Contacts of the strand formed by residues 444 - 449 (chain B) in PDB entry 1YA8


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 THR 444 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346B  TYR      3.5    10.1    -      -       -      +
    348B  VAL*     5.4     2.0    -      -       +      -
    434B  ALA*     3.6    39.9    -      -       +      +
    437B  HIS*     2.9    25.6    -      -       +      -
    438B  ARG*     3.4     9.8    +      -       -      -
    442B  ALA      2.9    10.0    +      -       -      -
    443B  PRO*     1.3    70.8    -      -       -      +
    445B  TYR*     1.3    65.6    +      -       -      +
    519B  GLU*     3.5    15.1    +      -       -      +
    520B  TYR*     2.8    48.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 445 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346B  TYR      3.1     6.6    +      -       -      +
    347B  MET*     3.3    16.9    -      -       +      -
    348B  VAL      2.8    26.3    +      -       -      -
    443B  PRO*     5.0     6.1    -      -       +      +
    444B  THR*     1.3    85.1    -      -       -      +
    446B  MET*     1.3    64.3    +      -       -      +
    503B  PHE*     4.0    14.8    -      +       -      -
    507B  GLY      3.5    17.2    +      -       -      -
    508B  ASN*     2.9    28.7    +      -       -      +
    509B  PRO*     3.5    37.0    -      -       +      -
    510B  ASN*     4.9     0.5    +      -       -      -
    517B  TRP*     4.0    19.1    -      +       +      +
    518B  PRO      3.5    17.0    -      -       -      -
    519B  GLU*     3.5    35.9    +      -       +      +
    520B  TYR*     4.1     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 446 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348B  VAL*     2.9    20.0    -      -       +      +
    349B  GLY*     5.0     2.0    -      -       -      +
    350B  ILE*     5.4     1.3    -      -       +      -
    430B  SER*     3.5    17.7    -      -       -      +
    431B  VAL*     3.3    44.0    -      -       +      +
    434B  ALA*     3.5    27.1    -      -       +      -
    445B  TYR*     1.3    75.1    -      -       -      +
    447B  TYR*     1.3    62.1    +      -       -      +
    517B  TRP*     2.9    25.9    +      -       -      +
    520B  TYR*     3.8    29.7    -      -       +      +
    525B  GLY      5.0     0.4    +      -       -      -
    526B  TYR*     3.6    18.6    -      -       +      +
    527B  LEU      3.2     7.4    +      -       -      -
    539B  LEU*     3.9    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 447 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244B  ILE*     5.1     0.9    -      -       +      -
    245B  SER      5.1     0.9    -      -       -      -
    246B  GLU*     3.3    34.7    -      -       +      +
    247B  SER*     4.7     0.5    +      -       -      -
    347B  MET*     4.1    12.8    -      -       +      -
    348B  VAL      3.4     2.8    +      -       -      -
    349B  GLY*     3.3    21.9    +      -       -      -
    350B  ILE      3.0    31.1    +      -       -      -
    351B  ASN*     4.4     2.6    +      -       -      -
    446B  MET*     1.3    77.9    -      -       -      +
    448B  GLU*     1.3    64.5    +      -       -      +
    449B  PHE*     3.6    22.0    -      +       +      -
    471B  GLU*     4.1     9.6    -      -       +      +
    500B  TRP*     3.5    32.4    -      +       -      -
    517B  TRP*     3.4    22.2    -      +       +      -
    526B  TYR*     4.3     4.2    -      -       -      +
    527B  LEU      3.0    17.0    -      -       -      +
    529B  ILE*     4.3    11.0    -      -       +      -
    539B  LEU*     4.4     6.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 448 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350B  ILE*     3.1    16.4    -      -       +      +
    351B  ASN      4.3     2.6    -      -       -      +
    352B  LYS*     3.2    39.7    -      -       -      +
    447B  TYR*     1.3    75.9    -      -       -      +
    449B  PHE*     1.3    61.6    +      -       -      +
    450B  GLN*     3.4    26.7    +      -       -      +
    526B  TYR*     3.9    20.1    +      -       +      -
    527B  LEU      2.9     9.7    +      -       -      -
    528B  GLN*     3.5     2.6    +      -       -      -
    529B  ILE      3.1    20.4    +      -       -      -
    539B  LEU*     3.3    26.4    -      -       +      +
    540B  LYS*     4.8    11.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 449 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350B  ILE      2.8     8.5    +      -       -      -
    351B  ASN*     3.2    23.2    -      -       -      +
    352B  LYS      2.9    26.9    +      -       -      -
    447B  TYR*     3.6    13.4    -      +       +      -
    448B  GLU*     1.3    70.3    -      -       -      +
    450B  GLN*     1.3    59.9    +      -       -      +
    451B  TYR*     3.5    43.7    -      +       +      -
    453B  PRO*     5.2     0.4    -      -       +      -
    466B  GLY*     4.0     1.8    -      -       -      -
    470B  ASP*     3.9    11.9    -      -       +      -
    471B  GLU*     3.6    42.4    -      -       +      -
    474B  SER*     3.8    26.5    -      -       -      -
    492B  LEU*     4.3     4.5    -      -       +      -
    496B  VAL*     4.8     3.8    -      -       +      -
    500B  TRP*     6.4     1.3    -      +       -      -
    529B  ILE*     3.7    35.2    -      -       +      -
----------------------------------------------------------
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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