Contacts of the strand formed by residues 227 - 240 (chain A) in PDB entry 1QQW


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 GLY 227 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  VAL*     3.8    16.2    -      -       -      -
    224A  ASN      3.1     5.7    +      -       -      -
    225A  ALA      3.5     1.8    +      -       -      -
    226A  ASN*     1.3    74.9    -      -       -      +
    228A  GLU*     1.3    60.6    +      -       -      +
    229A  ALA      3.6     0.3    +      -       -      -
    421A  HIS*     3.4    23.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  TYR      4.3     1.6    -      -       -      +
    222A  LEU      3.6     0.7    -      -       -      +
    223A  VAL*     3.3     2.5    -      -       -      -
    224A  ASN*     2.8    51.7    +      -       -      +
    226A  ASN*     3.4    17.1    -      -       +      +
    227A  GLY*     1.3    76.9    -      -       -      +
    229A  ALA*     1.3    60.4    +      -       -      +
    230A  VAL*     5.4     4.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 229 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  LYS*     4.0     7.0    -      -       +      -
    222A  LEU      2.9    11.2    -      -       -      +
    223A  VAL*     4.0     6.1    -      -       +      -
    227A  GLY      3.6     1.6    +      -       -      -
    228A  GLU*     1.3    74.0    -      -       -      +
    230A  VAL*     1.3    68.8    +      -       -      +
    286A  PHE*     3.3    28.9    +      -       +      -
    421A  HIS*     3.5    39.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 230 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  TYR*     4.0    33.2    -      -       +      +
    221A  LYS*     3.6     1.0    -      -       -      -
    222A  LEU*     2.7    50.8    +      -       +      +
    228A  GLU*     5.4     4.3    -      -       +      +
    229A  ALA*     1.3    80.1    -      -       -      +
    231A  TYR*     1.3    68.2    +      -       -      +
    283A  VAL*     4.2     9.6    -      -       +      -
    284A  MET      3.9     8.7    -      -       -      +
    285A  THR*     4.5    16.8    -      -       +      -
    286A  PHE*     4.0     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  THR*     3.9    13.0    -      -       +      -
    220A  PHE      3.2    16.4    -      -       -      +
    221A  LYS*     4.3    15.7    -      -       +      -
    230A  VAL*     1.3    74.4    -      -       -      +
    232A  CYS*     1.3    65.6    +      -       -      +
    283A  VAL*     3.6     5.5    -      -       -      +
    284A  MET*     2.8    39.6    +      -       +      +
    286A  PHE*     3.4    35.0    -      +       -      -
    289A  ALA*     4.2    20.4    -      -       +      -
    297A  PHE*     3.7    31.6    -      +       -      -
    303A  TRP*     3.8    17.0    -      +       +      -
    346A  SER*     4.2    11.9    -      -       -      -
    347A  PRO*     4.3     7.9    -      -       +      +
    423A  ILE*     3.8    21.5    -      -       -      +
    425A  TYR*     5.0     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  THR*     3.5     2.4    -      -       -      -
    220A  PHE*     2.8    56.3    +      -       -      -
    222A  LEU*     3.4    41.3    -      -       +      -
    231A  TYR*     1.3    78.1    -      -       -      +
    233A  LYS*     1.3    73.8    +      -       -      +
    234A  PHE*     4.1    14.1    -      -       -      -
    281A  ILE*     5.1     6.3    -      -       +      -
    282A  GLN      2.9    14.6    -      -       -      +
    283A  VAL*     4.9     1.8    -      -       +      -
    303A  TRP*     4.0     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  PRO      5.3     1.0    +      -       -      -
    217A  SER      3.4    20.5    +      -       -      +
    218A  HIS      3.4    22.3    -      -       -      +
    219A  THR*     3.2    23.0    +      -       -      +
    232A  CYS*     1.3    80.0    -      -       -      +
    234A  PHE*     1.3    64.4    +      -       -      +
    235A  HIS*     3.4    22.6    -      -       +      +
    281A  ILE*     3.3     7.1    -      -       -      +
    282A  GLN*     3.0    31.5    +      -       +      +
    296A  PRO      4.3     3.4    +      -       -      -
    297A  PHE*     6.0     0.4    -      -       -      +
    298A  ASP      4.8     6.7    +      -       -      -
    299A  LEU*     5.7     1.4    -      -       -      +
    301A  LYS      4.2    16.0    +      -       -      -
    302A  VAL*     5.4     0.4    -      -       -      +
    303A  TRP*     3.5    50.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  PHE*     4.8     7.2    -      +       -      -
    143A  TRP*     3.9    27.6    -      +       -      -
    145A  LEU*     4.0    24.7    -      -       +      -
    215A  TYR*     3.0     8.7    -      -       -      +
    216A  GLY*     2.8    36.0    +      -       -      +
    217A  SER      4.5     0.7    +      -       -      +
    218A  HIS      5.0     1.0    +      -       -      -
    220A  PHE*     3.8    39.9    -      +       +      -
    222A  LEU*     4.7    13.0    -      -       +      -
    232A  CYS*     4.1    14.8    -      -       -      -
    233A  LYS*     1.3    71.3    -      -       -      +
    235A  HIS*     1.3    65.2    +      -       -      +
    236A  TYR*     4.5     2.0    -      -       +      -
    279A  PHE*     3.3    33.0    -      +       +      -
    280A  TYR      3.9     1.6    -      -       -      -
    281A  ILE*     3.5    21.1    -      -       +      -
    343A  ILE*     4.8     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  PRO*     5.2     7.9    -      -       +      -
    214A  GLY      3.4     5.4    -      -       -      -
    215A  TYR*     3.2    32.1    -      +       +      -
    233A  LYS*     3.4    28.0    +      -       +      +
    234A  PHE*     1.3    76.3    +      -       -      +
    236A  TYR*     1.3    64.5    +      -       -      +
    237A  LYS*     4.1    10.7    +      -       +      +
    278A  THR      3.6     0.7    -      -       -      +
    279A  PHE*     3.7     1.2    -      -       -      -
    280A  TYR*     2.8    40.9    +      -       +      +
    282A  GLN*     3.6    34.1    +      -       -      +
    305A  HIS*     5.2     7.4    +      +       -      -
    310A  LEU*     3.6    28.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  PHE*     3.3    57.6    +      +       -      +
    134A  VAL*     4.7     7.4    -      -       +      -
    145A  LEU*     4.1    21.4    +      -       +      +
    147A  GLY*     3.5    17.0    +      -       -      -
    214A  GLY*     2.8    67.7    +      -       -      -
    215A  TYR*     3.6    12.4    +      -       -      -
    216A  GLY      4.2     2.7    -      -       -      -
    234A  PHE      4.4     1.3    -      -       -      -
    235A  HIS*     1.3    79.0    -      -       -      +
    237A  LYS*     1.3    62.7    +      -       -      +
    277A  TRP*     3.3    20.1    -      +       +      -
    278A  THR      3.0    10.8    -      -       -      +
    279A  PHE*     3.8    26.0    -      +       +      -
    316A  LEU*     4.3     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  ASN*     3.2    30.8    -      -       +      +
    215A  TYR*     5.1     8.9    +      -       +      -
    235A  HIS*     4.8    11.3    +      -       +      +
    236A  TYR*     1.3    73.0    -      -       -      +
    238A  THR*     1.3    64.9    +      -       -      +
    239A  ASP*     3.4     2.6    +      -       -      +
    277A  TRP*     2.9     6.5    -      -       -      -
    278A  THR*     2.8    32.4    +      -       -      +
    280A  TYR*     3.5    31.9    -      -       +      -
    305A  HIS*     4.5    10.7    +      -       -      -
    310A  LEU*     4.2    23.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  ARG      2.6    28.1    +      -       -      -
    212A  MET*     3.4    22.7    -      -       -      +
    213A  ASN*     3.0    16.8    +      -       -      +
    237A  LYS*     1.3    72.7    -      -       -      +
    239A  ASP*     1.3    59.9    +      -       -      +
    240A  GLN*     2.9    15.6    +      -       -      +
    241A  GLY*     3.2    33.3    +      -       -      +
    242A  ILE*     4.0     4.9    -      -       +      +
    276A  SER      3.7     0.7    -      -       -      -
    277A  TRP*     3.3    13.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  LYS*     3.5     7.4    -      -       -      +
    238A  THR*     1.3    71.1    -      -       -      +
    240A  GLN*     1.3    65.9    +      -       -      +
    241A  GLY      3.4     0.7    -      -       -      -
    276A  SER*     2.7    44.6    +      -       -      +
    277A  TRP      4.0     0.2    -      -       -      -
    278A  THR*     2.8    21.2    +      -       -      -
    315A  LYS*     3.2    22.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  ARG*     3.2    29.7    +      -       -      +
    211A  HIS*     3.2    35.7    +      -       +      +
    238A  THR*     2.9     5.6    +      -       -      +
    239A  ASP*     1.3    85.3    -      -       -      +
    241A  GLY*     1.3    59.0    -      -       -      +
    243A  LYS*     5.3     2.1    -      -       -      +
    273A  LYS      6.0     0.9    -      -       -      +
    274A  TYR      4.7     1.0    -      -       -      +
    275A  PRO*     3.4    22.5    -      -       +      +
    276A  SER*     2.7    47.4    +      -       -      +
    277A  TRP*     4.0     3.2    -      -       -      -
----------------------------------------------------------
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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