIS*     4.9     8.1    -      -       +      +
    402A  TRP      3.2     7.9    -      -       -      +
    403A  ALA*     4.4     2.2    -      -       +      +
    433A  ALA      3.9     0.7    -      -       -      +
    434A  TRP*     3.5     2.8    -      -       -      -
    435A  ARG*     2.8    73.1    +      -       -      +
    497A  THR*     1.3    76.8    +      -       -      +
    499A  GLU*     1.3    63.3    +      -       -      +
    500A  GLN      4.2     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 499 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    378A  HIS*     5.5     1.1    -      -       -      -
    400A  GLN      4.0     0.7    -      -       -      +
    401A  LEU*     3.1     9.2    -      -       -      +
    402A  TRP*     2.7    64.6    +      -       +      +
    421A  LEU*     6.1     0.2    -      -       -      +
    432A  ASP*     3.9    10.6    -      -       -      +
    433A  ALA      3.6     3.8    -      -       -      -
    434A  TRP*     3.7    20.2    -      -       +      +
    487A  TRP*     2.9    45.1    +      -       +      +
    489A  ARG*     3.0    35.5    +      -       -      +
    498A  ALA*     1.3    74.7    -      -       -      +
    500A  GLN*     1.3    60.9    +      -       -      +
    501A  PHE*     3.9     2.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 500 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    378A  HIS*     3.2    25.8    -      -       +      +
    395A  LEU*     4.6     3.2    -      -       -      +
    399A  GLU*     3.1    29.9    +      -       -      +
    401A  LEU*     3.7    26.4    -      -       +      +
    431A  ALA      3.6     1.7    -      -       -      +
    432A  ASP*     3.3     6.8    -      -       -      +
    433A  ALA*     2.7    55.7    +      -       +      +
    435A  ARG*     5.9     0.7    -      -       -      +
    498A  ALA      4.2     0.4    -      -       -      -
    499A  GLU*     1.3    72.8    -      -       -      +
    501A  PHE*     1.3    58.6    +      -       -      +
    502A  ARG*     3.8    19.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 501 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399A  GLU*     3.0    23.4    -      -       -      +
    400A  GLN*     2.9    28.8    +      -       -      +
    425A  HIS*     3.2    43.7    -      +       +      -
    427A  PRO*     3.8    16.8    -      -       +      -
    430A  PRO*     3.2    33.9    -      -       +      -
    431A  ALA      3.5     4.7    -      -       -      -
    432A  ASP*     4.6    11.2    -      -       +      +
    478A  ASN*     4.4     2.7    -      -       -      -
    480A  LEU*     3.5    29.4    -      -       +      -
    487A  TRP*     3.5    31.2    -      +       +      -
    499A  GLU*     3.9     2.6    -      -       +      -
    500A  GLN*     1.3    73.5    -      -       -      +
    502A  ARG*     1.3    65.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 502 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397A  ASP*     3.0    25.3    +      -       -      -
    399A  GLU*     3.0    39.5    +      -       +      +
    430A  PRO*     3.5     4.7    -      -       -      +
    431A  ALA*     2.8    45.8    +      -       +      +
    500A  GLN*     3.8    16.4    -      -       +      +
    501A  PHE*     1.3    78.9    -      -       -      +
    503A  ARG*     1.3    71.8    +      -       +      +
----------------------------------------------------------
 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
----------------------------------------------------------
    398A  GLU*     4.9     7.2    +      -       -      +
    399A  GLU*     5.0     2.6    -      -       -      +
    426A  ARG*     3.5    17.2    +      -       -      +
    427A  PRO*     3.3    59.8    -      -       +      +
    428A  GLN*     3.4    18.8    +      -       -      +
    429A  GLY      3.6     6.3    -      -       -      +
    431A  ALA*     4.5     2.0    -      -       -      +
    502A  ARG*     1.3    89.2    -      -       +      +
    504A  MET*     1.3    71.9    +      -       -      +
    505A  ARG*     4.1    21.7    +      -       -      +
----------------------------------------------------------
 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