Contacts of the helix formed by residues 46 - 58 (chain B) in PDB entry 3ORH


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 46 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  VAL      5.0     1.4    -      -       -      +
     42B  MET*     3.3    34.4    -      -       +      +
     43B  GLU      3.3    12.1    -      -       -      +
     44B  ARG      3.0     0.4    +      -       -      -
     45B  TRP*     1.4   103.6    -      -       +      +
     47B  THR*     1.3    61.8    +      -       -      +
     48B  PRO*     3.4     1.6    -      -       -      -
     49B  TYR*     2.9    10.8    +      -       +      +
     50B  MET*     2.9    39.9    +      -       +      +
    135B  ASP*     4.9     1.0    -      -       -      +
    171B  LEU*     3.6    19.0    -      -       +      +
    214B  LEU*     4.5     3.1    -      -       -      -
    222B  TYR*     2.4    36.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  GLU      4.7     0.2    +      -       -      -
     44B  ARG*     2.7    36.7    +      -       -      +
     45B  TRP      3.2     1.2    -      -       -      -
     46B  GLU*     1.3    74.4    -      -       -      +
     48B  PRO*     1.4    70.0    -      -       +      +
     50B  MET*     3.2     1.8    +      -       -      +
     51B  HIS*     2.9    55.7    +      -       +      +
     73B  ILE*     3.7    24.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  TRP      3.4    14.1    -      -       -      +
     46B  GLU      3.6     2.0    -      -       -      -
     47B  THR*     1.4    93.2    -      -       +      +
     49B  TYR*     1.4    59.4    +      -       -      +
     51B  HIS*     3.4    13.2    +      -       +      +
     52B  ALA      3.2    16.3    +      -       -      -
    212B  MET*     3.8    21.1    -      -       +      +
    214B  LEU*     3.8    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  GLU*     2.9    10.4    +      -       +      +
     48B  PRO*     1.4    77.2    -      -       -      +
     50B  MET*     1.4    81.8    +      -       +      +
     52B  ALA*     3.0    13.7    +      -       -      +
     53B  LEU*     3.1    23.7    +      -       +      +
    168B  TYR      4.3     0.2    +      -       -      -
    169B  CYS*     3.2    28.6    -      -       +      +
    171B  LEU*     3.4    28.5    -      -       +      -
    174B  TRP*     3.4     7.2    -      +       -      -
    212B  MET*     3.8    10.3    -      -       +      -
    214B  LEU*     4.0    17.0    -      -       +      +
    228B  MET*     3.4    37.7    -      -       +      -
    229B  ILE      2.7    24.8    +      -       -      -
    230B  THR*     3.3    25.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  MET*     3.5    24.9    -      -       +      -
     46B  GLU*     2.9    34.5    +      -       +      +
     47B  THR      3.2     6.7    +      -       -      +
     49B  TYR*     1.4   103.7    -      -       +      +
     51B  HIS*     1.4    59.2    +      -       -      +
     53B  LEU*     3.4    22.0    +      -       +      +
     54B  ALA*     2.9    29.7    +      -       -      +
     73B  ILE*     3.7    17.3    -      -       +      -
     74B  ALA*     3.9    13.9    -      -       -      +
    133B  LEU*     5.9     0.2    -      -       -      -
    135B  ASP*     3.5    21.5    -      -       -      +
    169B  CYS*     4.2     3.1    -      -       -      -
   4001B  SAH      3.4    20.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  THR*     2.9    42.2    +      -       +      +
     48B  PRO*     3.4    13.3    -      -       +      +
     50B  MET*     1.4    76.5    -      -       -      +
     52B  ALA*     1.4    56.9    +      -       -      +
     54B  ALA*     3.6     1.6    -      -       -      +
     55B  ALA*     2.9    30.8    +      -       -      +
     73B  ILE*     4.2    13.5    +      -       +      +
     77B  LYS*     3.7    49.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  PRO      3.2     4.4    +      -       -      -
     49B  TYR*     3.0    11.5    +      -       -      +
     51B  HIS*     1.4    72.0    -      -       -      +
     53B  LEU*     1.3    63.4    +      -       -      +
     55B  ALA*     3.5     6.7    +      -       -      +
     56B  ALA*     3.2    22.3    +      -       -      +
    210B  GLU*     5.1     6.0    -      -       -      +
    212B  MET*     3.7    27.6    -      -       +      -
    230B  THR*     3.5    25.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  TYR*     3.1    29.7    +      -       +      +
     50B  MET*     3.7    29.4    -      -       +      +
     51B  HIS      3.4     0.2    -      -       -      -
     52B  ALA*     1.3    72.3    -      -       -      +
     54B  ALA*     1.3    59.7    +      -       -      +
     56B  ALA      3.1     2.3    +      -       -      -
     57B  ALA*     2.9    26.0    +      -       -      +
    133B  LEU*     3.8    24.0    -      -       +      -
    167B  THR*     3.3    33.1    -      -       +      +
    168B  TYR      3.8    18.8    -      -       -      +
    169B  CYS*     3.6    28.5    -      -       +      -
    230B  THR*     3.9    13.5    -      -       +      -
    231B  PRO*     4.2     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  MET      2.9    17.2    +      -       -      +
     51B  HIS      3.6     0.2    -      -       -      +
     53B  LEU*     1.3    75.4    -      -       -      +
     55B  ALA*     1.4    52.4    +      -       -      +
     57B  ALA      3.4     0.5    +      -       -      -
     58B  SER*     2.7    39.3    +      -       -      -
     74B  ALA*     3.4    27.8    -      -       -      +
     77B  LYS*     3.5    23.3    -      -       +      -
     78B  VAL*     3.8     9.9    -      -       +      +
    133B  LEU*     3.7    10.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  HIS      2.9    17.8    +      -       -      +
     52B  ALA*     3.7     7.0    -      -       -      +
     53B  LEU      3.3     0.2    -      -       -      -
     54B  ALA*     1.4    74.6    -      -       -      +
     56B  ALA*     1.4    58.2    +      -       -      +
     58B  SER*     3.6     5.8    +      -       -      -
     59B  SER*     3.0    31.0    +      -       -      -
     77B  LYS*     4.8    10.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  ALA      3.2    12.9    +      -       -      +
     53B  LEU      3.1     8.2    +      -       -      +
     55B  ALA*     1.4    75.3    -      -       -      +
     57B  ALA*     1.4    60.5    +      -       -      +
     59B  SER*     2.8    25.8    +      -       -      -
    165B  VAL*     3.2    14.2    -      -       +      +
    167B  THR*     3.9    20.4    -      -       -      +
    210B  GLU*     5.6     0.7    -      -       -      +
    230B  THR*     4.4     3.8    -      -       +      -
    232B  LEU*     3.8    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  LEU      2.9    18.8    +      -       -      +
     54B  ALA*     4.1     3.4    -      -       -      +
     56B  ALA*     1.4    72.5    -      -       -      +
     58B  SER*     1.3    58.5    +      -       -      +
     59B  SER      3.4     0.4    +      -       -      -
     60B  LYS      4.8     1.4    +      -       -      -
     61B  GLY      5.1     0.3    -      -       -      +
     64B  VAL*     3.5    19.1    -      -       +      +
     78B  VAL*     5.0     0.9    -      -       +      -
    130B  ASP      4.8     0.2    -      -       -      -
    131B  GLY*     3.3    22.9    -      -       -      -
    132B  ILE      3.9    12.8    -      -       -      +
    133B  LEU*     3.8    29.2    -      -       +      +
    165B  VAL*     4.3     7.6    -      -       -      +
    167B  THR*     3.8     8.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  ALA      2.7    22.9    +      -       -      -
     55B  ALA*     3.6     6.8    +      -       -      -
     57B  ALA*     1.3    75.7    -      -       -      +
     59B  SER*     1.4    62.6    +      -       -      +
     60B  LYS      3.2     3.4    -      -       -      -
     61B  GLY*     3.2    15.2    +      -       -      -
     64B  VAL*     4.1     7.6    -      -       -      -
     77B  LYS      5.0     1.0    +      -       -      -
     78B  VAL*     4.2    17.9    -      -       -      -
     81B  ALA*     3.5    32.5    -      -       -      +
     82B  PRO*     5.6     1.4    -      -       -      +
     83B  ILE*     4.0    11.2    -      -       -      -
----------------------------------------------------------
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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