Contacts of the strand formed by residues 412 - 417 (chain A) in PDB entry 1MOX


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 PHE 412 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380A  PHE*     3.6     5.4    -      -       -      +
    407A  LYS*     3.2     7.4    -      -       -      -
    408A  GLN*     2.7    44.6    +      -       +      +
    409A  HIS*     4.9     2.2    -      +       +      -
    411A  GLN*     1.3   114.9    -      -       +      +
    413A  SER*     1.3    60.6    -      -       -      +
    414A  LEU      4.4     7.4    -      -       -      +
    415A  ALA*     4.7     2.0    -      -       +      -
    436A  ASP*     3.5    23.3    -      -       +      +
    437A  VAL      4.9     0.9    -      -       -      -
    438A  ILE*     3.5    28.9    -      -       +      -
    463A  LYS*     5.7     0.4    -      -       -      -
    465A  LYS*     5.2     5.8    -      -       +      -
     48C  LEU*     3.3    54.7    -      -       +      -
     49C  LEU*     3.7    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 413 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380A  PHE*     3.1    12.9    -      -       -      +
    381A  LEU      3.0    22.7    +      -       -      -
    402A  ILE*     3.2    25.8    -      -       -      +
    404A  GLY*     3.7     7.9    -      -       -      -
    407A  LYS*     4.6     2.7    -      -       -      -
    412A  PHE*     1.3    75.3    -      -       -      +
    414A  LEU*     1.3    58.5    +      -       -      +
    415A  ALA      4.3     0.2    -      -       -      -
    432A  ILE*     3.5     9.7    -      -       -      +
    434A  ASP      3.1    27.9    +      -       -      -
    435A  GLY*     3.6    11.0    -      -       -      -
    436A  ASP      2.8     8.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 414 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381A  LEU*     3.5    38.6    -      -       +      +
    402A  ILE*     3.8    12.3    -      -       +      -
    412A  PHE*     4.4     0.6    -      -       -      +
    413A  SER*     1.3    80.5    -      -       -      +
    415A  ALA*     1.3    61.8    +      -       -      +
    416A  VAL*     4.3    17.3    -      -       +      +
    426A  LEU*     4.7    11.4    -      -       +      -
    429A  LEU*     4.3    10.5    -      -       +      -
    432A  ILE*     4.1    12.3    -      -       +      -
    436A  ASP      3.4     2.4    +      -       -      +
    437A  VAL*     3.4    29.1    -      -       +      -
    438A  ILE*     2.9    26.5    +      -       -      +
    439A  ILE*     4.8     4.9    -      -       +      -
    453A  TRP*     4.1    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 415 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380A  PHE*     6.2     0.7    -      -       +      -
    381A  LEU      2.9    12.0    +      -       -      +
    382A  LEU*     3.5    17.7    -      -       +      +
    383A  ILE      2.8    30.5    +      -       -      +
    408A  GLN*     5.4     1.1    -      -       +      -
    412A  PHE*     4.7     2.2    -      -       +      -
    413A  SER      4.3     0.2    -      -       -      -
    414A  LEU*     1.3    75.8    -      -       -      +
    416A  VAL*     1.3    62.5    +      -       -      +
    417A  VAL*     3.9     1.6    -      -       +      -
    438A  ILE*     3.4    12.3    -      -       +      -
     48C  LEU*     3.5    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 416 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    383A  ILE*     3.7    10.8    -      -       +      +
    393A  LEU*     4.4    17.0    -      -       +      -
    414A  LEU*     4.3    23.3    -      -       +      -
    415A  ALA*     1.3    75.7    -      -       -      +
    417A  VAL*     1.3    60.3    +      -       -      +
    419A  LEU*     3.7    27.4    -      -       +      -
    421A  ILE*     4.4     2.2    -      -       +      -
    424A  LEU*     4.2    22.0    -      -       +      -
    426A  LEU*     5.5     1.6    -      -       +      -
    438A  ILE      2.9     8.1    +      -       -      -
    439A  ILE*     3.3    26.8    -      -       +      -
    440A  SER      3.3     0.9    +      -       -      -
    442A  ASN*     3.0    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 417 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382A  LEU*     5.4     0.4    -      -       +      -
    383A  ILE      3.1    14.2    +      -       -      +
    384A  GLN*     3.7    25.0    -      -       +      -
    415A  ALA      4.7     1.6    -      -       -      +
    416A  VAL*     1.3    84.3    -      -       -      +
    418A  SER*     1.3    79.3    +      -       -      +
    419A  LEU*     3.3     9.6    +      -       -      +
    438A  ILE*     4.3     7.4    -      -       +      +
    440A  SER*     3.1    31.2    -      -       -      +
    442A  ASN*     3.5     2.0    -      -       -      -
     46C  ALA*     4.4    17.5    -      -       +      -
     48C  LEU*     4.4    19.5    -      -       +      -
----------------------------------------------------------
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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