Contacts of the strand formed by residues 447 - 458 (chain A) in PDB entry 2HD5


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 VAL 447 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    430A  ASP*     3.0    37.0    -      -       -      +
    431A  LEU      3.3     4.5    -      -       -      +
    432A  ASP*     3.7    23.6    -      -       -      +
    443A  HIS*     4.1     9.1    -      -       +      -
    446A  ALA*     1.3    83.0    -      -       -      +
    448A  TYR*     1.3    58.0    +      -       -      +
    449A  ASN*     5.2     0.7    -      -       -      +
    520A  LEU*     3.6     7.4    -      -       -      +
    521A  ALA*     2.7    46.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 448 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398A  PHE*     3.3    28.3    -      +       -      +
    399A  PRO*     2.7    35.3    +      -       -      +
    402A  LEU*     3.5    21.8    -      -       +      -
    430A  ASP      3.2     6.1    +      -       -      -
    431A  LEU*     2.9    39.0    +      -       +      +
    433A  LEU*     3.8    30.1    -      -       +      -
    446A  ALA      4.1     8.7    -      -       -      -
    447A  VAL*     1.3    75.9    -      -       -      +
    449A  ASN*     1.3    62.9    +      -       -      +
    518A  TYR*     3.7    30.7    -      -       +      -
    519A  GLU      3.3     7.0    -      -       -      -
    520A  LEU*     3.4    40.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 449 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429A  LEU      3.7     8.5    -      -       -      +
    430A  ARG*     3.0    45.3    +      -       -      +
    447A  VAL*     5.2     0.7    -      -       -      +
    448A  TYR*     1.3    73.2    -      -       -      +
    450A  LEU*     1.3    68.1    +      -       -      +
    470A  ARG*     5.1     4.9    -      -       -      +
    518A  TYR*     3.4     5.6    -      -       -      -
    519A  GLU*     2.8    46.5    +      -       +      +
    521A  ALA*     3.9    22.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 450 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427A  PHE*     3.6    28.5    -      -       +      -
    428A  PRO      3.9     2.9    -      -       -      +
    429A  LEU*     2.9    30.2    +      -       +      +
    449A  ASN*     1.3    76.2    -      -       -      +
    451A  TYR*     1.3    62.5    +      -       -      +
    452A  ALA      3.6    12.6    -      -       -      +
    453A  VAL*     3.7     9.6    -      -       +      -
    470A  ARG*     4.1    13.0    +      -       -      -
    477A  TRP*     3.7    29.9    -      -       +      -
    493A  VAL*     3.8     6.7    -      -       +      -
    516A  LEU*     4.2     6.5    -      -       +      -
    517A  PHE      3.4    19.3    -      -       -      +
    518A  TYR*     3.3    36.8    -      -       +      +
    519A  GLU*     4.9     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 451 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  CYS      3.7     9.2    -      -       -      -
    234A  ASN*     3.3    24.0    -      -       +      +
    235A  THR*     2.7    41.3    +      -       +      +
    236A  ARG      5.5     0.7    -      -       -      -
    324A  PHE*     5.0     0.3    -      -       -      -
    401A  ILE*     3.3    23.5    -      -       +      +
    450A  LEU*     1.3    74.7    -      -       -      +
    452A  ALA*     1.3    69.1    +      -       +      +
    469A  CYS*     4.2     0.2    -      -       -      +
    470A  ARG*     2.7    43.0    +      -       +      +
    477A  TRP*     3.5    10.8    -      -       -      -
    517A  PHE*     2.9    46.5    +      -       +      -
    518A  TYR      3.8    11.7    -      -       -      -
    519A  GLU*     3.8    36.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 452 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  CYS*     3.8    27.1    -      -       +      +
    450A  LEU*     3.6     1.9    -      -       -      +
    451A  TYR*     1.3    95.6    -      -       +      +
    453A  VAL*     1.3    69.6    +      -       -      +
    468A  TYR      3.3    10.3    -      -       -      +
    469A  CYS*     4.2     5.6    -      -       +      -
    477A  TRP*     3.9     2.7    -      -       -      -
    517A  PHE*     2.9    38.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 453 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  CYS*     3.8     4.2    -      -       -      -
    427A  PHE*     4.0    10.1    -      -       +      -
    450A  LEU*     3.7    24.5    -      -       +      -
    452A  ALA*     1.3    79.8    -      -       -      +
    454A  SER*     1.3    65.3    +      -       -      +
    455A  ASN*     3.3    24.6    +      -       -      +
    467A  ALA*     3.3     5.9    -      -       -      +
    468A  TYR*     2.8    42.3    +      -       +      +
    477A  TRP*     4.9     0.2    -      -       +      -
    493A  VAL*     3.8    16.4    -      -       +      +
    513A  ALA*     3.7    20.6    -      -       +      -
    515A  LEU      3.2    11.4    -      -       -      +
    516A  LEU*     4.1     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 454 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  SER*     2.7    26.9    +      -       -      -
    228A  ILE*     4.3     7.9    -      -       -      +
    231A  CYS*     4.1     6.8    -      -       -      -
    296A  ALA*     3.9     6.9    -      -       -      +
    453A  VAL*     1.3    71.9    -      -       -      +
    455A  ASN*     1.3    59.9    +      -       -      +
    465A  TYR*     3.6    18.4    -      -       -      -
    466A  THR      3.7     0.2    -      -       -      -
    514A  TYR*     3.0    27.4    +      -       -      +
    515A  LEU*     2.8    34.3    +      -       -      +
    517A  PHE*     4.5     0.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 455 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453A  VAL*     3.3    19.2    +      -       -      +
    454A  SER*     1.3    73.7    -      -       -      +
    456A  HIS*     1.3    59.5    +      -       -      +
    464A  HIS      3.8     0.3    -      -       -      +
    465A  TYR*     3.0    31.2    -      -       -      -
    466A  THR*     2.9    33.5    +      -       -      +
    468A  TYR*     3.2    53.2    -      -       -      +
    493A  VAL      5.0     0.3    -      -       -      +
    495A  THR*     3.9     2.8    +      -       -      -
    512A  ASP*     3.3    19.0    -      -       +      +
    513A  ALA*     3.5    13.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 456 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420A  LYS*     2.9    40.5    +      -       +      +
    454A  SER      4.2     1.0    +      -       -      -
    455A  ASN*     1.3    75.5    -      -       -      +
    457A  SER*     1.3    66.8    +      -       -      +
    458A  GLY*     3.7    18.6    -      -       -      -
    459A  THR      3.2    25.1    -      -       -      -
    462A  GLY      4.0     1.0    +      -       -      -
    463A  GLY*     4.0     0.8    -      -       -      -
    464A  HIS      3.5     7.4    -      -       -      -
    465A  TYR*     3.6    38.6    -      +       +      -
    512A  ASP*     2.9    27.6    +      -       -      +
    514A  TYR*     4.3     5.3    -      -       +      +
     73B  LEU*     3.7    26.1    +      -       +      +
     74B  ARG      2.9    23.1    +      -       -      -
     75B  GLY*     4.3     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 457 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420A  LYS*     3.9     1.3    -      -       -      +
    456A  HIS*     1.3    79.1    -      -       -      +
    458A  GLY*     1.3    59.6    +      -       -      +
    463A  GLY*     3.0     4.9    -      -       -      -
    464A  HIS*     2.9    41.4    +      -       -      -
    512A  ASP*     3.7    20.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 458 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420A  LYS*     3.2    19.9    +      -       -      +
    422A  THR*     4.9     5.2    -      -       -      +
    456A  HIS*     3.7     5.7    +      -       -      -
    457A  SER*     1.3    77.5    +      -       -      +
    459A  THR*     1.3    67.3    +      -       -      +
    462A  GLY      3.6     7.6    -      -       -      -
    463A  GLY*     4.2     2.0    -      -       -      -
----------------------------------------------------------
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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