Contacts of the strand formed by residues 290 - 297 (chain A) in PDB entry 1Y57


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 290 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  THR*     3.3     6.2    -      -       -      +
    286A  TRP*     2.8    53.5    +      -       +      -
    287A  ASN*     5.4     1.2    +      -       -      +
    289A  THR*     1.3    91.6    +      -       -      +
    291A  ARG*     1.3    72.4    +      -       -      +
    292A  VAL*     3.6     4.2    +      -       +      +
    326A  TYR*     4.1    22.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270A  GLU*     4.8     3.2    +      -       -      -
    283A  MET*     3.5    30.6    -      -       +      +
    284A  GLY      3.5    10.8    -      -       -      +
    285A  THR*     4.7     2.7    +      -       -      +
    289A  THR      4.0     2.2    +      -       -      -
    290A  THR*     1.3    78.1    -      -       -      +
    292A  VAL*     1.3    66.6    +      -       -      +
    326A  TYR*     4.2     6.1    +      -       -      -
    340A  TYR*     3.5    47.8    +      -       +      +
    342A  SER*     6.0     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 292 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  LEU*     4.5     0.4    -      -       +      -
    283A  MET*     3.5     8.8    -      -       -      +
    284A  GLY      2.9    46.9    +      -       -      +
    285A  THR      4.1     8.3    -      -       -      +
    286A  TRP*     3.7    24.0    -      -       +      -
    290A  THR*     3.7     2.2    -      -       +      +
    291A  ARG*     1.3    80.3    -      -       -      +
    293A  ALA*     1.3    59.3    +      -       -      +
    294A  ILE*     3.9    22.7    -      -       +      -
    326A  TYR*     3.6    27.1    -      -       +      -
    337A  VAL*     3.7    14.1    -      -       +      -
    338A  THR      3.4     8.1    -      -       -      +
    340A  TYR*     3.8     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 293 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273A  LEU*     5.1     0.4    -      -       +      -
    281A  VAL*     4.8     4.7    -      -       +      -
    282A  TRP      3.2     8.3    -      -       -      +
    292A  VAL*     1.3    73.6    -      -       -      +
    294A  ILE*     1.3    61.7    +      -       -      +
    295A  LYS      4.1     0.4    -      -       -      -
    336A  ILE      3.7     1.0    -      -       -      +
    337A  VAL*     3.4     5.4    -      -       -      +
    338A  THR*     2.9    38.4    +      -       -      +
    339A  GLU      3.9     0.7    -      -       -      +
    340A  TYR*     3.9     8.1    -      -       +      +
    600A  MPZ      3.4    46.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 294 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  LEU*     4.2    20.9    -      -       +      -
    268A  ARG      4.5     2.0    -      -       -      +
    269A  LEU*     3.6    26.5    -      -       +      -
    280A  GLU      3.9     0.2    -      -       -      +
    281A  VAL*     3.4     5.1    -      -       -      -
    282A  TRP*     2.8    40.0    +      -       +      +
    284A  GLY*     4.4    13.7    -      -       -      +
    285A  THR      5.1     0.2    -      -       -      +
    292A  VAL*     3.9    22.9    -      -       +      -
    293A  ALA*     1.3    77.6    -      -       -      +
    295A  LYS*     1.3    62.2    +      -       -      +
    296A  THR*     3.8     9.2    +      -       +      +
    335A  TYR*     3.7    42.0    -      -       +      -
    336A  ILE      3.5     3.6    -      -       -      +
    337A  VAL*     4.3     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 295 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  GLU      3.5     9.4    -      -       -      +
    281A  VAL*     4.4     9.6    -      -       +      +
    293A  ALA*     4.1     0.8    -      -       -      +
    294A  ILE*     1.3    73.0    -      -       -      +
    296A  THR*     1.3    61.5    +      -       -      +
    307A  PHE*     3.8    26.8    -      -       +      -
    310A  GLU*     2.8    37.4    +      -       -      +
    334A  ILE      3.7     0.5    -      -       -      +
    335A  TYR*     3.2     5.5    -      -       -      -
    336A  ILE*     2.8    48.9    +      -       +      +
    338A  THR*     6.5     0.4    -      -       +      -
    404A  ASP*     4.4    13.9    +      -       -      -
    406A  GLY*     5.6     0.4    -      -       -      -
    600A  MPZ      3.9    31.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 296 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  LEU*     5.4     2.5    -      -       +      -
    278A  PHE      3.7     1.0    -      -       -      +
    279A  GLY*     3.3     6.1    -      -       -      -
    280A  GLU*     2.9    47.5    +      -       -      +
    282A  TRP*     4.2    15.0    -      -       +      +
    294A  ILE*     4.1    14.4    -      -       +      +
    295A  LYS*     1.3    78.1    -      -       -      +
    297A  LEU*     1.3    61.8    +      -       -      +
    307A  PHE*     3.9     7.5    -      -       -      -
    333A  PRO*     5.1     4.0    -      -       -      -
    334A  ILE      3.4     4.3    -      -       -      -
    335A  TYR*     3.5    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 297 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    278A  PHE*     3.5    16.2    -      -       +      +
    296A  THR*     1.3    74.0    -      -       -      +
    298A  LYS*     1.3    66.5    +      -       -      +
    299A  PRO*     3.3    13.5    -      -       +      +
    301A  THR*     3.6    17.0    -      -       -      +
    302A  MET*     3.7    37.0    -      -       +      +
    304A  PRO*     3.9    11.7    -      -       +      -
    307A  PHE*     3.8    37.0    -      -       +      -
    332A  GLU*     5.9     1.8    -      -       +      +
    333A  PRO*     3.7    16.3    -      -       -      +
    334A  ILE*     3.0    35.8    +      -       +      +
----------------------------------------------------------
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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