Contacts of the helix formed by residues 324 - 341 (chain A) in PDB entry 5HI7


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 ASN 324 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275A  MET      3.2    15.9    +      -       -      -
    276A  LEU*     3.6     3.8    -      -       -      +
    277A  THR*     2.9    29.7    +      -       -      +
    283A  TRP*     3.4    31.7    -      -       -      +
    320A  LEU*     3.9     7.9    -      -       +      +
    321A  PRO      3.0    16.3    +      -       -      +
    322A  ASP      3.6     0.2    -      -       -      +
    323A  ILE*     1.3    79.3    -      -       -      +
    325A  ILE*     1.3    54.0    +      -       -      +
    326A  TYR*     3.0    33.8    +      -       -      +
    327A  GLN*     3.1    13.1    +      -       +      +
    328A  LEU*     2.7    34.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 325 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  LEU*     4.1    23.1    -      -       +      +
    244A  MET*     4.2    12.6    -      -       -      +
    245A  THR*     4.2     9.4    -      -       +      -
    248A  GLU*     3.9    21.8    -      -       -      +
    275A  MET*     3.0    51.3    +      -       +      +
    276A  LEU*     4.7     0.2    -      -       +      -
    323A  ILE      4.1     0.4    -      -       -      -
    324A  ASN*     1.3    72.5    +      -       -      +
    326A  TYR*     1.3    85.3    +      -       +      +
    328A  LEU*     3.6     8.3    -      -       -      +
    329A  LYS*     2.9    35.0    +      -       -      +
    361A  PHE*     4.1    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 326 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  THR*     4.9     0.3    -      -       -      +
    248A  GLU*     2.5    34.9    +      -       -      -
    276A  LEU*     4.0    17.1    -      -       +      +
    283A  TRP*     3.5    41.9    -      +       +      +
    286A  VAL*     3.9    15.9    -      -       +      -
    287A  GLN*     3.1    31.5    +      -       +      +
    290A  LEU*     3.6    26.9    -      -       +      +
    324A  ASN*     3.0    13.8    +      -       -      +
    325A  ILE*     1.3    94.3    -      -       +      +
    327A  GLN*     1.3    65.4    +      -       -      +
    329A  LYS*     3.3    10.1    +      -       +      -
    330A  VAL*     3.0    27.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 327 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  VAL*     4.2     4.0    -      -       -      +
    312A  ILE*     4.0    21.0    -      -       -      +
    313A  ILE*     4.5    16.4    +      -       -      +
    319A  ARG*     5.8     2.9    -      -       -      +
    320A  LEU*     3.9    34.2    +      -       +      +
    321A  PRO      3.4    22.2    -      -       -      +
    322A  ASP*     3.7    22.5    +      -       -      +
    324A  ASN*     3.1    14.9    +      -       +      +
    326A  TYR*     1.3    74.5    -      -       -      +
    328A  LEU*     1.3    58.3    +      -       -      +
    330A  VAL*     3.1     7.1    +      -       -      +
    331A  LEU*     2.9    38.7    +      -       +      +
    353A  ARG*     3.8    12.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 328 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  LEU*     4.0    20.0    -      -       +      -
    322A  ASP      3.5    10.7    +      -       -      +
    324A  ASN      2.7    18.6    +      -       -      +
    325A  ILE*     3.6     7.2    -      -       -      +
    327A  GLN*     1.3    73.5    -      -       -      +
    329A  LYS*     1.3    62.1    +      -       -      +
    331A  LEU*     3.4     8.5    +      -       +      +
    332A  ASP*     3.0    22.9    +      -       -      +
    354A  THR*     3.7    32.3    -      -       +      -
    357A  PRO*     3.6    34.8    -      -       +      -
    358A  TYR*     4.0    18.4    -      -       +      -
    361A  PHE*     3.8    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 329 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241A  ASP*     2.6    30.3    +      -       -      -
    243A  LEU*     3.2    34.2    +      -       +      +
    244A  MET*     5.2     1.2    -      -       -      +
    248A  GLU*     6.2     0.2    -      -       -      -
    290A  LEU*     3.8    28.7    -      -       +      -
    294A  GLU*     4.2    16.4    +      -       -      +
    325A  ILE*     2.9    26.1    +      -       -      +
    326A  TYR*     3.7    16.4    -      -       +      +
    328A  LEU*     1.3    75.2    -      -       -      +
    330A  VAL*     1.3    59.2    +      -       -      +
    332A  ASP*     3.2     8.3    +      -       -      +
    333A  CYS*     2.9    33.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 330 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  VAL*     3.7    21.1    -      -       +      -
    290A  LEU*     3.8    18.8    -      -       +      -
    293A  ILE*     4.5     3.6    -      -       +      -
    309A  CYS*     3.6    27.6    -      -       +      +
    312A  ILE*     4.1    20.2    -      -       +      -
    313A  ILE*     3.7    25.1    -      -       +      -
    326A  TYR      3.0    18.3    +      -       -      +
    327A  GLN*     3.1    10.7    +      -       -      +
    329A  LYS*     1.3    73.6    -      -       -      +
    331A  LEU*     1.3    66.0    +      -       -      +
    333A  CYS*     3.2     1.4    +      -       -      -
    334A  ALA*     2.9    22.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 331 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313A  ILE*     3.9    26.7    -      -       +      -
    322A  ASP*     3.5    38.6    -      -       +      +
    327A  GLN*     2.9    25.2    +      -       +      +
    328A  LEU*     3.7    11.7    -      -       +      +
    330A  VAL*     1.3    75.7    -      -       -      +
    332A  ASP*     1.3    57.4    +      -       -      +
    334A  ALA*     3.5     1.9    +      -       -      +
    335A  MET*     2.9    28.4    +      -       -      +
    350A  TYR*     3.7    27.0    -      -       +      +
    353A  ARG*     4.0    28.9    -      -       +      +
    354A  THR*     3.8    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 332 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  GLU      4.9     0.2    -      -       -      +
    190A  MET*     4.3    13.7    -      -       -      +
    297A  LYS*     5.6     1.4    +      -       -      -
    328A  LEU      3.0    14.9    +      -       -      +
    329A  LYS*     3.5    11.4    -      -       -      +
    330A  VAL      3.1     0.4    -      -       -      -
    331A  LEU*     1.3    75.2    -      -       -      +
    333A  CYS*     1.3    68.0    +      -       -      +
    335A  MET*     3.2     7.8    +      -       -      +
    336A  ASP*     3.0    29.6    +      -       -      +
    354A  THR*     4.4     4.9    -      -       +      +
    358A  TYR*     3.2    15.2    +      -       -      +
    372A  GLN*     2.8    23.9    +      -       -      +
    505A   MG      2.8    28.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 333 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290A  LEU*     4.8     2.5    -      -       -      -
    293A  ILE*     4.0    14.8    -      -       +      -
    294A  GLU*     4.6    13.5    -      -       -      -
    297A  LYS*     3.6    35.7    -      -       +      -
    302A  TRP*     4.3     1.2    -      -       -      -
    305A  VAL*     3.8    14.1    -      -       +      +
    309A  CYS*     3.8    17.5    -      -       -      -
    329A  LYS*     2.9    21.0    +      -       -      +
    332A  ASP*     1.3    79.2    -      -       -      +
    334A  ALA*     1.3    57.6    +      -       -      +
    336A  ASP*     3.3     4.0    +      -       -      +
    337A  ALA*     2.9    29.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 334 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    306A  LEU*     4.3     5.1    -      -       +      +
    309A  CYS*     3.7    23.4    -      -       +      -
    310A  GLN      5.5     0.2    -      -       -      +
    313A  ILE*     3.7     7.9    -      -       +      -
    330A  VAL      2.9    16.5    +      -       -      +
    331A  LEU      3.7     2.7    -      -       -      +
    333A  CYS*     1.3    74.7    -      -       -      +
    335A  MET*     1.3    59.6    +      -       -      +
    337A  ALA*     3.2     6.3    +      -       -      +
    338A  CYS*     2.8    34.0    +      -       -      -
    350A  TYR*     3.4    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 335 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331A  LEU      2.9    19.1    +      -       -      +
    332A  ASP*     3.2     6.7    +      -       -      +
    334A  ALA*     1.3    76.1    -      -       -      +
    336A  ASP*     1.3    61.0    +      -       -      +
    338A  CYS*     3.2     3.3    +      -       -      +
    339A  ILE*     3.0    42.1    +      -       +      +
    347A  ALA*     3.6    20.1    -      -       -      +
    350A  TYR*     3.9    12.0    -      -       +      -
    351A  GLY*     3.5    17.3    -      -       -      +
    354A  THR*     5.8     0.2    -      -       +      -
    372A  GLN*     3.8    26.5    -      -       -      +
    375A  LYS*     3.6    31.6    -      -       +      -
    376A  VAL*     3.9    17.5    -      -       +      -
    379A  LEU*     3.9    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 336 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  GLU*     3.0    33.2    -      -       +      +
    297A  LYS*     4.8     1.1    +      -       +      -
    302A  TRP*     3.9    20.0    -      -       +      -
    332A  ASP*     3.0    29.7    +      -       -      +
    333A  CYS*     3.8     6.0    -      -       -      +
    335A  MET*     1.3    81.1    -      -       -      +
    337A  ALA*     1.3    61.8    +      -       -      +
    339A  ILE*     3.5     9.9    +      -       -      +
    340A  ASN*     2.9    29.5    +      -       -      +
    375A  LYS*     2.9    31.3    +      -       -      +
    505A   MG      3.8     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 337 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302A  TRP*     3.4    40.7    -      -       +      +
    305A  VAL*     4.0     1.3    -      -       +      -
    306A  LEU*     3.8    21.1    -      -       +      +
    333A  CYS      2.9    17.2    +      -       -      +
    334A  ALA      3.2     5.4    +      -       -      +
    336A  ASP*     1.3    75.2    -      -       -      +
    338A  CYS*     1.3    60.4    +      -       -      +
    340A  ASN*     3.3     1.6    +      -       -      +
    341A  LEU*     2.8    36.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 338 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    306A  LEU*     3.7    17.7    -      -       -      -
    334A  ALA      2.8    20.3    +      -       -      +
    337A  ALA*     1.3    76.7    -      -       -      +
    339A  ILE*     1.3    58.9    +      -       -      +
    341A  LEU*     4.5     3.6    -      -       -      +
    342A  GLY      2.9     7.4    +      -       -      -
    343A  LEU*     2.7    50.7    +      -       +      +
    346A  GLU*     3.6    42.0    -      -       -      -
    347A  ALA*     3.5    13.5    -      -       +      -
    350A  TYR*     3.8     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 339 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  GLU*     5.8     6.3    -      -       +      +
    335A  MET*     3.0    43.3    +      -       +      +
    336A  ASP*     3.8    15.7    -      -       -      +
    337A  ALA      3.2     0.2    -      -       -      -
    338A  CYS*     1.3    77.1    -      -       -      +
    340A  ASN*     1.3    67.1    +      -       -      +
    342A  GLY*     3.2    12.5    +      -       -      -
    343A  LEU      4.6     0.7    -      -       -      -
    344A  LEU*     4.8    11.4    -      -       +      +
    347A  ALA*     3.7    14.4    -      -       +      -
    375A  LYS*     4.5    15.0    -      -       +      +
    379A  LEU*     4.3    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 340 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  GLU*     4.2    14.0    +      -       -      +
    300A  TRP*     5.4     7.3    -      -       -      -
    302A  TRP*     3.0    51.5    -      -       +      +
    336A  ASP      2.9    20.9    +      -       -      +
    337A  ALA      3.9     0.2    -      -       -      +
    339A  ILE*     1.3    83.6    -      -       -      +
    341A  LEU*     1.3    61.0    +      -       -      +
    342A  GLY*     3.2     1.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302A  TRP*     4.0    14.6    -      -       +      +
    303A  GLU*     3.8    40.2    -      -       +      +
    306A  LEU*     3.7    29.2    -      -       +      -
    337A  ALA      2.8    20.6    +      -       -      +
    338A  CYS*     4.2     4.0    -      -       -      +
    340A  ASN*     1.3    76.6    -      -       -      +
    342A  GLY*     1.3    60.4    +      -       -      +
    343A  LEU*     3.4    15.4    +      -       +      +
----------------------------------------------------------
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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