Contacts of the strand formed by residues 219 - 227 (chain A) in PDB entry 3ANX


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 TYR 219 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  PHE      3.3     0.2    -      -       -      -
    218A  ARG*     1.3   119.3    +      -       +      +
    220A  VAL*     1.3    60.4    +      -       -      +
    221A  ARG*     4.1     8.7    -      -       -      +
    238A  LEU      3.5     1.9    -      -       -      +
    239A  ALA*     3.3     4.3    -      -       -      -
    240A  SER      2.8    46.5    +      -       -      +
    241A  ASP      3.9     7.4    -      -       -      -
    242A  ALA      4.9     0.4    -      -       -      -
    243A  PHE*     3.4    28.3    -      -       -      +
    244A  ASP*     3.7    28.0    -      -       +      -
    245A  PRO*     3.7    20.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  HIS*     3.3    31.6    +      -       +      +
    213A  VAL*     3.5    22.4    -      -       +      +
    214A  ARG*     3.3    45.6    -      -       -      +
    217A  PHE*     3.9     9.4    -      -       +      -
    218A  ARG      3.8     2.2    +      -       -      -
    219A  TYR*     1.3    73.1    -      -       -      +
    221A  ARG*     1.3    76.5    +      -       -      +
    237A  LEU*     3.4    35.2    -      -       +      -
    238A  LEU      3.4     4.7    -      -       -      +
    239A  ALA*     4.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  ARG*     5.7     1.8    -      -       -      +
    219A  TYR*     4.7     9.2    -      -       -      +
    220A  VAL*     1.3    90.7    +      -       -      +
    222A  SER*     1.3    62.9    +      -       -      +
    223A  TYR      3.7     0.7    +      -       -      -
    237A  LEU*     3.4     1.8    -      -       -      +
    238A  LEU*     2.8    39.2    +      -       +      +
    244A  ASP*     2.8    45.1    +      -       -      -
    245A  PRO*     3.8    15.5    -      -       +      -
    246A  ALA*     3.7    22.9    -      -       +      +
    276A  PHE*     4.2     9.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206A  HIS*     2.7    30.9    +      -       -      -
    210A  HIS*     3.2    31.6    -      -       -      -
    221A  ARG*     1.3    74.4    -      -       -      +
    223A  TYR*     1.3    60.5    +      -       -      +
    236A  PHE      3.7     4.2    +      -       -      -
    237A  LEU*     3.9     2.5    -      -       -      -
    276A  PHE*     4.2     8.0    -      -       -      +
    278A  LEU*     3.3    23.8    -      -       -      +
    282A  LEU*     5.0     2.4    -      -       -      +
    286A  LEU*     4.0    14.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  THR*     3.0    38.4    +      -       +      -
     67A  LEU*     4.1     9.7    +      -       -      -
     70A  PRO*     3.7    13.2    -      -       +      +
    192A  GLY*     5.6     0.2    -      -       -      -
    193A  MET      4.8     2.9    +      -       -      -
    206A  HIS*     5.4     0.2    +      -       -      -
    222A  SER*     1.3    74.7    +      -       -      +
    224A  LYS*     1.3    64.6    +      -       -      +
    235A  GLY*     4.0     0.5    -      -       -      -
    236A  PHE*     2.8    63.6    +      +       +      +
    237A  LEU*     3.6    21.1    +      -       -      -
    238A  LEU*     4.0     9.7    -      -       +      +
    275A  MET*     3.4    40.2    -      -       +      +
    276A  PHE*     3.3    37.7    -      +       +      -
    278A  LEU*     4.7     1.3    -      -       -      -
    282A  LEU*     6.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  ILE*     4.1    16.6    -      -       +      -
    223A  TYR*     1.3    77.9    -      -       -      +
    225A  ASN*     1.3    66.3    +      -       -      +
    233A  ASN*     3.8    29.4    -      -       -      +
    234A  PHE      3.7    11.4    -      -       -      +
    236A  PHE*     4.5     2.5    -      -       -      -
    271A  TYR*     5.4     0.3    +      -       -      -
    274A  ALA      5.5     0.4    +      -       -      -
    275A  MET*     3.0    32.5    +      -       -      +
    277A  VAL      4.2     7.5    +      -       -      -
    278A  LEU*     3.7    16.2    -      -       +      -
    279A  PRO*     4.4     7.4    -      -       +      -
    282A  LEU*     4.2    18.2    -      -       +      -
    225B  ASN*     5.4     0.4    -      -       -      -
    226B  HIS*     6.0     2.0    -      -       -      -
    271B  TYR*     3.5    39.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  ILE*     3.6     9.5    -      -       -      +
     66A  THR*     2.6    44.0    +      -       +      +
    224A  LYS*     1.3    81.4    -      -       -      +
    226A  HIS*     1.4    69.4    +      -       -      +
    227A  ILE*     3.5    10.2    +      -       +      +
    233A  ASN*     3.6     7.3    +      -       -      -
    234A  PHE*     3.0    28.5    +      -       -      +
    236A  PHE*     4.6     0.7    -      -       +      -
    266A  HIS*     3.2    23.2    +      -       -      -
    271A  TYR*     2.6    29.5    +      -       -      -
    275A  MET*     3.9     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  ILE*     4.5     7.1    -      -       -      +
    225A  ASN*     1.4    75.7    +      -       -      +
    227A  ILE*     1.3    60.6    +      -       -      +
    228A  PRO*     3.4    38.3    +      -       +      +
    231A  PHE*     4.2     2.5    -      -       -      -
    232A  LEU      3.8    20.5    +      -       -      -
    233A  ASN*     3.8     7.2    +      -       -      +
    266A  HIS*     5.7     0.7    +      -       -      -
    198B  ILE      4.9     3.3    +      -       -      -
    199B  LEU*     5.3     2.0    -      -       -      +
    224B  LYS*     6.0     1.6    -      -       -      +
    226B  HIS*     2.7    43.8    +      +       +      +
    231B  PHE      4.3     0.7    -      -       -      -
    232B  LEU*     3.8     5.2    -      -       -      +
    233B  ASN*     3.4    48.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  ASP*     3.4    18.4    -      -       -      +
     62A  ILE*     4.4    10.1    -      -       +      -
     63A  TYR*     4.1    36.1    -      -       +      +
     66A  THR*     4.8     0.2    -      -       -      +
    225A  ASN*     3.8    22.0    -      -       -      +
    226A  HIS*     1.3    74.6    -      -       -      +
    228A  PRO*     1.4    68.1    -      -       +      +
    230A  PHE*     2.9    51.4    +      -       +      +
    231A  PHE      3.3     7.1    +      -       -      -
    232A  LEU      3.3    10.3    +      -       -      +
    234A  PHE*     3.9    18.2    -      -       +      -
    236A  PHE*     4.3    15.3    -      -       +      -
----------------------------------------------------------
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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