Contacts of the helix formed by residues 203 - 221 (chain 2) in PDB entry 5IY8


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 PHE 203 (chain 2).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1602  LEU*     4.3    10.2    -      -       +      +
    2012  PHE      3.4     2.8    +      -       -      +
    2022  GLN*     1.3    73.5    -      -       -      +
    2042  LEU*     1.3    94.0    +      -       +      +
    2052  LEU*     2.9    37.2    -      -       +      -
    2062  LEU*     3.3    22.3    +      -       +      +
    2072  ASP*     2.9    28.3    +      -       -      +
    2542  MET*     4.5     1.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 204 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2032  PHE*     1.3    99.8    -      -       +      +
    2052  LEU*     1.3    65.6    +      -       +      +
    2072  ASP*     3.1     6.8    +      -       +      +
    2082  THR*     3.0    25.7    +      -       -      +
    2512  VAL*     3.6    13.7    -      -       +      -
    2532  GLY*     4.9     8.7    -      -       -      +
    2542  MET*     3.4    45.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 205 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1602  LEU*     5.9     0.7    -      -       +      -
    1642  VAL*     4.5     7.1    -      -       +      +
    2032  PHE*     2.9    34.9    -      -       +      -
    2042  LEU*     1.3    76.8    -      -       +      +
    2062  LEU*     1.3    66.9    +      -       +      +
    2082  THR*     3.9     9.2    -      -       +      -
    2092  PRO*     2.8    32.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 206 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1602  LEU*     2.9    75.6    -      -       +      +
    1632  MET*     2.9    37.0    -      -       +      +
    1642  VAL*     3.6     9.8    -      -       +      -
    1962  ILE*     4.2     2.6    -      -       +      +
    2022  GLN*     4.3    11.9    -      -       +      -
    2032  PHE*     3.3    23.5    +      -       +      +
    2052  LEU*     1.3    81.0    -      -       +      +
    2072  ASP*     1.3    63.8    +      -       -      +
    2082  THR      3.4     0.2    +      -       -      -
    2092  PRO*     3.4     2.6    -      -       -      +
    2102  ALA*     3.0    22.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 207 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1962  ILE*     4.5     6.6    -      -       -      +
    1972  THR*     5.5     2.8    -      -       -      +
    2022  GLN*     3.4    19.6    -      -       -      +
    2032  PHE      2.9    15.5    +      -       -      +
    2042  LEU*     3.1     9.5    +      -       +      +
    2062  LEU*     1.3    76.6    -      -       -      +
    2082  THR*     1.3    63.1    +      -       -      +
    2102  ALA*     3.0     6.9    +      -       -      +
    2112  GLN*     2.7    42.0    +      -       +      +
    2422  PHE*     4.5     9.3    -      -       -      -
    2542  MET*     3.0    45.9    -      -       +      +
    2572  SER*     5.0     4.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 208 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2042  LEU      3.0    13.0    +      -       -      +
    2052  LEU*     3.3    19.7    -      -       +      +
    2072  ASP*     1.3    75.5    -      -       -      +
    2092  PRO*     1.3    83.2    -      -       +      +
    2112  GLN*     3.2     8.6    +      -       -      +
    2122  LEU*     3.0    40.9    +      -       -      +
    2572  SER*     4.6     6.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 209 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1642  VAL*     3.3    45.5    -      -       +      +
    1672  PRO*     4.2     6.7    -      -       +      +
    1682  SER*     5.0     8.5    -      -       -      +
    1712  VAL*     4.3     2.3    -      -       -      +
    2052  LEU      2.8    24.5    -      -       -      +
    2062  LEU      4.1     2.9    -      -       -      +
    2072  ASP      3.4     0.2    -      -       -      -
    2082  THR*     1.3    93.4    -      -       +      +
    2102  ALA*     1.3    62.2    +      -       -      +
    2122  LEU*     3.7    13.9    -      -       +      +
    2132  TRP*     3.1    22.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 210 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1672  PRO*     4.8     5.8    -      -       -      -
    1932  PRO*     4.4     7.1    -      -       +      +
    1962  ILE*     2.9    41.5    -      -       +      +
    1972  THR*     4.1     6.7    +      -       -      +
    2062  LEU      3.0     8.4    +      -       -      +
    2072  ASP*     3.0     9.2    +      -       -      +
    2092  PRO*     1.3    75.7    -      -       -      +
    2112  GLN*     1.3    72.4    +      -       -      +
    2132  TRP*     3.2    12.0    +      -       -      +
    2142  TYR*     3.2    19.9    +      -       -      +
    2612  PHE*     4.0     1.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 211 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1972  THR*     3.6    17.7    +      -       -      +
    2072  ASP*     2.7    32.3    +      -       -      +
    2082  THR*     3.6     5.4    -      -       -      +
    2102  ALA*     1.3    80.5    -      -       -      +
    2122  LEU*     1.3    67.7    +      -       +      +
    2142  TYR*     3.1     5.9    +      -       -      +
    2152  PHE*     3.0    21.8    +      -       -      +
    2392  GLN*     4.3     7.7    -      -       -      +
    2422  PHE*     5.7     6.1    -      -       -      -
    2542  MET*     4.5     2.8    +      -       -      +
    2572  SER*     3.0    45.8    -      -       -      +
    2582  LEU*     4.1     2.2    -      -       -      +
    2602  ASN*     5.9     2.2    -      -       +      -
    2612  PHE*     2.9    39.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 212 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1712  VAL*     3.8    12.6    -      -       +      +
    2082  THR*     3.0    39.7    +      -       -      +
    2092  PRO*     3.7    11.9    -      -       +      +
    2112  GLN*     1.3    80.4    -      -       +      +
    2132  TRP*     1.3    57.2    +      -       -      +
    2152  PHE*     3.2    10.0    +      -       +      +
    2162  MET*     2.8    31.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 213 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1672  PRO*     4.0    10.8    -      -       +      -
    1702  ALA*     2.9    40.6    -      -       +      -
    1712  VAL*     2.9    46.4    -      -       +      +
    1742  ASP*     2.7    34.3    -      -       -      -
    1792  LEU*     4.6     6.1    -      -       +      -
    1842  LEU*     5.2     6.7    -      -       +      -
    1892  GLU*     5.4     6.5    -      -       +      -
    1902  PRO*     4.7    19.9    -      -       +      +
    1932  PRO*     3.3    39.1    -      -       +      +
    1942  PRO*     5.5     1.0    -      -       +      +
    2092  PRO      3.1    11.1    +      -       -      +
    2102  ALA*     3.4     7.0    -      -       -      +
    2112  GLN      3.2     0.2    -      -       -      -
    2122  LEU*     1.3    76.1    -      -       -      +
    2142  TYR*     1.3    64.5    +      +       +      +
    2162  MET      3.2     1.2    +      -       -      -
    2172  LEU*     2.8    52.6    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 214 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1932  PRO*     5.9     1.6    -      -       +      -
    1942  PRO*     5.5    12.6    -      -       +      -
    2102  ALA      3.2     4.1    +      -       -      +
    2112  GLN      3.1     2.0    +      -       -      -
    2132  TRP*     1.3    87.5    -      +       +      +
    2152  PHE*     1.3    70.1    +      -       -      +
    2172  LEU*     3.1     7.5    +      -       +      +
    2182  GLN*     3.0    35.5    +      -       +      +
    2332  ILE*     2.8    58.9    +      -       +      +
    2352  SER*     6.0     0.7    -      -       -      -
    2362  PHE*     3.5    16.0    -      -       +      +
    2392  GLN*     4.9     1.1    -      -       -      -
    2612  PHE*     2.9    64.8    -      +       +      -
    2642  HIS*     5.1     0.4    -      -       +      -
    2652  LEU*     3.1    19.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 215 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2112  GLN      3.0    12.5    +      -       -      +
    2122  LEU*     3.4    15.7    -      -       +      +
    2142  TYR*     1.3    81.1    -      -       +      +
    2162  MET*     1.3    71.7    +      -       +      +
    2192  TYR*     2.9    35.4    +      +       +      -
    2602  ASN*     4.1    22.9    -      -       +      -
    2612  PHE*     6.0     0.7    -      -       +      -
    2632  GLN*     6.3     0.9    -      -       +      -
    2642  HIS*     2.9    69.5    +      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 216 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1712  VAL*     2.9    57.7    -      -       +      +
    1742  ASP*     3.6     3.1    -      -       +      +
    1752  LEU*     3.1    50.7    -      -       +      +
    2122  LEU      2.8     8.5    +      -       -      +
    2132  TRP      3.8     2.0    -      -       -      +
    2152  PHE*     1.3    86.2    -      -       +      +
    2172  LEU*     1.3    59.7    +      -       -      +
    2192  TYR*     3.1    12.2    +      -       +      +
    2202  LEU*     2.8    28.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 217 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1742  ASP*     3.2    24.8    +      -       -      +
    1812  GLN*     4.7     5.9    -      -       -      +
    1842  LEU*     4.1    20.9    -      -       +      -
    1902  PRO*     5.0    14.1    -      -       +      -
    2132  TRP*     2.8    38.0    +      -       +      +
    2142  TYR*     3.1    11.8    +      -       +      +
    2162  MET*     1.3    75.6    -      -       -      +
    2182  GLN*     1.3    64.4    +      -       -      +
    2202  LEU*     3.2    18.4    +      -       +      +
    2212  GLN*     3.5     5.9    +      -       -      +
    2292  ASP*     4.1    15.7    -      -       +      +
    2322  GLU*     6.2     2.0    -      -       +      -
    2332  ILE*     2.9    31.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 218 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2142  TYR*     3.0    37.4    +      -       -      +
    2152  PHE      3.8     0.2    -      -       -      +
    2172  LEU*     1.3    74.0    -      -       -      +
    2192  TYR*     1.3    64.2    +      -       -      +
    2212  GLN*     3.1    23.7    +      -       -      +
    2302  LEU*     4.1     3.7    -      -       +      +
    2332  ILE*     4.2    13.7    -      -       +      +
    2642  HIS*     3.0    19.4    +      -       +      +
    2652  LEU*     2.6    61.8    -      -       -      +
    2682  PHE*     2.7    32.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 219 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1752  LEU*     5.1    16.6    -      -       +      -
    1772  GLN*     3.7    18.0    +      -       +      -
    2152  PHE*     2.9    22.3    +      +       +      +
    2162  MET*     3.3    18.4    -      -       +      +
    2182  GLN*     1.3    73.1    -      -       -      +
    2202  LEU*     1.3    69.0    +      -       -      +
    2212  GLN      3.2     7.3    +      -       -      +
    2222  THR*     4.3     4.7    +      -       -      -
    2642  HIS*     2.7    28.2    +      +       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 220 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1742  ASP*     2.7    40.2    -      -       +      +
    1772  GLN*     2.8    70.4    +      -       -      +
    1792  LEU*     4.6    16.4    -      -       +      +
    1812  GLN*     3.2    28.9    -      -       +      +
    1842  LEU*     5.6     0.4    -      -       +      -
    2162  MET      2.8    11.1    +      -       -      +
    2172  LEU*     3.2    14.8    -      -       +      +
    2192  TYR*     1.3    78.6    -      -       -      +
    2212  GLN*     1.3    62.8    +      -       -      +
    2222  THR*     3.2     6.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 221 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1812  GLN*     2.7    28.2    +      -       -      +
    2172  LEU      3.5     4.7    +      -       -      +
    2182  GLN*     3.1    13.7    +      -       -      +
    2192  TYR      3.5     4.1    -      -       -      +
    2202  LEU*     1.3    81.7    -      -       -      +
    2222  THR*     1.3    54.2    +      -       -      +
    2232  ALA*     4.0     2.5    -      -       +      +
    2242  GLN*     2.7    29.3    -      -       -      +
    2262  ARG      5.3     0.7    -      -       -      +
    2272  GLY*     3.1    17.4    -      -       -      +
    2292  ASP*     4.1     1.0    -      -       -      +
    2302  LEU*     2.9    37.1    -      -       -      +
    2332  ILE*     4.6     2.4    -      -       -      +
    2682  PHE*     2.7    57.2    -      -       +      -
----------------------------------------------------------
 Back to top of page


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