Contacts of the strand formed by residues 284 - 289 (chain A) in PDB entry 1LE9


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 MET 284 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196A  ILE*     3.9    42.2    -      -       +      +
    197A  CYS      5.2     1.8    -      -       -      +
    198A  ARG*     5.0     7.9    -      -       -      -
    199A  VAL*     4.0    30.1    -      -       +      -
    202A  ASN*     5.2     2.7    -      -       -      +
    269A  SER*     3.4     3.8    -      -       -      -
    270A  MET*     2.5    61.3    +      -       +      +
    283A  PRO*     1.3    76.2    -      -       -      +
    285A  GLU*     1.3    75.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  ASN*     3.6    20.4    -      -       -      +
    267A  ARG*     4.9    15.5    -      -       +      +
    268A  VAL      3.4    14.1    -      -       -      +
    269A  SER*     4.5     4.5    +      -       -      +
    270A  MET*     4.7     2.5    -      -       -      +
    283A  PRO*     4.5     3.5    -      -       -      +
    284A  MET*     1.3    86.8    -      -       -      +
    286A  PHE*     1.3    61.0    +      -       -      +
    287A  GLN*     4.1     4.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  ASN*     3.2    20.4    -      -       -      -
    203A  SER*     3.2    33.2    -      -       -      -
    204A  GLY*     3.6     9.2    -      -       -      -
    210A  ASP*     5.3     0.4    -      -       +      -
    212A  ILE*     3.6    25.1    -      -       +      -
    228A  PHE*     3.9     8.3    -      +       -      -
    254A  THR*     3.2    20.0    -      -       +      -
    268A  VAL*     3.2    32.0    +      -       +      +
    270A  MET*     4.4    25.6    -      -       +      -
    284A  MET      3.9     0.2    +      -       -      -
    285A  GLU*     1.3    75.0    -      -       -      +
    287A  GLN*     1.3    59.6    +      -       -      +
    288A  TYR*     3.2    50.1    +      +       -      -
----------------------------------------------------------
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Residues in contact with GLN 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  ASN      3.1     8.5    +      -       -      +
    203A  SER*     3.1    32.6    -      -       -      -
    204A  GLY      3.1     4.2    +      -       -      -
    265A  PRO*     3.6    23.6    -      -       +      +
    267A  ARG*     3.7    48.3    +      -       +      +
    285A  GLU*     4.1     4.5    -      -       +      -
    286A  PHE*     1.3    69.7    -      -       -      +
    288A  TYR*     1.3    59.7    +      -       -      +
    289A  LEU*     3.3    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  GLY      3.4     4.0    -      -       -      -
    205A  SER      3.9    21.8    -      -       -      -
    206A  CYS*     4.0     3.8    -      -       -      -
    228A  PHE*     3.3    12.7    -      +       -      -
    233A  TRP*     3.0    30.7    -      +       -      -
    254A  THR*     3.5     4.9    -      -       +      +
    255A  PRO*     2.5    32.1    +      -       -      +
    257A  TYR*     4.0    21.1    -      +       +      -
    262A  LEU*     2.9    22.5    -      -       +      +
    264A  ALA      3.5     0.7    -      -       -      +
    265A  PRO*     3.7     0.3    -      -       -      +
    266A  VAL*     3.2    36.2    +      -       +      -
    268A  VAL*     3.4    30.5    -      -       +      -
    286A  PHE*     3.2    36.8    +      +       -      -
    287A  GLN*     1.3    70.5    -      -       -      +
    289A  LEU*     1.3    61.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  SER*     4.0    19.1    -      -       -      +
    204A  GLY*     2.7    15.3    +      -       -      +
    205A  SER*     3.7     1.8    -      -       -      -
    206A  CYS      3.2    23.7    +      -       -      -
    262A  LEU*     3.5     5.2    -      -       -      +
    264A  ALA      4.8     0.2    -      -       -      -
    265A  PRO*     4.5     9.4    -      -       +      -
    287A  GLN*     3.3    37.0    -      -       +      +
    288A  TYR*     1.3    79.3    -      -       -      +
    290A  PRO*     1.3    75.5    -      -       +      +
----------------------------------------------------------
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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