Contacts of the helix formed by residues 629 - 638 (chain C) in PDB entry 5UH8


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 GLY 629 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  ASN*     4.8     6.5    -      -       -      -
     30C  ASN*     3.4    24.1    +      -       -      +
     38C  ARG*     4.6     3.8    -      -       -      -
    584C  ARG*     4.8     5.3    +      -       -      -
    628C  THR*     1.3    78.5    -      -       -      +
    630C  MET*     1.3    61.5    +      -       -      +
    631C  GLU*     2.8    12.3    +      -       -      -
    632C  LEU*     3.7    12.7    +      -       -      +
    633C  ARG*     4.5     2.3    +      -       -      +
    712C  GLU*     6.0     0.2    -      -       -      -
    973C  SER*     3.3    16.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 630 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50C  VAL*     4.3    18.2    -      -       +      -
     53C  LEU*     5.7     1.3    -      -       -      -
    502C  VAL*     4.2    25.4    -      -       +      -
    584C  ARG*     4.1    30.9    -      -       +      +
    589C  VAL*     4.0    33.0    -      -       +      +
    592C  ALA*     3.6    25.8    -      -       +      +
    593C  MET*     4.2     8.5    -      -       +      -
    628C  THR*     3.2    17.5    +      -       -      +
    629C  GLY*     1.3    73.9    -      -       -      +
    631C  GLU*     1.3    65.3    +      -       -      +
    632C  LEU      3.1     4.5    +      -       -      -
    633C  ARG*     3.5    10.5    +      -       -      +
    634C  ALA*     3.1    23.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 631 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  ARG*     4.0    10.4    +      -       -      +
    593C  MET*     4.1    17.4    -      -       +      +
    624C  PRO*     4.4    18.6    -      -       +      -
    627C  GLY*     3.1    12.2    -      -       -      -
    628C  THR*     2.4    38.7    +      -       -      +
    629C  GLY*     2.8    24.1    +      -       -      -
    630C  MET*     1.3    78.8    -      -       -      +
    632C  LEU*     1.3    61.3    +      -       -      +
    634C  ALA      4.3     0.2    -      -       -      -
    635C  ALA*     3.6     1.0    +      -       -      +
    712C  GLU*     3.3    13.1    -      -       +      +
    713C  MET*     2.7    54.4    +      -       +      +
    888C  ARG*     4.6     5.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 632 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30C  ASN*     3.7    31.2    -      -       +      +
     33C  PRO*     3.9    11.4    -      -       +      -
     35C  ALA*     3.6    35.0    -      -       +      -
     36C  PRO      5.9     0.4    -      -       -      +
    629C  GLY      3.7    10.2    +      -       -      +
    630C  MET      3.1     0.6    -      -       -      -
    631C  GLU*     1.3    78.3    +      -       -      +
    633C  ARG*     1.3    71.5    +      -       +      +
    634C  ALA      3.1     0.9    +      -       -      -
    635C  ALA      3.2     9.9    +      -       -      -
    636C  ILE*     3.3    28.8    +      -       +      +
    701C  VAL*     5.6     1.3    -      -       +      -
    710C  ASP      5.1     1.1    -      -       -      +
    711C  GLY*     3.3    31.3    -      -       -      +
    712C  GLU*     4.1    16.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 633 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30C  ASN*     4.0    27.8    -      -       -      +
     32C  VAL*     6.5     1.6    -      -       -      -
     33C  PRO*     5.6     4.5    -      -       -      -
     49C  GLU*     3.9    13.9    +      -       -      +
     50C  VAL*     2.6    59.5    +      -       +      +
     51C  PRO      3.6     6.9    +      -       -      -
     52C  GLY*     4.5     1.2    -      -       -      +
     53C  LEU*     4.2     2.4    -      -       +      +
    629C  GLY      4.5     1.7    +      -       -      +
    630C  MET*     3.5    14.7    +      -       -      +
    632C  LEU*     1.3    87.8    -      -       +      +
    634C  ALA*     1.3    62.0    +      -       -      +
    636C  ILE*     4.0    10.4    -      -       -      +
    637C  ASP*     3.0    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 634 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53C  LEU*     4.3    10.7    -      -       -      +
    446C  LEU*     5.0     2.9    -      -       +      -
    449C  LEU*     4.0     8.5    -      -       +      +
    589C  VAL*     4.4    20.4    -      -       +      -
    593C  MET*     4.8     8.5    -      -       +      -
    630C  MET*     3.1    21.7    +      -       +      +
    633C  ARG*     1.3    75.4    -      -       -      +
    635C  ALA*     1.3    65.2    +      -       -      +
    637C  ASP      3.9     0.3    -      -       -      -
    638C  ALA*     3.0    25.6    +      -       -      +
    713C  MET*     3.8    18.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 635 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445C  PRO*     5.7     0.6    -      -       -      +
    631C  GLU      3.6     1.5    +      -       -      +
    632C  LEU      3.2     1.6    +      -       -      -
    634C  ALA*     1.3    79.0    -      -       -      +
    636C  ILE*     1.3    62.8    +      -       -      +
    638C  ALA*     3.5    12.5    -      -       -      +
    639C  GLY      4.2     0.7    +      -       -      -
    641C  VAL*     3.4    18.4    +      -       -      +
    708C  THR*     3.8    13.7    -      -       +      +
    711C  GLY*     3.6    19.1    -      -       -      +
    712C  GLU      3.8     3.1    -      -       -      -
    713C  MET*     3.6    43.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 636 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33C  PRO*     4.3    21.3    -      -       +      -
    632C  LEU*     3.3    33.5    +      -       +      +
    633C  ARG*     4.0    10.1    -      -       -      +
    634C  ALA      3.2     0.6    -      -       -      -
    635C  ALA*     1.3    78.2    -      -       -      +
    637C  ASP*     1.3    72.9    +      -       -      +
    638C  ALA      3.2     0.9    +      -       -      -
    639C  GLY*     3.3    12.3    +      -       -      -
    641C  VAL*     3.9    10.7    -      -       +      +
    643C  VAL*     3.9    29.5    -      -       +      +
    699C  GLY      4.8     4.3    -      -       -      +
    701C  VAL*     3.8    25.8    -      -       +      -
    711C  GLY      4.3     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 637 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  GLY*     3.9     3.6    -      -       -      -
     53C  LEU*     3.2    47.3    +      -       +      +
     54C  LEU*     3.2    27.9    -      -       +      +
    449C  LEU*     4.7     1.8    -      -       +      -
    633C  ARG*     3.0    47.9    +      -       -      +
    634C  ALA      4.2     0.4    -      -       -      +
    636C  ILE*     1.3    81.0    -      -       -      +
    638C  ALA*     1.3    64.6    +      -       -      +
    639C  GLY*     3.1     1.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 638 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54C  LEU*     4.7     2.5    -      -       -      +
    163C  LYS*     4.7     1.9    -      -       -      +
    445C  PRO*     4.1    37.1    -      -       +      +
    446C  LEU*     5.0     0.4    -      -       -      +
    449C  LEU*     4.6    16.1    +      -       +      +
    452C  LYS*     4.0    17.3    +      -       -      -
    634C  ALA      3.0    18.3    +      -       -      +
    635C  ALA*     3.5    10.5    -      -       -      +
    636C  ILE      3.1     0.8    -      -       -      -
    637C  ASP*     1.3    77.8    -      -       -      +
    639C  GLY*     1.3    58.6    +      -       -      +
    640C  ASP*     3.1    14.7    +      -       +      +
    713C  MET*     5.3     0.4    -      -       -      -
----------------------------------------------------------
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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