Contacts of the strand formed by residues 449 - 459 (chain A) in PDB entry 2E3S


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 ILE 449 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    442A  ARG*     4.6    14.1    -      -       +      +
    443A  ASN*     6.0     1.6    -      -       -      +
    446A  GLU*     3.4    39.6    -      -       +      +
    447A  THR      3.5     2.5    -      -       -      -
    448A  THR*     1.3    80.5    -      -       -      +
    450A  GLU*     1.3    65.6    +      -       -      +
    451A  ASN*     3.5    28.7    -      -       -      +
    452A  PHE*     4.2    13.5    -      -       +      -
    467A  GLN*     3.4    39.7    -      -       +      +
    468A  THR      3.6     4.9    -      -       -      +
    469A  HIS*     3.9     8.7    -      -       +      +
    470A  LYS*     2.9    18.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 450 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449A  ILE*     1.3    75.5    -      -       -      +
    451A  ASN*     1.3    82.3    +      -       -      +
    468A  THR*     2.9    23.7    +      -       -      +
    469A  HIS      4.2     7.4    -      -       -      -
    470A  LYS*     3.8    19.5    +      -       +      +
    477A  GLN*     2.7    37.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 451 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449A  ILE*     3.5     4.1    -      -       -      +
    450A  GLU*     1.3   108.7    +      -       -      +
    452A  PHE*     1.3    64.6    +      -       -      +
    466A  TYR*     6.1     1.3    -      -       +      -
    467A  GLN*     3.3     1.1    -      -       -      +
    468A  THR*     2.9    37.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 452 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439A  VAL*     3.8    45.5    -      -       +      -
    442A  ARG*     3.8    24.0    -      -       +      -
    443A  ASN*     3.8    27.8    -      -       -      -
    449A  ILE*     4.2    13.5    -      -       +      -
    451A  ASN*     1.3    79.4    -      -       -      +
    453A  HIS*     1.3    75.7    +      -       -      +
    454A  VAL*     4.9     4.0    -      -       +      -
    465A  ILE*     4.0    14.8    -      -       +      -
    466A  TYR*     3.2     7.4    -      -       -      +
    467A  GLN*     3.4    24.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 453 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452A  PHE*     1.3    85.4    -      -       -      +
    454A  VAL*     1.3    72.8    +      -       -      +
    455A  VAL*     3.4    26.7    +      -       +      -
    465A  ILE*     3.5     2.1    -      -       -      -
    466A  TYR*     2.9    59.3    +      +       +      +
    512A  ALA*     6.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 454 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439A  VAL*     4.0    36.8    -      -       +      -
    452A  PHE*     4.9     3.4    -      -       +      -
    453A  HIS*     1.3    78.0    +      -       -      +
    455A  VAL*     1.3    62.1    +      -       -      +
    456A  GLU*     3.6    26.5    -      -       -      +
    457A  THR*     4.0    12.1    -      -       -      +
    463A  ILE*     4.1    18.6    -      -       +      -
    464A  ILE      3.5     6.7    -      -       -      +
    465A  ILE*     4.5     3.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 455 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453A  HIS*     3.6    26.0    -      -       +      -
    454A  VAL*     1.3    74.2    -      -       -      +
    456A  GLU*     1.3    58.5    +      -       +      +
    464A  ILE*     2.7    17.9    +      -       +      +
    466A  TYR*     3.7    26.9    -      -       +      +
    481A  LEU*     4.0     9.2    -      -       +      -
    509A  HIS*     3.5    45.0    +      -       +      +
    511A  SER*     4.5     9.0    -      -       -      -
    512A  ALA*     4.8     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 456 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366A  ARG*     2.8    45.4    +      -       -      -
    454A  VAL*     3.4     8.1    -      -       -      +
    455A  VAL*     1.3    81.5    -      -       +      +
    457A  THR*     1.3    75.2    +      -       -      +
    458A  LEU*     3.4    13.9    +      -       +      +
    463A  ILE*     3.5     3.1    -      -       -      -
    464A  ILE*     2.9    36.1    +      -       +      +
    509A  HIS*     2.8    21.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 457 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  VAL*     4.0    12.6    -      -       -      +
    456A  GLU*     1.3    82.1    -      -       -      +
    458A  LEU*     1.3    61.1    +      -       -      +
    459A  ALA*     3.4    24.9    -      -       -      +
    460A  ASP*     5.5     1.1    -      -       -      -
    462A  ALA      4.1     1.6    -      -       -      -
    463A  ILE*     4.0    11.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 458 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365A  HIS*     3.8    42.2    -      -       +      +
    366A  ARG*     3.7    14.4    -      -       -      +
    367A  PHE*     3.9    13.2    -      -       +      -
    456A  GLU*     3.4    29.4    +      -       +      +
    457A  THR*     1.3    75.2    -      -       -      +
    459A  ALA*     1.3    63.2    +      -       -      +
    462A  ALA*     2.9    19.7    +      -       +      +
    463A  ILE*     4.8     0.7    -      -       -      -
    464A  ILE*     3.9    19.1    -      -       +      -
    483A  LEU*     3.6    36.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 459 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365A  HIS*     4.2    15.9    -      -       +      -
    457A  THR*     3.4    16.8    -      -       -      +
    458A  LEU*     1.3    78.4    -      -       -      +
    460A  ASP*     1.3    67.7    +      -       -      +
    461A  ASN*     3.1    19.5    -      -       -      +
    462A  ALA*     3.0    17.1    +      -       +      +
    463A  ILE*     4.8     1.0    -      -       -      +
----------------------------------------------------------
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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