Contacts of the helix formed by residues 46 - 59 (chain k) in PDB entry 4B2Q


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 THR 46 (chain k).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43k  ILE*     3.6    29.0    -      -       +      +
     44k  LYS      2.9     0.8    +      -       -      -
     45k  ASP*     1.3    81.6    +      -       -      +
     47k  VAL*     1.3    61.7    +      -       -      +
     49k  PRO*     3.2    17.0    -      -       -      +
     50k  MET*     3.0    26.0    +      -       +      +
     37l  VAL*     5.9     1.8    -      -       +      -
     44l  LYS*     3.5    37.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 47 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33k  LEU*     3.6    16.2    -      -       +      -
     37k  VAL*     5.4     2.7    -      -       +      -
     43k  ILE*     3.4    37.2    -      -       +      +
     44k  LYS      3.4     3.4    +      -       -      +
     46k  THR*     1.3    78.2    -      -       -      +
     48k  PHE*     1.3    59.7    +      -       -      +
     49k  PRO      3.4     0.4    -      -       -      -
     50k  MET*     3.1     7.9    -      -       +      +
     51k  ALA*     2.9    27.4    +      -       -      +
     34l  ILE*     3.4    39.5    -      -       +      +
     37l  VAL*     3.6    19.5    -      -       +      -
     38l  SER*     4.0    11.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 48 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50j  MET*     4.8    25.4    -      -       +      -
     53j  LEU*     4.9    15.3    -      -       +      -
     30k  PHE*     6.3     2.5    -      +       -      -
     33k  LEU*     4.1    24.8    -      -       +      +
     44k  LYS*     3.1    35.2    +      -       +      +
     45k  ASP*     4.8     2.5    -      -       -      +
     47k  VAL*     1.3    78.3    -      -       -      +
     49k  PRO*     1.3    66.0    -      -       +      +
     51k  ALA*     3.3     7.6    +      -       -      +
     52k  ILE*     3.3    44.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 49 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45k  ASP*     3.7    19.3    -      -       -      +
     46k  THR*     3.2    22.0    -      -       -      +
     48k  PHE*     1.3    98.8    -      -       +      +
     50k  MET*     1.3    66.2    +      -       +      +
     52k  ILE*     3.3    19.3    +      -       +      +
     53k  LEU*     3.4    16.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 50 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46k  THR*     3.0    33.7    -      -       +      +
     47k  VAL*     3.1    25.8    -      -       +      +
     49k  PRO*     1.3    78.6    -      -       +      +
     51k  ALA*     1.3    65.6    +      -       -      +
     53k  LEU*     3.0    24.4    +      -       +      +
     30l  PHE*     3.0    31.6    -      -       +      -
     33l  LEU*     4.2    26.2    -      -       +      +
     34l  ILE*     4.7     6.1    -      -       +      -
     37l  VAL*     4.3    25.1    -      -       +      -
     44l  LYS*     4.9     7.4    -      -       +      -
     48l  PHE*     4.6    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 51 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29k  VAL*     4.2     9.2    -      -       -      +
     30k  PHE*     6.1     2.7    -      -       +      -
     33k  LEU*     3.8    26.0    -      -       +      -
     47k  VAL      2.9    18.8    +      -       -      +
     48k  PHE      3.4     7.0    -      -       -      +
     49k  PRO      3.2     0.4    -      -       -      -
     50k  MET*     1.3    78.5    -      -       -      +
     52k  ILE*     1.3    62.2    +      -       +      +
     54k  GLY*     3.2    11.1    +      -       -      -
     55k  PHE*     3.3     9.9    +      -       -      +
     30l  PHE*     4.5     0.7    -      -       -      -
     34l  ILE*     4.4    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 52 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48k  PHE*     3.3    41.5    +      -       +      +
     49k  PRO*     3.6    10.8    -      -       +      +
     50k  MET      3.2     0.4    -      -       -      -
     51k  ALA*     1.3    74.1    -      -       +      +
     53k  LEU*     1.3    67.3    +      -       +      +
     55k  PHE*     3.0    32.7    +      -       +      +
     56k  ALA*     3.5     6.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 53 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49k  PRO      3.5    11.9    -      -       -      +
     50k  MET*     3.0    25.9    +      -       +      +
     52k  ILE*     1.3    81.4    -      -       +      +
     54k  GLY*     1.3    59.9    +      -       -      +
     55k  PHE      3.3     0.7    +      -       -      -
     56k  ALA*     3.5     7.6    +      -       -      +
     57k  LEU*     3.1    26.7    +      -       +      +
     30l  PHE*     4.1     9.2    -      -       +      -
     48l  PHE*     4.7    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 54 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29k  VAL*     4.3    11.5    -      -       -      +
     50k  MET      3.1    10.3    +      -       -      -
     51k  ALA      3.2     5.1    +      -       -      -
     52k  ILE      3.2     0.4    -      -       -      -
     53k  LEU*     1.3    74.3    -      -       -      +
     55k  PHE*     1.3    63.4    +      -       -      +
     56k  ALA      3.5     0.2    -      -       -      -
     57k  LEU*     3.4     4.7    +      -       -      +
     58k  SER*     3.1    25.3    +      -       -      -
     26l  ILE*     5.8     0.3    -      -       -      +
     30l  PHE*     3.4    33.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 55 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57j  LEU*     3.6    42.8    -      -       +      -
     26k  ILE*     3.5    34.1    -      -       +      -
     29k  VAL*     4.7     2.2    -      -       -      +
     30k  PHE*     6.4     0.7    -      -       +      -
     51k  ALA      3.3     8.4    +      -       -      +
     52k  ILE*     3.0    26.8    +      -       +      +
     54k  GLY*     1.3    77.6    -      -       -      +
     56k  ALA*     1.3    55.1    +      -       +      +
     58k  SER*     3.1     4.8    +      -       -      -
     59k  GLU*     2.7    68.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 56 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52k  ILE      3.5     6.2    +      -       -      +
     53k  LEU*     4.0     8.1    -      -       -      +
     54k  GLY      3.5     0.2    -      -       -      -
     55k  PHE*     1.3    83.6    -      -       +      +
     57k  LEU*     1.3    64.0    +      -       +      +
     59k  GLU*     3.8     9.2    -      -       -      +
     60k  ALA*     3.5    17.5    +      -       -      +
     63k  LEU*     5.9     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 57 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53k  LEU*     3.1    13.5    -      -       +      +
     54k  GLY      3.6     5.4    -      -       -      +
     55k  PHE      3.1     0.4    -      -       -      -
     56k  ALA*     1.3    81.2    -      -       +      +
     58k  SER*     1.3    59.5    +      -       -      +
     60k  ALA*     3.5    18.2    -      -       -      +
     61k  THR*     4.8     1.7    +      -       -      +
     22l  ALA      5.0     0.9    -      -       -      +
     26l  ILE*     4.2    20.5    -      -       +      +
     30l  PHE*     3.4    39.3    -      -       +      -
     55l  PHE*     3.4    51.6    -      -       +      -
     59l  GLU*     4.9     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 58 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21k  GLY      3.7     2.8    +      -       -      -
     22k  ALA*     3.9     7.8    -      -       -      +
     25k  GLY      3.7     1.5    -      -       -      -
     26k  ILE*     3.3    36.9    +      -       -      +
     29k  VAL*     4.8     6.3    -      -       -      -
     54k  GLY      3.1    16.6    +      -       -      -
     55k  PHE*     4.9     0.2    -      -       -      -
     57k  LEU*     1.3    73.0    -      -       -      +
     59k  GLU*     1.3    57.3    +      -       -      +
     60k  ALA      3.1     5.2    -      -       -      -
     61k  THR*     3.1    23.9    +      -       -      -
     22l  ALA      5.1     2.5    -      -       -      -
     23l  GLY*     3.3    25.7    +      -       -      -
     26l  ILE*     5.6     2.0    -      -       -      -
     27l  ALA*     5.2     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 59 (chain k). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57j  LEU      5.1     2.3    -      -       -      +
     60j  ALA*     5.4     6.4    -      -       -      +
     64j  PHE*     5.1    10.0    -      -       -      -
     22k  ALA*     5.0     1.6    -      -       -      +
     26k  ILE*     3.3    23.5    -      -       -      +
     55k  PHE*     2.7    40.7    +      -       +      +
     56k  ALA*     3.9    11.0    -      -       -      +
     57k  LEU      3.3     0.4    -      -       -      -
     58k  SER*     1.3    75.4    -      -       -      +
     60k  ALA*     1.3    64.8    +      -       -      +
     61k  THR      3.4     0.2    -      -       -      -
     62k  GLY*     3.0    21.6    +      -       -      +
     63k  LEU*     3.1    40.5    +      -       +      +
----------------------------------------------------------
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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