Contacts of the strand formed by residues 446 - 451 (chain A) in PDB entry 4X8P


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 GLU 446 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    395A  TYR*     4.0     5.9    +      -       +      +
    396A  ILE*     3.3     7.7    -      -       -      +
    397A  ASN*     2.9    52.6    +      -       +      +
    444A  GLY      4.2     7.3    -      -       -      +
    445A  SER*     1.4    79.5    -      -       -      +
    447A  ILE*     1.3    62.3    +      -       -      +
    448A  ILE*     3.6    22.7    +      -       +      +
    458A  VAL*     3.4    31.1    -      -       +      +
    460A  TYR      3.4     7.0    -      -       -      +
    461A  LYS*     5.0     5.8    -      -       +      +
    463A  ILE*     5.3     1.8    -      -       -      +
    495A  LEU*     5.9     3.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 447 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346A  TRP*     4.0    16.8    -      -       +      -
    364A  TYR*     3.5    41.5    -      -       +      -
    395A  TYR      3.6     2.9    -      -       -      +
    396A  ILE*     3.8    24.7    -      -       +      -
    446A  GLU*     1.3    73.5    -      -       -      +
    448A  ILE*     1.4    66.9    -      -       -      +
    449A  PHE*     3.6    36.6    -      -       +      -
    458A  VAL*     3.8     1.0    -      -       -      -
    459A  ALA*     2.9    26.8    +      -       +      -
    460A  TYR*     2.8    20.4    +      -       +      +
    463A  ILE*     3.8    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 448 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382A  TYR*     4.5     0.2    -      -       -      -
    393A  GLY      4.0     0.2    -      -       -      +
    394A  PHE*     3.9     1.7    -      -       -      -
    395A  TYR*     2.9    64.3    +      -       +      +
    446A  GLU*     3.6    24.7    -      -       +      +
    447A  ILE*     1.4    79.7    -      -       -      +
    449A  PHE*     1.3    69.1    +      -       -      +
    450A  TYR*     3.7    12.1    -      -       +      -
    455A  ASN*     3.3    36.6    -      -       -      +
    457A  GLY      3.6     8.3    -      -       -      +
    458A  VAL*     4.2    17.5    -      -       +      -
    495A  LEU*     3.7    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 449 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344A  LEU      3.9     6.3    -      -       -      -
    345A  GLY*     4.1     4.9    -      -       -      -
    346A  TRP*     4.8     1.8    -      +       -      -
    364A  TYR*     4.3     9.0    -      -       +      -
    365A  SER      4.0    17.9    -      -       -      -
    366A  TRP*     3.4    39.3    -      +       +      -
    373A  LYS*     5.0     0.9    -      -       +      -
    382A  TYR*     3.2    33.8    +      +       +      +
    393A  GLY      3.4     1.6    -      -       -      -
    394A  PHE*     3.4    39.9    -      +       -      -
    447A  ILE*     3.6    21.5    -      -       +      -
    448A  ILE*     1.3    78.0    -      -       -      +
    450A  TYR*     1.3    58.8    +      -       -      +
    456A  GLN*     2.8    33.8    +      -       -      +
    459A  ALA*     3.5    26.9    -      -       +      -
    460A  TYR*     4.9     2.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with TYR 450 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328A  TYR*     3.7    38.4    -      +       -      +
    366A  TRP*     3.2    14.4    -      -       -      -
    392A  LEU*     3.3     1.4    -      -       -      -
    393A  GLY*     2.8    32.2    +      -       -      +
    395A  TYR*     3.9    11.0    -      -       +      -
    448A  ILE*     3.7    19.3    -      -       +      -
    449A  PHE*     1.3    78.5    -      -       -      +
    451A  LYS*     1.3    60.4    +      -       -      +
    452A  ASN      4.2     0.2    -      -       -      -
    453A  GLY*     4.2    15.9    -      -       -      +
    454A  VAL      3.3     9.6    -      -       -      +
    455A  ASN*     3.3    26.1    +      -       +      -
    456A  GLN*     4.2     0.2    -      -       -      -
    492A  PRO*     3.6    20.0    -      -       +      +
    494A  ASP*     2.7    37.5    +      -       -      -
    495A  LEU*     3.3    20.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 451 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366A  TRP*     3.7    15.7    -      -       +      -
    384A  SER*     4.2    14.2    +      -       -      +
    385A  GLY      2.7    29.4    +      -       -      +
    386A  TYR*     3.9    14.6    -      -       +      +
    390A  ASP*     4.1    12.4    +      -       -      +
    391A  VAL      4.0     2.2    -      -       -      -
    392A  LEU*     3.8    10.5    -      -       +      -
    450A  TYR*     1.3    73.4    -      -       -      +
    452A  ASN*     1.3    87.6    -      -       -      +
    453A  GLY      3.2     0.4    -      -       -      -
    454A  VAL*     2.9    26.5    +      -       -      +
    456A  GLN*     3.8    17.2    -      -       -      +
----------------------------------------------------------
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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