Contacts of the strand formed by residues 449 - 454 (chain B) in PDB entry 3HO5


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 THR 449 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    436B  ALA      3.8     0.3    -      -       -      +
    437B  VAL*     3.4     3.3    -      -       -      -
    438B  ASP*     2.7    51.0    +      -       -      +
    440B  HIS*     3.2    14.6    +      -       -      -
    448B  LEU*     1.3    76.9    -      -       -      +
    450B  ILE*     1.3    67.7    +      -       -      +
    451B  LEU*     4.7     0.9    -      -       +      +
    465B  ILE*     3.7    29.6    -      -       +      -
    466B  LEU      3.4     9.4    -      -       -      +
    467B  GLN*     3.2    23.9    +      -       +      +
    509B  TYR*     3.6    16.5    +      -       +      +
    530B  TRP*     6.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 450 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358B  LEU*     5.1     6.1    -      -       +      -
    366B  TYR*     5.3     7.2    -      -       +      -
    368B  ILE*     3.9    20.6    -      -       +      -
    392B  VAL*     4.9    10.8    -      -       +      -
    429B  LEU*     6.5     0.2    -      -       +      -
    435B  CYS*     3.6    20.0    -      -       +      -
    436B  ALA      3.3     6.1    -      -       -      +
    437B  VAL*     4.5    10.3    -      -       +      -
    448B  LEU*     4.6    17.7    -      -       +      +
    449B  THR*     1.3    78.0    -      -       -      +
    451B  LEU*     1.3    61.7    +      -       -      +
    452B  CYS*     3.4    22.0    -      -       -      -
    464B  ARG      3.9     0.3    -      -       -      +
    465B  ILE*     3.5     2.6    -      -       -      +
    466B  LEU*     2.9    56.2    +      -       +      +
    468B  ILE*     5.9     1.3    -      -       +      -
    480B  LEU*     6.3     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 451 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    435B  CYS*     3.6     0.3    -      -       -      -
    436B  ALA      3.0    31.2    +      -       -      +
    449B  THR*     4.2     0.4    -      -       +      -
    450B  ILE*     1.3    72.5    -      -       -      +
    452B  CYS*     1.3    70.3    +      -       -      +
    463B  ALA*     4.2    15.3    -      -       +      -
    464B  ARG      3.4     8.1    -      -       -      +
    465B  ILE*     4.5     9.0    -      -       +      +
    483B  PHE*     4.0    21.5    -      -       +      -
    486B  PHE*     4.8     1.3    -      -       +      -
    509B  TYR*     3.5    39.0    -      -       +      +
    511B  PHE*     3.5    30.6    -      -       +      -
    521B  LEU*     4.2    13.2    -      -       +      -
    530B  TRP*     4.1    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 452 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368B  ILE*     4.4     7.2    -      -       -      -
    429B  LEU*     5.0    11.0    -      -       +      -
    432B  PRO*     4.5     7.6    -      -       +      -
    435B  CYS*     2.0    49.1    -      -       -      +
    450B  ILE*     3.4    21.3    -      -       -      -
    451B  LEU*     1.3    77.4    -      -       -      +
    453B  SER*     1.3    66.3    +      -       -      +
    454B  ASP*     5.8     0.7    -      -       +      -
    463B  ALA*     3.3     6.9    -      -       -      +
    464B  ARG*     2.9    43.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 453 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    431B  ASP      3.6     0.2    -      -       -      +
    432B  PRO*     3.2     4.7    -      -       -      +
    433B  GLY*     2.9    36.7    +      -       -      +
    434B  ARG      5.4     1.6    +      -       -      -
    435B  CYS*     5.1     0.2    -      -       -      -
    451B  LEU      4.3     0.4    +      -       -      -
    452B  CYS*     1.3    73.9    -      -       -      +
    454B  ASP*     1.3    59.9    +      -       -      +
    455B  SER      4.2     0.4    -      -       -      -
    461B  SER*     4.8     5.8    -      -       -      -
    462B  SER      3.8     4.9    -      -       -      -
    463B  ALA*     4.6     2.9    -      -       -      +
    486B  PHE*     5.0     2.7    -      -       -      -
    491B  LEU*     4.0    37.4    +      -       -      +
    493B  GLY*     4.0    12.1    +      -       -      -
    511B  PHE*     4.4    10.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 454 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429B  LEU*     3.8     2.4    -      -       +      +
    430B  HIS*     2.9    20.9    +      -       -      +
    431B  ASP      2.5    33.5    +      -       -      -
    432B  PRO*     4.4     2.9    -      -       +      -
    452B  CYS*     5.5     1.1    -      -       +      -
    453B  SER*     1.3    75.2    -      -       -      +
    455B  SER*     1.3    57.9    +      -       -      +
    456B  ASN*     2.8    37.9    +      -       -      +
    461B  SER*     3.7     3.7    -      -       -      -
    462B  SER*     2.8    32.0    +      -       -      +
    464B  ARG*     2.9    34.8    +      -       +      +
----------------------------------------------------------
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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