Contacts of the helix formed by residues 250 - 272 (chain B) in PDB entry 1O4X


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 250 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  LEU      3.7     1.4    +      -       -      -
    249B  LEU*     1.3    74.7    -      -       -      +
    251B  GLU*     1.3    58.6    +      -       -      +
    252B  THR*     3.6     7.7    +      -       -      -
    253B  GLU*     3.1    36.0    +      -       -      +
    254B  LYS*     2.8    31.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 251 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250B  SER*     1.3    75.4    -      -       -      +
    252B  THR*     1.3    54.4    +      -       -      +
    254B  LYS*     4.2     8.5    -      -       +      +
    255B  ARG*     1.5    83.2    +      -       -      +
    258B  ILE*     5.2     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 252 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250B  SER*     3.3     7.6    +      -       -      -
    251B  GLU*     1.3    77.4    -      -       -      +
    253B  GLU*     1.3    61.1    +      -       +      +
    255B  ARG*     3.4     8.9    -      -       +      +
    256B  PRO*     2.8    25.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 253 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249B  LEU*     3.9    26.1    -      -       +      +
    250B  SER*     3.1    27.5    +      -       -      +
    252B  THR*     1.3    79.8    -      -       +      +
    254B  LYS*     1.3    59.4    +      -       -      +
    256B  PRO*     3.0    23.0    -      -       -      +
    257B  PHE*     3.5    13.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 254 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  TRP*     3.3    68.0    +      -       +      +
    247B  LYS*     4.6     6.1    +      -       -      +
    249B  LEU*     3.5    27.7    +      -       +      +
    250B  SER      2.8    22.4    +      -       -      +
    251B  GLU*     3.8     7.9    -      -       -      +
    253B  GLU*     1.3    75.8    -      -       -      +
    255B  ARG*     1.3    67.3    +      -       -      +
    257B  PHE*     2.8    22.5    +      -       -      +
    258B  ILE*     3.0    24.5    +      -       +      +
    308C    G      4.3     7.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 255 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251B  GLU*     1.5    79.5    +      -       -      +
    252B  THR*     3.4     8.7    -      -       +      +
    254B  LYS*     1.3    71.6    -      -       -      +
    256B  PRO*     1.3    72.6    -      -       +      +
    258B  ILE*     2.8    33.9    +      -       +      +
    259B  ASP*     2.9    33.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 256 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  THR      2.8    28.0    -      -       -      +
    253B  GLU*     3.0    18.2    -      -       -      +
    255B  ARG*     1.3    82.8    -      -       +      +
    257B  PHE*     1.3    67.9    +      -       +      +
    259B  ASP*     4.2     7.7    -      -       +      +
    260B  GLU*     3.4    23.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 257 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214B  ALA*     3.6    22.1    -      -       -      +
    217B  VAL*     5.4     7.5    -      -       +      +
    218B  TRP*     3.6    48.7    -      +       +      -
    246B  TRP*     4.3    12.3    -      +       +      -
    249B  LEU*     5.7     3.8    -      -       +      -
    253B  GLU      3.5    22.2    -      -       -      -
    254B  LYS*     2.8    14.8    +      -       -      +
    256B  PRO*     1.3    80.5    -      -       +      +
    258B  ILE*     1.3    64.9    +      -       -      +
    260B  GLU*     3.5    11.3    +      -       -      +
    261B  ALA*     3.1    17.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 258 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214B  ALA*     3.8    20.6    -      -       +      -
    246B  TRP*     5.7     2.0    -      -       +      -
    251B  GLU*     5.2     3.4    -      -       +      +
    254B  LYS*     3.0    28.0    +      -       +      +
    255B  ARG*     2.8    31.2    +      -       +      +
    257B  PHE*     1.3    76.8    -      -       -      +
    259B  ASP*     1.3    64.7    +      -       -      +
    261B  ALA*     3.1     3.2    +      -       +      +
    262B  LYS*     2.8    52.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 259 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255B  ARG*     2.9    34.1    +      -       -      +
    256B  PRO*     4.2     7.3    -      -       +      +
    258B  ILE*     1.3    81.2    -      -       -      +
    260B  GLU*     1.3    58.5    +      -       -      +
    262B  LYS*     3.1    10.5    +      -       -      +
    263B  ARG*     2.7    52.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 260 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217B  VAL*     4.6    15.6    -      -       +      +
    256B  PRO      3.4    17.4    +      -       -      +
    257B  PHE*     3.8    12.5    -      -       -      +
    258B  ILE      3.2     0.6    -      -       -      -
    259B  ASP*     1.3    78.7    -      -       -      +
    261B  ALA*     1.3    57.5    +      -       -      +
    263B  ARG*     3.0    14.9    +      -       +      +
    264B  LEU*     2.7    53.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 261 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  MET      3.8    10.3    -      -       -      +
    213B  ASN*     3.8     2.0    -      -       -      -
    214B  ALA*     3.3    32.5    -      -       +      +
    217B  VAL*     4.7     1.9    -      -       +      +
    257B  PHE      3.1    11.7    +      -       -      +
    258B  ILE*     3.5     7.6    -      -       +      +
    260B  GLU*     1.3    77.2    -      -       -      +
    262B  LYS*     1.3    58.9    +      -       +      +
    264B  LEU*     3.3    12.7    +      -       -      +
    265B  ARG*     2.8    40.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 262 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  ILE*     5.0    16.8    +      -       +      +
     28A  GLY*     3.7    35.2    +      -       -      -
     29A  PHE      3.9    18.0    +      -       -      -
     30A  THR*     4.1    14.6    -      -       -      +
    258B  ILE*     2.8    36.1    +      -       +      +
    259B  ASP*     3.2    13.7    -      -       -      +
    261B  ALA*     1.3    79.1    -      -       +      +
    263B  ARG*     1.3    58.3    +      -       +      +
    265B  ARG*     3.2    33.5    +      -       -      +
    266B  ALA*     2.9    28.1    +      -       -      +
    309C    T      5.3     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 263 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259B  ASP*     2.7    39.1    +      -       +      +
    260B  GLU*     3.5    15.1    -      -       +      +
    262B  LYS*     1.3    71.6    -      -       +      +
    264B  LEU*     1.3    62.1    +      -       +      +
    266B  ALA*     3.2     5.8    +      -       -      +
    267B  LEU*     2.8    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 264 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211B  PRO*     4.8     4.5    -      -       +      -
    212B  MET*     4.7    19.3    -      -       +      +
    217B  VAL*     3.7    33.4    -      -       +      -
    260B  GLU*     2.7    47.3    +      -       +      +
    261B  ALA*     3.6     6.1    -      -       -      +
    263B  ARG*     1.3    72.9    -      -       +      +
    265B  ARG*     1.3    58.0    +      -       +      +
    267B  LEU*     4.0    12.4    -      -       +      +
    268B  HIS*     2.7    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 265 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  ARG*     5.1     2.2    -      -       -      +
     25A  ILE*     5.0    26.5    -      -       +      +
     30A  THR*     6.0     1.4    -      -       -      +
    211B  PRO*     3.5    34.0    -      -       +      +
    212B  MET      5.0     2.9    -      -       -      +
    213B  ASN*     6.0     2.2    -      -       -      +
    261B  ALA*     2.8    30.2    +      -       -      +
    262B  LYS*     3.4    35.1    -      -       -      +
    264B  LEU*     1.3    77.7    -      -       -      +
    266B  ALA*     1.3    58.1    +      -       -      +
    268B  HIS*     3.4     2.1    +      -       -      +
    269B  MET*     2.9    29.7    +      -       -      +
    309C    T      3.8    31.3    +      -       -      -
    310C    C      3.5    23.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 266 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  ILE*     4.6    16.7    -      -       +      +
     26A  LYS*     6.3     4.0    -      -       +      -
    262B  LYS      2.9    16.0    +      -       -      +
    263B  ARG*     3.8     6.5    -      -       -      +
    265B  ARG*     1.3    76.2    -      -       -      +
    267B  LEU*     1.3    65.3    +      -       -      +
    269B  MET*     3.1    12.1    +      -       -      +
    270B  LYS*     3.0    21.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 267 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263B  ARG      2.8    22.7    +      -       -      +
    264B  LEU*     4.0    12.1    -      -       +      +
    266B  ALA*     1.3    73.1    -      -       -      +
    268B  HIS*     1.3    62.2    +      -       -      +
    270B  LYS*     3.0    28.3    +      -       +      +
    271B  GLU*     3.2    27.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 268 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208B  VAL*     3.4    30.4    -      -       +      +
    209B  LYS      3.3    20.2    +      -       -      -
    211B  PRO*     3.6    33.2    -      -       +      +
    264B  LEU      2.7    25.2    +      -       -      +
    265B  ARG      3.6     4.5    -      -       -      +
    267B  LEU*     1.3    73.7    -      -       -      +
    269B  MET*     1.3    65.8    +      -       -      +
    271B  GLU*     3.2    18.7    +      -       -      +
    272B  HIS*     3.2    25.1    +      +       -      +
    275B  TYR*     4.7    16.7    -      +       +      +
----------------------------------------------------------
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Residues in contact with MET 269 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  LYS*     4.7    11.7    -      -       +      +
     22A  GLN*     2.6    40.4    -      -       -      +
     25A  ILE*     3.2    38.6    -      -       +      -
    265B  ARG      2.9    14.3    +      -       -      +
    266B  ALA*     3.1    12.1    +      -       -      +
    268B  HIS*     1.3    80.6    -      -       -      +
    270B  LYS*     1.3    58.3    +      -       -      +
    272B  HIS      4.1     6.1    -      -       -      +
    273B  PRO*     2.9    42.1    -      -       +      +
    275B  TYR*     6.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 270 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  ALA      3.0    12.4    +      -       -      +
    267B  LEU*     3.0    25.3    +      -       +      +
    269B  MET*     1.3    78.1    -      -       -      +
    271B  GLU*     1.3    64.2    +      -       +      +
    273B  PRO*     3.4    15.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 271 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267B  LEU*     3.2    28.3    +      -       +      +
    268B  HIS*     3.2    19.9    +      -       -      +
    270B  LYS*     1.3    79.2    -      -       +      +
    272B  HIS*     1.3    83.4    +      -       +      +
    273B  PRO*     3.4     5.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 272 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208B  VAL*     3.7    41.1    -      -       +      +
    268B  HIS*     3.2    14.3    +      +       -      +
    269B  MET*     3.1    11.6    -      -       -      +
    271B  GLU*     1.3   102.4    +      -       +      +
    273B  PRO*     1.3    62.2    -      -       -      +
    274B  ASP      3.1     5.8    -      -       -      -
    275B  TYR*     3.0    33.6    +      -       +      +
----------------------------------------------------------
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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