Contacts of the strand formed by residues 280 - 286 (chain A) in PDB entry 1L6O


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 GLY 280 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271A  GLY*     3.7     0.2    -      -       -      -
    272A  GLN*     3.0    28.6    +      -       -      +
    278A  ASP      3.1     5.4    +      -       -      -
    279A  GLY*     1.3    77.3    -      -       -      +
    281A  ILE*     1.3    67.2    +      -       -      -
    282A  TYR*     3.8     5.7    -      -       -      -
    303A  MSE      5.0     7.2    -      -       -      -
    304A  LEU      6.1     0.2    -      -       -      -
    312A  PHE      6.1     0.9    -      -       -      -
    315A  MSE      6.2     0.2    -      -       -      -
    317A  ASN*     3.3    16.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  ILE*     3.9    20.2    -      -       +      -
    270A  VAL      3.4     5.2    -      -       -      +
    271A  GLY*     4.5     2.9    -      -       -      -
    280A  GLY*     1.3    63.3    -      -       -      +
    282A  TYR*     1.3    62.0    +      -       -      +
    303A  MSE      3.6     7.6    -      -       -      +
    304A  LEU*     3.0    53.5    +      -       +      +
    312A  PHE*     4.0    26.2    -      -       +      -
    317A  ASN*     3.9    33.0    -      -       +      +
    320A  ALA*     4.0    15.5    -      -       +      -
    321A  VAL*     4.3    13.7    -      -       +      -
    324A  LEU*     4.8     2.7    -      -       +      -
      5D  MET*     4.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  ILE*     3.4     9.8    -      -       -      +
    270A  VAL*     2.9    46.2    +      -       +      +
    272A  GLN*     2.7    47.9    +      -       +      -
    279A  GLY      4.3     2.1    +      -       -      -
    280A  GLY      3.8    10.1    -      -       -      -
    281A  ILE*     1.3    73.3    -      -       -      +
    283A  ILE*     1.4    69.1    +      -       -      +
    301A  GLY*     3.4    24.7    -      -       -      +
    302A  ASP      3.2    11.4    -      -       -      +
    303A  MSE      3.8    33.2    -      -       +      -
    304A  LEU*     4.5     2.2    -      -       -      +
      2D  LEU*     5.3     2.0    -      -       +      -
      1E  SER*     3.8    11.8    -      -       -      -
      2E  LEU*     3.8    36.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  ILE*     3.9    29.2    -      -       +      -
    268A  SER      3.4     6.3    -      -       -      +
    269A  ILE*     4.4     6.3    -      -       +      -
    270A  VAL*     5.0     0.7    -      -       -      -
    282A  TYR*     1.4    74.3    -      -       -      +
    284A  GLY*     1.3    57.0    +      -       -      +
    285A  SER      4.2     7.0    -      -       -      +
    286A  ILE*     3.8    34.8    -      -       +      -
    298A  ILE*     4.0    15.3    -      -       +      -
    299A  GLU      4.0     8.5    -      -       -      +
    300A  PRO*     3.3     3.0    -      -       +      +
    301A  GLY*     2.8    30.7    +      -       -      -
    302A  ASP*     3.0    28.3    +      -       +      +
    304A  LEU*     4.6    13.9    -      -       +      -
    336A  LEU*     5.7     2.7    -      -       +      -
    338A  VAL*     5.3     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268A  SER*     2.9    19.5    +      -       -      -
    270A  VAL*     3.9    18.9    -      -       -      +
    282A  TYR      3.6     3.2    +      -       -      -
    283A  ILE*     1.3    71.2    -      -       -      +
    285A  SER*     1.3    60.8    +      -       -      +
    300A  PRO*     3.2    19.9    -      -       -      +
    284B  GLY      4.6     0.2    -      -       -      +
    285B  SER*     5.9     0.2    -      -       -      -
    300B  PRO*     4.0    19.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  GLY      3.8     0.2    -      -       -      +
    267A  ILE*     3.5     5.2    -      -       -      +
    268A  SER*     2.7    42.1    +      -       -      -
    283A  ILE*     4.2     0.5    -      -       -      +
    284A  GLY*     1.3    77.0    -      -       -      +
    286A  ILE*     1.3    71.4    +      -       -      +
    287A  MSE      4.3    18.5    +      -       -      +
    300A  PRO*     4.6     5.4    -      -       -      -
    300B  PRO*     4.6    18.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  GLY      3.3     5.8    -      -       -      +
    267A  ILE*     4.5     1.3    -      -       +      -
    283A  ILE*     3.8    14.4    -      -       +      -
    285A  SER*     1.3    84.8    -      -       -      +
    287A  MSE      1.3    65.9    +      -       -      +
    288A  LYS      3.8     0.9    +      -       -      -
    292A  VAL*     4.0    15.7    -      -       +      -
    293A  ALA*     3.8    37.1    -      -       +      +
    298A  ILE*     3.5    28.0    -      -       +      +
    299A  GLU*     3.7    22.4    -      -       -      -
    300A  PRO*     3.9     9.5    -      -       +      +
----------------------------------------------------------
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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