Contacts of the helix formed by residues 340 - 360 (chain A) in PDB entry 4IX8


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 PRO 340 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ILE*     5.1     7.0    -      -       +      -
    338A  LYS      3.3     6.6    -      -       -      +
    339A  CYS*     1.3    87.8    -      -       +      +
    341A  THR*     1.3    68.6    +      -       +      +
    342A  GLU*     3.0    12.7    +      -       +      +
    343A  CYS*     3.1    45.0    +      -       -      +
    344A  THR*     4.2     3.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339A  CYS      3.8     1.6    +      -       -      -
    340A  PRO*     1.3    72.8    -      -       +      +
    342A  GLU*     1.3    67.2    +      -       +      +
    344A  THR*     3.2    17.6    +      -       -      -
    345A  GLU*     3.2    27.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  PRO*     3.0    11.1    -      -       +      +
    341A  THR*     1.3    84.1    -      -       +      +
    343A  CYS*     1.3    62.9    +      -       -      +
    345A  GLU*     3.2    33.9    -      -       -      +
    346A  HIS*     3.3    11.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  LYS      5.4     1.7    -      -       -      +
     90A  PRO*     4.0    34.8    -      -       +      -
     92A  ILE*     5.8     0.4    -      -       -      -
    339A  CYS*     5.6     1.8    -      -       +      -
    340A  PRO*     3.1    39.9    +      -       +      +
    342A  GLU*     1.3    79.7    -      -       -      +
    344A  THR*     1.3    60.6    +      -       -      +
    346A  HIS*     3.8    10.6    +      -       -      +
    347A  ILE*     3.7    20.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258A  GLU*     3.2    40.8    +      -       +      +
    259A  MET*     5.3     4.0    -      -       +      -
    287A  TYR*     3.7    26.2    +      -       +      -
    340A  PRO      4.2     3.3    +      -       -      -
    341A  THR*     3.2    11.7    +      -       -      -
    342A  GLU      3.2     0.2    -      -       -      -
    343A  CYS*     1.3    77.9    -      -       -      +
    345A  GLU*     1.3    61.2    +      -       -      +
    346A  HIS      3.0     2.5    -      -       -      -
    347A  ILE*     2.9    25.9    +      -       +      +
    348A  VAL*     3.0    18.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  THR*     3.2    24.1    +      -       -      +
    342A  GLU*     3.2    32.4    -      -       +      +
    344A  THR*     1.3    79.5    -      -       -      +
    346A  HIS*     1.3    56.8    +      -       -      +
    348A  VAL*     3.7    10.3    -      -       +      +
    349A  THR*     2.9    33.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  ASN      3.3    26.2    +      -       -      -
     87A  LEU*     4.7     4.7    -      -       +      -
     88A  LYS*     5.3     5.8    +      -       +      +
    342A  GLU      3.3    11.9    +      -       -      +
    343A  CYS*     3.8    11.6    +      -       -      +
    345A  GLU*     1.3    76.9    -      -       -      +
    347A  ILE*     1.3    73.8    +      -       -      +
    349A  THR*     3.4     8.7    +      -       +      -
    350A  GLN*     3.2    40.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  LEU*     4.0    37.7    -      -       +      -
     88A  LYS      4.6     8.1    -      -       -      +
    259A  MET*     4.5    17.3    -      -       +      -
    286A  LLP      5.8     0.4    -      -       -      +
    287A  TYR*     3.2    29.4    -      -       +      +
    289A  VAL*     3.9    17.3    -      -       +      -
    343A  CYS      3.7    17.7    -      -       -      +
    344A  THR*     2.9    13.2    +      -       +      +
    346A  HIS*     1.3    83.2    -      -       -      +
    348A  VAL*     1.3    64.2    +      -       +      +
    350A  GLN*     3.1     5.4    +      -       -      +
    351A  LEU*     3.0    36.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258A  GLU      4.5     5.8    -      -       -      +
    259A  MET*     4.7     6.1    -      -       +      -
    260A  VAL      3.8    21.3    -      -       -      +
    261A  LEU*     4.0    14.1    -      -       +      -
    262A  ASN      4.8     0.4    -      -       -      +
    344A  THR*     3.0    25.0    +      -       +      +
    345A  GLU*     3.7    12.1    -      -       -      +
    347A  ILE*     1.3    74.9    -      -       +      +
    349A  THR*     1.3    59.5    +      -       -      +
    351A  LEU*     3.1    10.8    +      -       +      +
    352A  GLU*     2.9    53.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345A  GLU*     2.9    21.9    +      -       -      +
    346A  HIS*     3.6     9.6    -      -       +      -
    347A  ILE      3.3     0.2    -      -       -      -
    348A  VAL*     1.3    76.6    -      -       -      +
    350A  GLN*     1.3    69.7    +      -       -      +
    352A  GLU*     3.4    15.8    +      -       -      +
    353A  ALA*     3.2    22.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  ASN*     3.4    33.2    +      -       -      +
     87A  LEU*     3.8    20.2    -      -       +      -
    346A  HIS*     3.2    35.2    +      -       -      +
    347A  ILE      3.1     7.7    +      -       -      +
    349A  THR*     1.3    82.9    -      -       -      +
    351A  LEU*     1.3    57.8    +      -       +      +
    353A  ALA*     3.4     8.4    +      -       -      +
    354A  GLY*     3.1    22.3    +      -       -      -
    425A  VAL      4.2     3.8    -      -       -      +
    426A  SER*     5.8     2.2    -      -       -      +
    427A  ARG      5.1     3.1    -      -       -      +
    428A  PRO*     5.6     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 351 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  LEU*     5.1     3.1    -      -       +      -
    259A  MET*     4.2    18.2    -      -       +      -
    261A  LEU*     4.0    22.8    -      -       +      +
    347A  ILE*     3.0    37.0    +      -       +      +
    348A  VAL*     3.1     6.5    +      -       -      +
    350A  GLN*     1.3    75.9    -      -       +      +
    352A  GLU*     1.3    65.6    +      -       -      +
    354A  GLY      3.2     0.2    +      -       -      -
    355A  ALA*     2.9    20.4    +      -       -      +
    376A  SER      3.7    18.6    -      -       -      +
    377A  MET*     3.9    16.4    -      -       +      -
    425A  VAL*     3.0    18.6    -      -       +      +
    426A  SER*     3.7    36.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 352 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261A  LEU*     4.0    14.1    -      -       +      -
    262A  ASN*     2.8    44.8    +      -       -      +
    263A  ASN      4.8     0.2    +      -       -      -
    348A  VAL*     2.9    34.2    +      -       -      +
    349A  THR*     3.7    14.0    +      -       -      +
    351A  LEU*     1.3    75.5    -      -       -      +
    353A  ALA*     1.3    63.6    +      -       -      +
    355A  ALA*     3.1     8.8    +      -       -      +
    356A  LYS*     3.0    21.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 353 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    349A  THR*     3.2    13.8    +      -       +      +
    350A  GLN*     3.7    11.2    -      -       -      +
    351A  LEU      3.2     0.2    -      -       -      -
    352A  GLU*     1.3    76.2    -      -       -      +
    354A  GLY*     1.3    62.9    +      -       -      +
    356A  LYS*     3.3    16.4    +      -       -      +
    357A  VAL*     3.3    17.8    +      -       -      +
    429A  SER*     4.1    15.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350A  GLN      3.1    12.4    +      -       -      -
    351A  LEU      3.2     3.9    +      -       -      -
    353A  ALA*     1.3    76.9    -      -       -      +
    355A  ALA*     1.3    61.1    +      -       -      +
    357A  VAL*     3.2    12.9    +      -       -      +
    358A  TYR*     3.4    18.9    +      -       -      -
    425A  VAL*     3.7    15.3    -      -       -      -
    427A  ARG      5.1     0.9    -      -       -      -
    429A  SER*     4.9     2.2    +      -       -      -
    432A  LEU*     3.5    25.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261A  LEU*     5.1     3.6    -      -       +      -
    351A  LEU      2.9    12.2    +      -       -      +
    352A  GLU*     3.1    13.4    +      -       -      +
    354A  GLY*     1.3    78.2    -      -       -      +
    356A  LYS*     1.3    62.1    +      -       -      +
    358A  TYR*     3.0    16.1    +      -       -      +
    359A  ALA*     3.2    11.3    +      -       -      +
    370A  MET*     5.0     2.6    -      -       -      +
    372A  ALA*     5.8     2.5    -      -       +      +
    373A  PRO*     3.8    31.6    -      -       +      +
    425A  VAL*     3.6     8.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 356 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352A  GLU      3.0    11.8    +      -       -      +
    353A  ALA*     3.3    11.6    +      -       -      +
    355A  ALA*     1.3    76.5    -      -       -      +
    357A  VAL*     1.3    63.4    +      -       +      +
    359A  ALA*     3.2    22.7    +      -       -      +
    360A  ARG*     3.6     8.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 357 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  ALA      3.4    14.4    -      -       -      +
    354A  GLY*     3.2     8.5    +      -       -      +
    355A  ALA      3.1     0.8    -      -       -      -
    356A  LYS*     1.3    78.3    -      -       +      +
    358A  TYR*     1.3    62.5    +      -       +      +
    360A  ARG*     3.2    26.8    +      -       -      +
    429A  SER*     4.4    12.1    -      -       -      +
    432A  LEU*     3.7    18.8    -      -       +      -
    433A  ASN*     3.4    57.0    -      -       -      +
    436A  VAL*     3.9    13.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 358 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  LEU*     3.4    28.9    -      -       +      +
    354A  GLY      3.4    20.4    +      -       -      -
    355A  ALA*     3.0     8.9    +      -       -      +
    357A  VAL*     1.3    73.9    -      -       +      +
    359A  ALA*     1.3    59.6    +      -       -      +
    360A  ARG      3.0     2.5    -      -       -      -
    361A  LEU*     2.8    49.5    +      -       +      +
    362A  LEU      4.2     0.2    +      -       -      -
    370A  MET*     3.8    25.4    -      -       +      +
    379A  VAL*     4.0    12.1    -      -       +      -
    381A  LEU*     4.7     3.8    -      -       +      -
    423A  ALA*     3.4    22.6    -      -       +      +
    424A  THR      2.6    30.2    +      -       -      -
    425A  VAL*     3.7    23.6    -      -       +      -
    432A  LEU*     3.6    16.8    -      -       +      +
    436A  VAL*     4.2    15.0    -      -       +      -
    439A  ILE*     5.5     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 359 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  ALA      3.2    10.2    +      -       -      +
    356A  LYS*     3.3    17.7    -      -       -      +
    357A  VAL      3.2     0.2    -      -       -      -
    358A  TYR*     1.3    77.6    -      -       -      +
    360A  ARG*     1.3    62.6    +      -       -      +
    362A  LEU*     2.9    36.1    +      -       +      +
    363A  GLU*     4.0     6.5    +      -       -      +
    370A  MET*     4.5     4.7    -      -       +      +
    372A  ALA*     6.3     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 360 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  LYS      3.6     7.8    +      -       -      +
    357A  VAL*     3.2    18.8    +      -       -      +
    358A  TYR      3.0     0.8    -      -       -      -
    359A  ALA*     1.3    78.3    -      -       -      +
    361A  LEU*     1.3    59.8    +      -       -      +
    363A  GLU*     3.1    41.7    +      -       -      +
    364A  HIS*     3.7    14.8    +      -       +      -
    433A  ASN*     2.6    48.3    +      -       -      +
    436A  VAL*     3.8    21.1    -      -       +      +
    437A  ASP*     2.6    30.7    +      -       -      -
    440A  ILE*     3.9    13.8    -      -       +      +
----------------------------------------------------------
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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