Contacts of the strand formed by residues 295 - 301 (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 ILE 295 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  TRP*     5.8     1.3    -      -       +      -
    248A  PHE*     3.4    36.8    -      -       +      -
    279A  VAL*     6.1     0.7    -      -       +      +
    282A  GLN*     3.7    33.2    -      -       +      +
    283A  ILE*     3.7    29.6    -      -       +      +
    285A  GLN*     5.5     3.1    -      -       +      +
    293A  THR*     3.6    12.8    +      -       -      +
    294A  PRO*     1.3    79.0    -      -       -      +
    296A  TYR*     1.3    59.6    +      -       -      +
    297A  ASN*     5.1     2.7    -      -       -      +
    330A  GLN      5.0     5.6    -      -       -      +
    331A  ASN*     2.8    36.4    -      -       -      +
    332A  LEU*     3.0    27.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 296 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  GLN*     5.7     0.4    -      -       -      -
    130A  PHE*     4.1    10.3    -      +       +      -
    176A  ASN*     4.0    14.3    +      -       -      -
    217A  ARG*     3.8    19.9    +      -       -      -
    247A  PHE*     3.7    40.8    -      +       +      -
    248A  PHE      2.7    11.3    +      -       -      +
    249A  THR*     3.2     6.3    -      -       +      -
    250A  GLY      3.0    23.9    +      -       -      -
    294A  PRO*     3.9    21.1    -      -       +      +
    295A  ILE*     1.3    77.5    -      -       -      +
    297A  ASN*     1.3    60.1    +      -       -      +
    298A  ASP*     3.2    20.5    -      -       -      +
    331A  ASN*     3.2     8.3    -      -       -      -
    332A  LEU*     4.2    14.5    -      -       +      +
    333A  LEU*     3.6    40.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 297 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250A  GLY*     3.1    27.0    +      -       -      +
    251A  GLU      5.2     0.2    -      -       -      -
    252A  ALA*     4.9    12.3    -      -       +      +
    278A  VAL      5.9     0.4    +      -       -      -
    279A  VAL*     3.2    27.8    -      -       -      +
    282A  GLN*     5.9     5.1    -      -       -      +
    295A  ILE*     5.1     3.0    -      -       -      +
    296A  TYR*     1.3    72.1    +      -       -      +
    298A  ASP*     1.3    52.4    +      -       -      +
    299A  GLU      2.9    10.2    +      -       -      +
    300A  ALA*     4.0     6.3    +      -       +      -
    331A  ASN*     3.1    21.9    +      -       -      +
    333A  LEU      2.8    11.7    +      -       -      -
    334A  LEU*     3.4    25.9    -      -       +      +
    335A  ALA*     2.8    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 298 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  CYS*     5.3     1.7    -      -       -      -
     89A  ARG*     3.0    36.8    +      -       +      +
    130A  PHE*     3.2    27.8    -      -       -      -
    132A  LEU*     3.6    29.9    -      -       +      +
    178A  GLU*     5.1     0.9    -      -       -      +
    249A  THR*     3.0    26.7    -      -       -      +
    250A  GLY      3.5     5.6    +      -       -      +
    296A  TYR*     3.2    15.4    -      -       -      +
    297A  ASN*     1.3    69.3    -      -       -      +
    299A  GLU*     1.3    57.4    +      -       -      +
    333A  LEU*     4.9     6.2    -      -       -      +
    335A  ALA*     3.5    17.7    -      -       -      +
    337A  THR*     4.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 299 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  ARG*     3.1    34.5    +      -       -      +
     91A  HIS*     4.6     1.0    +      -       -      -
    181A  ASN*     3.7    15.2    +      -       -      +
    182A  GLU*     3.8     6.8    -      -       -      +
    250A  GLY      4.2     2.1    +      -       -      +
    251A  GLU*     3.3    28.1    -      -       +      +
    252A  ALA*     2.7    33.5    +      -       -      +
    297A  ASN      2.9     3.6    +      -       -      -
    298A  ASP*     1.3    75.3    -      -       -      +
    300A  ALA*     1.3    54.6    +      -       -      +
    301A  ASP*     4.2     4.7    -      -       -      +
    304A  VAL*     3.3    28.4    -      -       -      +
    335A  ALA      3.6     2.9    -      -       -      -
    337A  THR*     3.5    17.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  ALA*     3.3    11.2    -      -       +      +
    275A  GLN*     4.6     8.5    -      -       -      +
    297A  ASN*     4.2     3.8    -      -       +      +
    299A  GLU*     1.3    73.2    -      -       -      +
    301A  ASP*     1.3    60.0    +      -       -      +
    323A  VAL*     6.0     1.6    -      -       +      -
    334A  LEU*     4.1    34.5    -      -       +      -
    335A  ALA      2.8    14.7    +      -       -      +
    336A  ASN*     3.2    19.5    +      -       -      +
    337A  THR*     3.0    22.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 301 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251A  GLU*     4.7     0.4    -      -       -      +
    252A  ALA      3.1     6.5    +      -       -      +
    253A  GLY*     3.6     3.6    -      -       -      -
    254A  VAL*     4.0     2.3    +      -       -      +
    275A  GLN*     3.3    20.2    +      -       -      +
    299A  GLU*     4.5     7.7    -      -       -      +
    300A  ALA*     1.3    73.6    -      -       -      +
    302A  PRO*     1.3    77.3    -      -       +      +
    303A  LEU      3.0    32.6    -      -       -      +
    304A  VAL*     3.3    20.1    +      -       -      +
    323A  VAL*     6.5     0.9    -      -       -      -
    336A  ASN*     5.5     1.6    -      -       -      +
    337A  THR*     3.1    37.5    +      -       -      +
    357A  PRO*     4.4     5.0    -      -       +      +
----------------------------------------------------------
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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