Contacts of the strand formed by residues 267 - 276 (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 LEU 267 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262A  ILE*     3.9    23.3    -      -       +      -
    264A  ARG*     3.0    17.3    +      -       -      +
    265A  GLU*     3.1     5.8    -      -       -      +
    266A  SER*     1.3    81.1    -      -       -      +
    268A  ARG*     1.3    60.5    +      -       -      +
    269A  LEU*     4.4     2.1    +      -       +      +
    285A  THR      3.4     4.0    -      -       -      +
    286A  TRP*     3.7    34.8    -      -       +      -
    292A  VAL*     4.5     0.7    -      -       +      -
    294A  ILE*     4.2    20.6    -      -       +      -
    329A  VAL*     4.3     5.8    -      -       +      -
    335A  TYR*     3.5    36.3    -      -       +      -
    337A  VAL*     3.9    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 268 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  LEU*     1.3    73.9    -      -       -      +
    269A  LEU*     1.3    71.9    +      -       -      +
    270A  GLU*     3.0    32.0    +      -       +      +
    284A  GLY*     3.1     6.2    -      -       -      -
    285A  THR*     2.9    46.4    +      -       -      +
    294A  ILE*     4.5     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 269 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  LEU*     4.2     2.2    +      -       +      +
    268A  ARG*     1.3    79.0    -      -       -      +
    270A  GLU*     1.3    61.0    +      -       -      +
    282A  TRP*     3.7    51.3    -      -       +      +
    283A  MET      4.2     2.7    -      -       -      -
    284A  GLY*     4.5     0.2    -      -       -      -
    294A  ILE*     3.6    32.5    -      -       +      -
    296A  THR*     5.6     1.1    -      -       +      -
    335A  TYR*     4.1    27.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 270 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268A  ARG*     3.0    42.1    +      -       -      +
    269A  LEU*     1.3    79.8    -      -       -      +
    271A  VAL*     1.3    69.4    +      -       +      +
    282A  TRP*     4.0     9.1    -      -       -      -
    283A  MET*     2.9    39.5    +      -       +      +
    284A  GLY*     4.1     1.3    -      -       -      -
    285A  THR*     2.4    30.5    +      -       -      -
    291A  ARG*     4.8     4.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 271 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270A  GLU*     1.3    91.4    -      -       +      +
    272A  LYS*     1.3    73.3    +      -       -      +
    273A  LEU*     3.4    12.4    +      -       +      +
    282A  TRP*     3.3     5.4    -      -       -      -
    283A  MET*     2.8    48.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 272 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271A  VAL*     1.3    79.8    -      -       -      +
    273A  LEU*     1.3    61.2    +      -       -      +
    274A  GLY*     4.0    12.8    -      -       -      +
    275A  GLN*     2.6    49.4    +      -       -      +
    280A  GLU*     3.0    26.8    +      -       -      +
    281A  VAL      4.0     1.8    -      -       -      +
    282A  TRP*     3.4    44.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 273 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271A  VAL*     4.3    14.8    -      -       +      +
    272A  LYS*     1.3    75.0    -      -       -      +
    274A  GLY*     1.3    59.1    +      -       -      +
    281A  VAL*     2.7    24.5    +      -       +      +
    282A  TRP      3.9     7.0    -      -       -      +
    283A  MET*     3.8    30.7    -      -       +      +
    293A  ALA*     5.1     0.4    -      -       +      -
    340A  TYR*     3.9    17.3    -      -       +      +
    600A  MPZ      3.7    76.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 274 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  LYS*     3.5     9.7    -      -       -      +
    273A  LEU*     1.3    82.3    -      -       -      +
    275A  GLN*     1.3    65.2    +      -       -      +
    280A  GLU*     3.4     4.5    -      -       -      +
    281A  VAL      2.9    25.5    +      -       -      +
    600A  MPZ      3.8    23.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 275 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  LYS*     2.6    36.3    +      -       -      +
    274A  GLY*     1.3    76.5    -      -       -      +
    276A  GLY*     1.3    60.1    +      -       -      +
    279A  GLY      3.4    12.6    -      -       -      +
    280A  GLU*     3.7    11.3    +      -       +      +
    281A  VAL*     6.2     0.2    -      -       -      -
    600A  MPZ      3.3    25.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 276 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275A  GLN*     1.3    78.2    +      -       -      +
    277A  CYS*     1.3    66.3    +      -       -      -
    278A  PHE      3.2     4.4    +      -       -      -
    279A  GLY*     2.9    17.0    +      -       -      +
    298A  LYS*     4.9     5.7    +      -       -      +
    600A  MPZ      4.2    12.3    -      -       -      -
----------------------------------------------------------
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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