Contacts of the helix formed by residues 276 - 289 (chain J) in PDB entry 1XFB


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 276 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274J  GLY      3.8     0.8    +      -       -      -
    275J  GLN*     1.3    76.1    -      -       -      +
    277J  GLU*     1.3    66.9    +      -       -      +
    278J  GLU*     3.0     6.2    +      -       -      +
    279J  GLU*     3.0    33.4    +      -       -      +
    280J  ALA*     2.9    21.4    +      -       -      +
    305J  ALA*     4.9     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 277 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276J  SER*     1.3    73.2    -      -       -      +
    278J  GLU*     1.3    60.9    +      -       +      +
    280J  ALA*     3.8     2.9    +      -       -      +
    281J  SER*     2.9    14.2    +      -       -      -
    305J  ALA*     3.5    24.5    -      -       -      +
    306J  LEU      4.0     2.9    -      -       -      +
    308J  ALA*     3.3    25.0    +      -       +      +
    309J  SER*     2.8    50.1    +      -       -      -
    331J  ARG*     2.8    52.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 278 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276J  SER*     3.1     5.6    +      -       -      +
    277J  GLU*     1.3    77.8    -      -       +      +
    279J  GLU*     1.3    56.6    +      -       -      +
    280J  ALA      3.1     1.8    -      -       -      -
    281J  SER*     2.9     3.7    +      -       -      -
    282J  PHE*     2.7    73.8    +      -       +      -
    331J  ARG*     2.5    35.0    +      -       -      -
    343J  TYR*     3.1    14.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 279 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241F  PRO*     5.4    14.9    -      -       +      +
    274J  GLY      4.7     1.4    -      -       -      +
    275J  GLN*     3.5    26.4    -      -       -      +
    276J  SER*     3.0    36.2    +      -       -      +
    278J  GLU*     1.3    76.4    -      -       -      +
    280J  ALA*     1.3    57.1    +      -       -      +
    282J  PHE*     3.9     5.1    -      -       -      +
    283J  ASN*     3.0    44.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 280 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272J  SER*     4.4     2.9    -      -       -      -
    275J  GLN*     3.6    19.8    +      -       +      +
    276J  SER      2.9    15.3    +      -       -      +
    277J  GLU      3.9     2.2    -      -       -      +
    279J  GLU*     1.3    77.4    -      -       -      +
    281J  SER*     1.3    57.5    +      -       -      +
    283J  ASN*     3.9     1.0    -      -       -      +
    284J  LEU*     2.8    26.0    +      -       -      +
    302J  TYR*     3.1    41.4    +      -       +      -
    305J  ALA*     3.8    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 281 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277J  GLU      2.9    15.3    +      -       -      -
    278J  GLU*     2.9     8.6    +      -       -      -
    280J  ALA*     1.3    78.3    -      -       -      +
    282J  PHE*     1.3    58.0    +      -       -      +
    284J  LEU*     4.5     0.2    -      -       -      -
    285J  ASN*     2.9    31.6    +      -       -      +
    331J  ARG*     3.0    17.5    +      -       -      -
    334J  VAL*     3.7    18.8    -      -       -      +
    335J  ASN*     2.7    27.0    +      -       -      -
    338J  ALA*     3.3     7.2    -      -       -      +
    343J  TYR*     4.4     9.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 282 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246J  PRO*     4.5    15.8    -      -       +      +
    278J  GLU*     2.7    56.9    +      -       +      +
    279J  GLU*     3.9     5.8    -      -       -      +
    281J  SER*     1.3    73.0    -      -       -      +
    283J  ASN*     1.3    62.2    +      -       -      +
    285J  ASN*     3.2     7.2    +      -       -      +
    286J  ALA*     2.8    30.5    +      -       -      +
    343J  TYR*     3.8    20.6    -      +       -      -
    344J  GLU      6.0     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 283 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233J  MET*     3.7    20.0    -      -       -      +
    235J  THR*     5.2     0.9    -      -       -      +
    246J  PRO*     3.1    32.9    -      -       -      +
    249J  ILE*     3.8    29.6    -      -       +      +
    250J  ALA*     4.6     0.3    +      -       -      +
    275J  GLN*     2.7    20.5    -      -       -      +
    279J  GLU*     3.0    26.5    +      -       -      +
    280J  ALA      3.9     0.9    -      -       -      +
    282J  PHE*     1.3    77.3    -      -       -      +
    284J  LEU*     1.3    64.5    +      -       -      +
    286J  ALA*     3.2     5.5    +      -       -      +
    287J  ILE*     2.9    28.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 284 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233J  MET*     4.1     5.3    -      -       +      +
    270J  PHE*     4.2    13.5    -      -       +      -
    280J  ALA      2.8    23.3    +      -       -      +
    281J  SER*     3.8     3.4    -      -       -      +
    283J  ASN*     1.3    72.4    -      -       -      +
    285J  ASN*     1.3    63.1    +      -       -      +
    287J  ILE*     3.1     9.1    +      -       +      +
    288J  ASN*     3.0    22.3    +      -       -      +
    298J  LEU      3.3    25.8    -      -       -      +
    299J  THR      3.8    12.1    -      -       -      +
    300J  PHE*     3.7    41.5    -      -       +      -
    302J  TYR*     3.5    11.0    -      -       +      +
    335J  ASN*     4.0    15.0    -      -       -      +
    338J  ALA*     3.7    11.7    -      -       +      +
    339J  ALA*     4.1     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 285 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281J  SER      2.9    19.1    +      -       -      +
    282J  PHE*     3.4     7.0    -      -       -      +
    284J  LEU*     1.3    75.8    -      -       -      +
    286J  ALA*     1.3    65.4    +      -       -      +
    288J  ASN*     2.9    13.9    +      -       -      +
    289J  ARG*     3.0    45.0    +      -       -      +
    338J  ALA*     3.2    15.7    -      -       +      +
    341J  GLY*     3.0    13.8    +      -       -      -
    343J  TYR*     2.9    52.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 286 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246J  PRO*     3.2    38.8    -      -       +      +
    247J  GLU*     4.1    14.1    -      -       -      +
    250J  ALA*     3.5     7.1    -      -       +      +
    282J  PHE      2.8    16.9    +      -       -      +
    283J  ASN      3.5     7.4    -      -       -      +
    285J  ASN*     1.3    73.4    -      -       -      +
    287J  ILE*     1.3    58.4    +      -       -      +
    289J  ARG*     2.9    24.7    +      -       -      +
    290J  CYS*     3.0    10.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 287 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233J  MET*     4.0    24.0    -      -       +      -
    249J  ILE*     5.3     1.1    -      -       +      -
    250J  ALA*     3.4    26.0    -      -       -      -
    253J  THR*     3.8    13.7    -      -       +      +
    254J  VAL*     3.8     9.9    -      -       +      +
    270J  PHE*     3.8    36.3    -      -       +      -
    283J  ASN*     2.9    18.8    +      -       +      +
    284J  LEU*     3.1    10.1    +      -       +      +
    286J  ALA*     1.3    76.1    -      -       -      +
    288J  ASN*     1.3    59.4    -      -       -      +
    290J  CYS*     3.0    25.2    +      -       -      +
    294J  ARG*     3.6     6.6    -      -       -      -
    298J  LEU*     3.4    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 288 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284J  LEU*     3.0    14.5    +      -       -      +
    285J  ASN      2.9     4.7    +      -       -      +
    287J  ILE*     1.3    73.1    -      -       -      +
    289J  ARG*     1.3    59.2    +      -       -      +
    294J  ARG*     2.8    33.6    +      -       -      +
    298J  LEU*     2.8    40.4    +      -       -      +
    338J  ALA      2.9    20.5    +      -       -      +
    339J  ALA*     3.2    21.1    -      -       -      +
    340J  GLN*     3.9     4.6    -      -       -      +
    341J  GLY*     3.4    23.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 289 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247J  GLU*     5.0     9.5    +      -       -      -
    285J  ASN*     3.0    27.2    +      -       -      +
    286J  ALA*     2.9    14.6    +      -       -      +
    288J  ASN*     1.3    79.8    -      -       -      +
    290J  CYS*     1.3    66.7    +      -       -      +
    291J  PRO*     3.5     6.1    -      -       -      +
    294J  ARG*     4.3     0.2    -      -       -      -
    341J  GLY*     2.8    31.4    +      -       -      +
    344J  GLU*     5.2     8.5    +      -       -      -
----------------------------------------------------------
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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