Contacts of the strand formed by residues 325 - 333 (chain F) 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 ALA 325 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284F  GLU*     4.7     6.7    -      -       -      +
    316F  TYR*     3.7    35.9    -      -       +      +
    321F  ILE*     4.7     5.5    -      -       +      +
    323F  LYS      3.6     3.3    +      -       -      +
    324F  PRO*     1.3    75.2    -      -       -      +
    326F  SER*     1.3    61.9    +      -       -      +
    327F  VAL*     3.5     2.6    +      -       -      +
    346F  LEU*     3.8     4.2    -      -       -      -
    347F  TYR*     2.9    35.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 326 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284F  GLU*     4.2    12.5    -      -       -      +
    325F  ALA*     1.3    70.9    -      -       -      +
    327F  VAL*     1.3    60.6    +      -       -      +
    328F  PHE*     5.7     2.1    -      -       -      -
    344F  PRO*     6.0     4.0    -      -       -      -
    345F  PHE      3.7     7.9    -      -       -      -
    346F  LEU*     3.7    17.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 327 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282F  PHE*     4.1     8.1    -      -       +      -
    283F  TYR      2.7    36.3    -      -       -      +
    284F  GLU*     3.3    18.8    -      -       +      +
    292F  TRP*     3.6    15.5    -      -       +      -
    316F  TYR*     4.8     4.0    -      -       +      -
    325F  ALA      3.5     1.4    +      -       -      +
    326F  SER*     1.3    77.1    -      -       -      +
    328F  PHE*     1.3    71.9    +      -       -      +
    344F  PRO*     3.7     5.0    -      -       -      +
    345F  PHE*     2.8    38.7    +      -       +      +
    347F  TYR*     3.4    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 328 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281F  ARG      4.3     0.2    -      -       -      -
    282F  PHE*     2.9    31.7    -      -       -      +
    283F  TYR*     2.9    54.2    +      +       +      +
    284F  GLU*     5.6     1.8    -      -       -      -
    285F  GLU      6.2     0.4    -      -       -      -
    326F  SER      5.7     1.8    -      -       -      -
    327F  VAL*     1.3    77.9    -      -       -      +
    329F  VAL*     1.3    62.7    +      -       -      +
    342F  PRO*     3.7    28.0    -      -       +      -
    343F  LYS      3.7    15.3    -      -       -      -
    344F  PRO*     3.9    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 329 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250F  ILE*     4.2    14.5    -      -       +      +
    253F  MET*     4.4    19.5    -      -       +      -
    268F  LEU*     5.2     0.7    -      -       +      -
    280F  ILE*     3.9    25.1    -      -       +      -
    281F  ARG      3.3     5.8    -      -       -      +
    282F  PHE*     3.5    20.4    -      -       +      -
    311F  PHE*     5.1     0.9    -      -       +      -
    328F  PHE*     1.3    75.0    -      -       -      +
    330F  GLN*     1.3    65.8    +      -       -      +
    342F  PRO*     3.2     7.1    -      -       -      +
    343F  LYS      2.8    37.6    +      -       -      +
    344F  PRO      4.5     1.3    -      -       -      +
    345F  PHE*     3.2    37.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 330 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250F  ILE*     4.2     4.3    -      -       -      -
    280F  ILE*     3.7     2.5    -      -       -      -
    281F  ARG*     2.8    64.6    +      -       +      +
    283F  TYR*     3.1    34.6    +      -       +      -
    329F  VAL*     1.3    81.1    -      -       -      +
    331F  LEU*     1.3    65.0    +      -       -      +
    332F  ARG      3.6     0.3    +      -       -      -
    339F  THR*     3.5    31.9    +      -       +      +
    340F  SER*     3.1    33.2    -      -       -      +
    342F  PRO*     3.9     9.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 331 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248F  LEU*     4.0    12.0    -      -       +      +
    249F  LYS      3.4    31.9    -      -       -      +
    250F  ILE*     3.5    21.2    -      -       +      +
    268F  LEU*     4.0    20.2    -      -       +      -
    270F  CYS*     3.8    16.6    -      -       +      -
    273F  VAL*     4.6     9.4    -      -       +      -
    278F  ILE*     4.2    15.0    -      -       +      -
    279F  GLN      3.7    10.3    -      -       -      +
    280F  ILE*     4.5    10.8    -      -       +      -
    309F  ILE*     4.5     5.4    -      -       +      -
    330F  GLN*     1.3    74.5    -      -       -      +
    332F  ARG*     1.3    57.5    +      -       -      +
    339F  THR*     3.1     6.1    -      -       -      -
    340F  SER*     2.8    41.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 332 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248F  LEU*     4.0     0.2    -      -       -      -
    278F  ILE*     3.5     6.3    -      -       -      +
    279F  GLN*     2.6    71.6    +      -       +      +
    281F  ARG*     3.9    31.5    -      -       +      +
    293F  GLU*     4.8     5.9    +      -       -      -
    295F  PHE*     3.7    21.0    -      -       -      -
    330F  GLN      4.6     3.4    -      -       -      +
    331F  LEU*     1.3    75.6    -      -       -      +
    333F  ARG*     1.3    74.2    +      -       -      +
    334F  LYS*     4.4     1.5    -      -       -      +
    337F  LEU*     3.8    33.5    +      -       -      +
    338F  GLU      3.2     5.4    -      -       -      +
    339F  THR*     3.2    24.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 333 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51F  ARG*     4.2     3.0    -      -       -      +
    243F  PRO      3.7     4.9    +      -       -      -
    244F  ASN*     2.7    40.4    +      -       -      +
    245F  ALA      3.5     7.3    +      -       -      +
    246F  SER*     3.2    26.5    +      -       -      -
    248F  LEU*     3.4    25.9    -      -       +      +
    274F  GLN*     2.7    27.9    +      -       -      +
    277F  ASP*     2.8    30.1    -      -       -      +
    278F  ILE*     4.2     1.6    -      -       -      -
    332F  ARG*     1.3    73.2    -      -       -      +
    334F  LYS*     1.3    59.7    +      -       -      +
    335F  SER*     3.0     6.1    -      -       -      +
    336F  ASP*     2.8    35.3    +      -       -      +
    337F  LEU*     2.7    35.9    +      -       -      -
    338F  GLU*     2.9    25.2    +      -       -      +
----------------------------------------------------------
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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