Contacts of the strand formed by residues 455 - 465 (chain A) in PDB entry 4HXG


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 455 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377A  LYS*     3.7     2.8    -      -       -      +
    380A  VAL*     3.7     6.7    -      -       +      -
    409A  TYR*     3.3    25.3    -      -       +      -
    448A  PHE*     3.6    31.2    -      -       +      -
    449A  LEU*     4.0     8.1    -      -       +      +
    452A  GLU      3.0    14.9    +      -       -      +
    453A  PRO      3.6     9.7    -      -       -      +
    454A  GLN*     1.3    78.1    -      -       -      +
    456A  ASP*     1.3    61.6    +      -       -      +
    457A  ARG*     3.4     7.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 456 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377A  LYS*     3.8    25.9    -      -       +      +
    378A  ALA      3.0    18.3    +      -       -      +
    379A  PRO*     4.7     0.4    -      -       +      -
    380A  VAL*     4.3     1.6    -      -       -      +
    454A  GLN      3.5     0.8    +      -       -      -
    455A  ALA*     1.3    71.0    -      -       -      +
    457A  ARG*     1.3    63.5    +      -       -      +
    458A  GLU*     2.7    27.3    +      -       -      +
    459A  ARG*     2.9    58.4    +      -       -      +
    460A  ILE*     3.7     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 457 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    446A  GLU*     3.7    16.6    +      -       -      -
    449A  LEU*     3.4    52.5    +      -       +      +
    453A  PRO*     6.4     0.4    -      -       -      +
    455A  ALA      3.4     7.8    +      -       -      +
    456A  ASP*     1.3    73.2    +      -       -      +
    458A  GLU*     1.3    77.4    +      -       +      +
    459A  ARG      3.5     0.2    -      -       -      -
    460A  ILE*     3.4    24.8    -      -       +      +
    481A  LEU*     4.5    13.6    -      -       +      +
    483A  LYS*     4.7     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 458 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    456A  ASP*     2.7    17.0    +      -       -      +
    457A  ARG*     1.3    94.2    -      -       +      +
    459A  ARG*     1.3    61.2    +      -       +      +
    460A  ILE      3.9     0.4    -      -       -      -
    483A  LYS*     3.0    52.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 459 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    376A  GLU*     6.1     0.2    -      -       -      +
    377A  LYS*     3.2    31.7    +      -       -      +
    379A  PRO*     3.5    30.5    -      -       +      +
    380A  VAL      2.9    22.7    +      -       -      -
    456A  ASP*     2.9    36.7    +      -       -      +
    458A  GLU*     1.3    82.5    -      -       +      +
    460A  ILE*     1.3    60.6    +      -       -      +
    483A  LYS*     4.3     5.4    -      -       +      -
    604A  LEU*     3.2    22.8    -      -       +      +
    605A  LYS*     3.0    41.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 460 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380A  VAL*     3.3    17.7    -      -       +      +
    382A  VAL*     4.2    10.8    -      -       +      -
    445A  ILE*     4.7     7.6    -      -       +      -
    449A  LEU*     4.0    26.9    -      -       +      -
    456A  ASP      3.7     5.8    -      -       -      +
    457A  ARG*     3.4    31.0    -      -       +      +
    458A  GLU      3.9     2.4    +      -       -      -
    459A  ARG*     1.3    79.9    -      -       -      +
    461A  GLY*     1.3    66.2    +      -       -      +
    481A  LEU*     4.3    22.8    +      -       +      +
    482A  PHE*     3.1    30.0    -      -       +      +
    483A  LYS*     3.0    25.2    +      -       -      +
    604A  LEU*     3.5     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 461 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380A  VAL      2.7    14.2    +      -       -      +
    381A  ILE*     4.3     2.5    -      -       -      -
    382A  VAL*     2.7    30.6    +      -       -      +
    460A  ILE*     1.3    74.7    -      -       -      +
    462A  ILE*     1.3    63.0    +      -       -      +
    482A  PHE*     4.1     1.3    -      -       -      -
    484A  ALA      3.1    14.6    -      -       -      -
    600A  PHE*     4.4     4.0    -      -       -      -
    604A  LEU*     3.3    19.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 462 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382A  VAL*     3.3    18.2    -      -       +      +
    384A  VAL*     3.9    24.0    -      -       +      -
    438A  PHE*     5.9     1.1    -      -       +      -
    441A  ILE*     5.1     4.9    -      -       +      -
    461A  GLY*     1.3    75.6    -      -       -      +
    463A  THR*     1.3    65.4    +      -       -      +
    471A  MET*     4.5     7.2    -      -       +      +
    472A  THR*     3.7    18.7    -      -       +      +
    475A  ALA*     3.8    22.7    -      -       +      -
    476A  LEU*     4.2    11.9    -      -       +      -
    482A  PHE*     3.6    39.9    -      -       +      -
    484A  ALA      3.1     8.4    +      -       -      +
    485A  GLY*     3.0     7.4    -      -       -      -
    486A  ILE      3.0    22.0    +      -       -      -
    600A  PHE*     4.1     3.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 463 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381A  ILE*     3.8    14.1    -      -       +      -
    382A  VAL      2.8    14.8    +      -       -      +
    383A  PHE*     3.5    31.4    -      -       +      +
    384A  VAL*     3.0    25.6    +      -       -      +
    462A  ILE*     1.3    76.7    -      -       -      +
    464A  GLY*     1.3    60.1    +      -       -      +
    472A  THR*     3.3     6.9    +      -       -      -
    486A  ILE*     2.9    20.7    +      -       -      +
    488A  GLU*     4.1     4.2    +      -       -      -
    596A  PHE*     3.4    20.7    -      -       +      -
    600A  PHE*     4.0    11.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 464 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    383A  PHE*     6.1     0.9    -      -       -      -
    384A  VAL      3.6    10.1    -      -       -      -
    392A  TYR*     5.8     0.9    -      -       -      -
    463A  THR*     1.3    81.8    +      -       -      +
    465A  ILE*     1.3    63.5    +      -       -      -
    468A  GLY      3.3    14.4    -      -       -      -
    469A  GLY*     3.3    11.2    -      -       -      -
    472A  THR*     3.2     5.5    +      -       -      -
    486A  ILE      3.3     1.4    +      -       -      +
    488A  GLU*     3.0    28.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 465 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384A  VAL      4.2     2.4    +      -       -      -
    386A  GLY*     3.7     9.9    +      -       -      -
    397A  LYS*     4.2    21.3    -      -       -      +
    464A  GLY*     1.3    77.6    -      -       -      -
    466A  ALA*     1.3    76.2    +      -       +      +
    468A  GLY*     2.9    15.6    +      -       -      -
    469A  GLY      3.4     0.4    -      -       -      -
    488A  GLU*     3.2    30.7    -      -       +      +
    489A  ASN*     4.2    12.3    -      -       +      +
    578A  HIS*     4.5    14.4    -      -       +      +
    579A  GLY*     6.1     0.2    -      -       -      -
    581A  SER*     3.6    28.5    -      -       -      +
    592A  ARG*     4.4     6.5    -      -       -      +
----------------------------------------------------------
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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