Contacts of the helix formed by residues 425 - 437 (chain J) in PDB entry 6H25


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 425 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422J  ASP*     3.6    27.3    +      -       -      +
    423J  VAL      3.6     3.0    +      -       -      -
    424J  GLY*     1.3    79.6    -      -       -      +
    426J  LYS*     1.3    66.2    +      -       -      +
    427J  GLU*     3.5     4.0    -      -       +      +
    428J  THR*     4.1     9.9    -      -       -      +
    429J  GLU*     3.4    22.5    +      -       -      +
    834J  PHE*     4.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 426 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    424J  GLY      3.8     0.6    +      -       -      -
    425J  GLU*     1.3    72.6    -      -       -      +
    427J  GLU*     1.3    59.0    +      -       -      +
    429J  GLU*     3.4     2.4    +      -       -      +
    430J  THR*     2.7    46.0    +      -       -      +
    534J  GLU*     4.6    16.6    -      -       +      +
    645J  THR      4.5     2.0    +      -       -      -
    646J  HIS*     2.4    48.2    +      -       +      +
    834J  PHE*     4.2    18.2    -      -       +      -
    835J  HIS*     3.1    34.3    -      -       -      +
    838J  LEU*     4.9    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 427 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    425J  GLU*     3.5     2.8    -      -       +      +
    426J  LYS*     1.3    80.7    -      -       -      +
    428J  THR*     1.3    58.6    +      -       -      +
    430J  THR*     3.4     3.9    +      -       -      -
    431J  GLU*     3.0    57.6    +      -       -      +
    535J  LYS*     4.2    21.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 428 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397J  ARG*     4.2    20.2    -      -       +      -
    420J  LEU*     4.0    11.4    +      -       +      +
    421J  GLY*     3.3    49.5    +      -       -      +
    422J  ASP*     3.7    15.7    +      -       -      +
    425J  GLU*     3.8    11.5    +      -       -      +
    426J  LYS      3.3     0.6    -      -       -      -
    427J  GLU*     1.3    78.9    -      -       -      +
    429J  GLU*     1.3    58.8    +      -       -      +
    431J  GLU*     3.3     5.7    +      -       -      +
    432J  VAL*     2.9    33.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 429 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397J  ARG*     2.5    46.3    +      -       -      -
    423J  VAL*     4.1    12.8    -      -       -      +
    424J  GLY*     4.2    11.0    +      -       -      +
    425J  GLU      3.4    17.5    +      -       -      +
    426J  LYS      4.0     0.2    -      -       -      +
    428J  THR*     1.3    78.8    -      -       -      +
    430J  THR*     1.3    57.4    +      -       -      +
    432J  VAL*     3.8     6.6    -      -       -      +
    433J  LEU*     3.0    37.0    +      -       +      +
    834J  PHE*     3.8    36.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 430 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    426J  LYS*     2.7    33.6    +      -       -      +
    427J  GLU*     3.6     7.8    -      -       -      -
    428J  THR      3.2     0.2    -      -       -      -
    429J  GLU*     1.3    76.5    -      -       -      +
    431J  GLU*     1.3    59.4    +      -       +      +
    433J  LEU*     3.3    13.5    +      -       -      +
    434J  LEU*     3.0    38.2    +      -       +      +
    532J  LEU*     3.8    25.0    -      -       +      +
    534J  GLU*     6.1     0.7    -      -       -      +
    535J  LYS*     3.5    28.3    -      -       -      +
    834J  PHE*     5.0     4.9    -      -       -      -
    835J  HIS*     5.7     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 431 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418J  ARG*     5.0     6.2    +      -       -      -
    420J  LEU*     4.4    22.4    -      -       +      +
    427J  GLU*     3.0    43.9    +      -       -      +
    428J  THR*     4.0     3.9    -      -       -      +
    430J  THR*     1.3    78.8    -      -       +      +
    432J  VAL*     1.3    57.8    +      -       -      +
    434J  LEU*     3.4    10.8    +      -       +      +
    435J  LEU*     2.9    35.9    +      -       +      +
    441J  HIS*     4.6    23.0    +      -       +      +
    535J  LYS*     5.9     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 432 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357J  CYS*     4.1    24.7    -      -       +      -
    376J  ALA*     5.2     1.1    -      -       +      -
    397J  ARG*     3.7    50.5    -      -       +      +
    399J  ILE*     6.1     0.2    -      -       +      -
    420J  LEU*     3.7    20.4    -      -       +      -
    428J  THR      2.9    20.4    +      -       -      +
    429J  GLU*     3.8     8.1    -      -       -      +
    431J  GLU*     1.3    77.6    -      -       -      +
    433J  LEU*     1.3    59.7    +      -       -      +
    435J  LEU*     3.2     1.6    +      -       -      +
    436J  GLU*     2.9    35.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 433 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429J  GLU*     3.0    28.3    +      -       +      +
    430J  THR*     3.3    12.8    -      -       -      +
    432J  VAL*     1.3    78.9    -      -       +      +
    434J  LEU*     1.3    68.2    +      -       +      +
    436J  GLU*     4.1     3.1    -      -       -      -
    437J  HIS*     3.2    30.4    +      -       +      +
    532J  LEU*     4.1    20.6    -      -       +      -
    827J  ALA*     3.8    27.7    -      -       -      +
    830J  ALA*     4.4    17.0    -      -       +      +
    831J  SER*     4.3    19.3    -      -       -      +
    834J  PHE*     4.7    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 434 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    430J  THR*     3.0    35.9    +      -       +      +
    431J  GLU*     3.7     9.9    -      -       +      +
    432J  VAL      3.1     0.2    -      -       -      -
    433J  LEU*     1.3    87.6    -      -       +      +
    435J  LEU*     1.3    65.1    +      -       -      +
    437J  HIS      3.6     1.2    +      -       -      -
    438J  ASP*     3.2     3.5    +      -       -      -
    439J  VAL*     3.2    50.4    +      -       +      +
    441J  HIS*     4.0    24.0    -      -       +      +
    530J  VAL*     4.9     0.9    -      -       +      -
    532J  LEU*     4.3    17.5    -      -       +      -
    535J  LYS*     5.2     4.5    -      -       -      +
    537J  ILE*     3.7    33.0    -      -       +      -
    827J  ALA*     4.9     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 435 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354J  ARG*     4.1    10.4    +      -       -      -
    355J  PRO      5.5     1.6    -      -       -      +
    357J  CYS*     4.0    16.4    -      -       -      -
    399J  ILE*     4.6    17.0    -      -       +      -
    418J  ARG*     5.4     4.9    -      -       -      +
    420J  LEU*     4.2    20.9    -      -       +      -
    431J  GLU*     2.9    22.4    +      -       +      +
    432J  VAL      3.2     2.4    +      -       -      +
    434J  LEU*     1.3    75.4    -      -       -      +
    436J  GLU*     1.3    64.9    +      -       -      +
    438J  ASP*     3.6    10.9    +      -       -      +
    439J  VAL      5.5     0.9    -      -       -      +
    441J  HIS*     3.5    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 436 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354J  ARG*     3.9    31.1    +      -       -      +
    356J  TYR*     4.1     5.8    -      -       -      +
    357J  CYS*     3.1    37.4    +      -       +      +
    376J  ALA*     3.4    23.9    -      -       +      +
    377J  ASP*     4.0    18.6    -      -       -      +
    432J  VAL*     2.9    23.3    +      -       +      +
    433J  LEU*     4.5     1.6    -      -       -      +
    434J  LEU      3.3     0.2    -      -       -      -
    435J  LEU*     1.3    79.5    -      -       -      +
    437J  HIS*     1.3    76.1    +      -       +      +
    438J  ASP*     3.2     2.5    +      -       -      +
    823J  MET*     4.5     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 437 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    433J  LEU*     3.2    23.3    +      -       +      +
    434J  LEU      3.6     2.9    +      -       -      +
    436J  GLU*     1.3    86.1    -      -       +      +
    438J  ASP*     1.3    66.9    +      -       -      +
    439J  VAL*     3.4     5.0    +      -       +      +
    823J  MET*     2.5    64.4    -      -       +      +
    826J  TYR*     3.8    30.2    +      +       +      +
    827J  ALA*     4.8     9.1    -      -       +      -
    830J  ALA*     4.8    18.6    -      -       +      -
----------------------------------------------------------
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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