Contacts of the helix formed by residues 217 - 238 (chain L) in PDB entry 4DVQ


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 SER 217 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211L  LEU*     3.5    19.0    -      -       -      +
    215L  SER      3.6     0.4    +      -       -      -
    216L  PRO*     1.3    76.1    -      -       -      +
    218L  SER*     1.3    62.4    +      -       -      +
    219L  ALA*     3.2    13.9    +      -       -      +
    220L  SER*     3.0    24.4    +      -       -      -
    221L  LEU*     3.1    25.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 218 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217L  SER*     1.3    70.9    -      -       -      +
    219L  ALA*     1.3    65.9    +      -       -      +
    220L  SER      3.3     0.2    +      -       -      -
    221L  LEU*     3.3     8.5    +      -       -      +
    222L  ASN*     3.0    41.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 219 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217L  SER*     3.2    10.7    +      -       -      +
    218L  SER*     1.3    80.1    +      -       -      +
    220L  SER*     1.3    56.8    +      -       -      +
    222L  ASN*     4.0     6.0    -      -       -      +
    223L  PHE*     3.0    29.3    +      -       -      +
    266L  TYR*     4.1    21.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 220 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194L  HIS*     3.5    26.9    -      -       -      -
    197L  ILE*     4.4     7.6    -      -       -      +
    211L  LEU*     3.0    32.3    -      -       -      +
    217L  SER*     3.0    21.0    +      -       -      -
    219L  ALA*     1.3    73.0    -      -       -      +
    221L  LEU*     1.3    61.8    +      -       -      +
    223L  PHE*     3.3     6.1    +      -       -      +
    224L  LEU*     2.9    35.1    +      -       -      +
    266L  TYR*     5.2     4.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 221 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194L  HIS*     4.7     8.5    -      -       +      +
    216L  PRO*     4.1    28.3    -      -       +      +
    217L  SER      3.1    21.1    +      -       -      +
    218L  SER*     3.3     7.2    +      -       -      +
    220L  SER*     1.3    79.2    -      -       -      +
    222L  ASN*     1.3    62.7    +      -       -      +
    224L  LEU*     3.5    10.2    +      -       +      +
    225L  HIS*     3.0    29.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 222 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218L  SER*     3.0    27.9    +      -       -      +
    219L  ALA*     4.0     5.2    -      -       -      +
    221L  LEU*     1.3    77.6    -      -       -      +
    223L  PHE*     1.3    54.8    +      -       -      +
    225L  HIS*     3.9     6.1    -      -       -      +
    226L  ALA*     2.8    35.0    +      -       -      +
    262L  CYS*     3.8    20.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 223 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197L  ILE*     4.4    18.2    -      -       +      -
    219L  ALA      3.0    19.3    +      -       -      +
    220L  SER*     3.5     5.2    -      -       -      +
    222L  ASN*     1.3    77.0    -      -       -      +
    224L  LEU*     1.3    62.1    +      -       -      +
    226L  ALA*     3.3     5.9    +      -       -      +
    227L  LEU*     3.0    46.5    +      -       +      +
    262L  CYS*     4.6     3.7    -      -       -      -
    263L  ILE*     4.2    29.6    -      -       +      -
    266L  TYR*     3.8    56.5    -      +       +      -
    312L  THR*     3.7    26.0    -      -       +      -
    313L  ALA*     4.4     2.2    -      -       -      -
    316L  VAL*     3.7    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 224 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190L  PRO*     5.6     1.6    -      -       +      +
    193L  PHE*     3.7    27.1    -      -       +      -
    194L  HIS*     3.9    28.3    -      -       +      +
    197L  ILE*     3.9    14.4    -      -       +      -
    220L  SER      2.9    21.0    +      -       -      +
    221L  LEU*     3.9    10.3    -      -       +      +
    223L  PHE*     1.3    69.7    -      -       +      +
    225L  HIS*     1.3    65.9    +      -       -      +
    227L  LEU*     3.2    11.4    +      -       +      +
    228L  GLU*     3.0    23.9    +      -       -      +
    316L  VAL*     3.7    30.7    -      -       +      -
    317L  ASP*     5.3     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 225 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221L  LEU      3.0    17.4    +      -       -      +
    222L  ASN*     3.9     6.5    -      -       -      +
    224L  LEU*     1.3    72.4    -      -       -      +
    226L  ALA*     1.3    66.2    +      -       -      +
    228L  GLU*     3.2    18.1    +      -       +      +
    229L  VAL*     3.1    43.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 226 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222L  ASN      2.8    23.1    +      -       -      +
    223L  PHE*     3.4     7.4    -      -       -      +
    225L  HIS*     1.3    74.0    +      -       -      +
    227L  LEU*     1.3    57.3    +      -       -      +
    229L  VAL*     5.0     1.3    -      -       -      -
    230L  MET*     2.8    30.1    +      -       -      +
    259L  ALA*     3.5    21.6    -      -       -      +
    262L  CYS*     3.9    16.2    -      -       +      -
    263L  ILE*     3.5    22.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 227 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223L  PHE*     3.0    47.4    +      -       +      +
    224L  LEU*     3.2    11.0    +      -       +      +
    226L  ALA*     1.3    74.8    -      -       -      +
    228L  GLU*     1.3    57.8    +      -       -      +
    230L  MET*     3.2    12.5    +      -       +      +
    231L  PHE*     2.9    40.4    +      -       +      -
    263L  ILE*     4.0    22.0    -      -       +      -
    313L  ALA*     3.6    30.5    -      -       +      +
    316L  VAL*     4.1    17.9    -      -       +      -
    317L  ASP*     3.5    26.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 228 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224L  LEU      3.0    12.9    +      -       -      +
    225L  HIS*     3.2    20.3    +      -       +      +
    227L  LEU*     1.3    78.1    -      -       -      +
    229L  VAL*     1.3    58.1    +      -       +      +
    231L  PHE*     3.4     5.0    +      -       -      +
    232L  LYS*     2.9    31.0    +      -       +      +
    317L  ASP*     5.4     1.5    +      -       -      +
    490L  ARG*     3.9    36.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 229 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225L  HIS*     3.1    39.1    +      -       +      +
    226L  ALA*     4.0     3.6    -      -       -      +
    228L  GLU*     1.3    73.9    -      -       +      +
    230L  MET*     1.3    63.5    +      -       -      +
    232L  LYS*     3.8     8.4    -      -       +      +
    233L  SER*     2.9    29.8    +      -       -      -
    255L  GLU*     3.7    48.9    -      -       +      +
    259L  ALA*     3.9     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 230 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116L  TRP*     3.6    26.7    -      -       +      -
    226L  ALA      2.8    15.1    +      -       -      +
    227L  LEU*     3.3    13.7    -      -       +      +
    229L  VAL*     1.3    78.2    -      -       -      +
    231L  PHE*     1.3    90.0    +      -       +      +
    233L  SER*     4.1     2.9    -      -       -      -
    234L  THR*     2.8    37.9    +      -       -      -
    256L  HIS*     3.3     6.3    -      -       +      -
    259L  ALA*     3.8     8.7    -      -       +      +
    260L  TRP*     3.4    55.4    -      -       +      +
    263L  ILE*     3.8    14.1    -      -       +      -
    313L  ALA*     5.9     1.3    -      -       +      -
    602L  1CA      5.8     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 231 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116L  TRP*     4.3     0.4    -      +       -      -
    227L  LEU*     2.9    34.3    +      -       +      +
    228L  GLU*     3.8     6.7    -      -       -      +
    230L  MET*     1.3   103.6    -      -       +      +
    232L  LYS*     1.3    62.2    +      -       -      +
    234L  THR*     3.1    13.6    +      -       -      -
    235L  VAL*     3.2    19.2    +      -       -      +
    313L  ALA      5.2     1.8    -      -       -      -
    317L  ASP*     3.6    31.9    -      -       +      -
    318L  THR*     5.9     0.7    -      -       +      -
    486L  SER      3.3    19.1    -      -       -      +
    487L  PHE*     3.5    31.9    -      +       +      +
    488L  ILE*     4.0    22.9    -      -       +      -
    490L  ARG*     4.6     8.3    -      -       -      +
    602L  1CA      4.0    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 232 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59L  GLN*     2.9    40.5    +      -       -      +
     60L  GLY*     5.7     0.8    -      -       -      -
    228L  GLU*     2.9    20.8    +      -       +      +
    229L  VAL*     3.8    11.2    -      -       +      +
    230L  MET      3.3     0.2    -      -       -      -
    231L  PHE*     1.3    78.2    -      -       -      +
    233L  SER*     1.3    63.5    +      -       -      +
    235L  VAL*     3.3    12.5    +      -       -      +
    236L  GLN*     3.1    44.4    +      -       -      +
    255L  GLU*     4.1    15.3    -      -       -      +
    486L  SER*     3.8    16.1    +      -       -      +
    490L  ARG*     6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 233 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229L  VAL      2.9    20.1    +      -       -      -
    232L  LYS*     1.3    75.9    -      -       -      +
    234L  THR*     1.3    63.9    +      -       -      +
    236L  GLN*     3.3    13.8    +      -       -      +
    237L  LEU*     3.0    28.1    +      -       -      +
    252L  VAL*     3.7    20.9    -      -       -      -
    255L  GLU*     4.6     7.6    -      -       -      -
    256L  HIS*     2.6    45.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 234 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113L  LEU*     4.3    15.7    -      -       +      -
    115L  PRO*     4.6     4.6    -      -       +      +
    116L  TRP*     3.0    35.9    +      -       +      +
    230L  MET*     2.8    25.4    +      -       -      -
    231L  PHE*     3.1    11.1    +      -       -      -
    233L  SER*     1.3    75.3    +      -       -      +
    235L  VAL*     1.3    64.3    +      -       -      +
    237L  LEU*     3.2     5.3    +      -       -      +
    238L  MET*     3.0    30.8    +      -       +      +
    256L  HIS*     3.0    10.6    -      -       -      -
    487L  PHE*     4.1    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 235 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55L  ILE*     4.0     3.6    -      -       +      +
     60L  GLY*     4.5     5.4    -      -       -      -
     61L  TYR*     3.9    28.9    -      -       +      +
    231L  PHE      3.2    15.4    +      -       -      +
    232L  LYS      3.6     6.7    -      -       -      +
    233L  SER      3.2     0.2    -      -       -      -
    234L  THR*     1.3    77.9    -      -       -      +
    236L  GLN*     1.3    61.3    +      -       -      +
    237L  LEU      3.3     0.7    +      -       -      -
    238L  MET*     3.5    17.3    +      -       +      -
    239L  PHE*     3.6    32.6    -      -       +      -
    485L  TYR*     4.3     9.9    -      -       +      +
    486L  SER*     3.6    12.1    -      -       -      +
    487L  PHE*     3.4    31.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 236 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55L  ILE*     3.4    34.7    -      -       +      +
     59L  GLN*     3.1    43.6    -      -       -      +
     60L  GLY*     4.4     1.6    -      -       -      +
    232L  LYS*     3.1    45.4    +      -       -      +
    233L  SER*     3.3    25.0    +      -       -      +
    235L  VAL*     1.3    76.6    -      -       -      +
    237L  LEU*     1.3    61.3    +      -       -      +
    238L  MET      3.5     0.2    -      -       -      -
    240L  MET*     4.1    10.9    -      -       -      +
    249L  SER*     5.6     0.7    +      -       -      -
    252L  VAL*     3.5    30.6    -      -       +      +
    255L  GLU*     4.2     5.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 237 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114L  GLU*     6.0     0.3    -      -       -      +
    115L  PRO*     3.8    23.7    -      -       +      +
    233L  SER      3.0    20.0    +      -       -      +
    234L  THR      3.7     0.4    -      -       -      +
    236L  GLN*     1.3    77.6    -      -       -      +
    238L  MET*     1.3    62.3    +      -       -      +
    239L  PHE      3.5     2.0    -      -       -      -
    240L  MET*     3.4    20.2    -      -       +      +
    245L  SER*     4.1    12.1    +      -       -      -
    249L  SER*     4.5     6.5    -      -       -      +
    252L  VAL*     3.5    25.1    -      -       +      +
    253L  TRP*     3.2    48.2    -      -       +      +
    256L  HIS*     3.7    36.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 238 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113L  LEU*     4.0    26.2    -      -       +      -
    115L  PRO*     4.7     7.2    -      -       -      -
    234L  THR*     3.0    13.4    +      -       +      +
    235L  VAL*     3.5    33.1    +      -       +      +
    237L  LEU*     1.3    78.1    -      -       -      +
    239L  PHE*     1.3    90.4    +      -       +      +
    240L  MET      3.5     5.6    +      -       -      +
    381L  PHE*     5.8     4.9    -      -       -      -
    485L  TYR*     4.2    16.8    -      -       +      +
    487L  PHE*     4.3    19.7    -      -       +      -
----------------------------------------------------------
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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