Contacts of the strand formed by residues 214 - 224 (chain B) 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 214 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  PHE*     4.1     2.7    -      -       -      -
    148B  ASN      3.5     8.1    -      -       -      -
    213B  ASN*     1.3    78.6    -      -       -      +
    215B  TYR*     1.3    67.2    +      -       -      -
    235B  HIS*     3.3     2.9    -      -       -      -
    236B  TYR*     2.7    61.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 215 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  GLY*     3.2    21.7    -      -       -      -
    148B  ASN      3.2     7.5    +      -       -      -
    149B  ASN      2.9    26.9    -      -       -      -
    150B  THR      3.4    19.1    -      -       -      +
    151B  PRO*     3.4    35.0    -      -       +      -
    203B  ARG*     3.1    27.2    +      -       -      -
    213B  ASN*     3.5    29.8    +      -       +      +
    214B  GLY*     1.3    78.9    -      -       -      -
    216B  GLY*     1.3    64.2    -      -       -      +
    217B  SER*     3.8     8.2    -      -       -      +
    234B  PHE      3.0     8.7    -      -       -      +
    235B  HIS*     3.1    33.2    -      +       +      +
    236B  TYR*     3.3     6.0    +      -       -      -
    237B  LYS*     5.4     4.7    -      -       +      -
    305B  HIS*     6.2     2.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 216 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  LEU*     4.2    24.7    -      -       -      -
    146B  VAL      4.1     2.8    -      -       -      +
    147B  GLY*     4.6     2.7    -      -       -      -
    215B  TYR*     1.3    71.8    -      -       -      +
    217B  SER*     1.3    65.5    +      -       -      +
    218B  HIS*     2.9    16.1    +      -       -      -
    220B  PHE*     4.1     9.7    -      -       -      -
    234B  PHE*     2.7    24.3    +      -       -      +
    236B  TYR*     4.7     0.7    -      -       -      -
    600B  HEM      3.6    12.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 217 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148B  ASN*     4.4     6.9    +      -       -      +
    150B  THR      3.0    23.7    +      -       -      -
    151B  PRO*     3.7    22.0    -      -       -      +
    152B  ILE      4.0     5.9    +      -       -      -
    215B  TYR*     3.1     8.1    +      -       -      +
    216B  GLY*     1.3    80.3    -      -       -      +
    218B  HIS*     1.3    63.2    +      -       -      -
    233B  LYS*     3.4    19.8    +      -       -      +
    234B  PHE      5.3     0.8    -      -       -      +
    299B  LEU*     3.4    21.9    -      -       -      +
    600B  HEM      3.8    19.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 218 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216B  GLY      2.9    19.1    +      -       -      -
    217B  SER*     1.3    77.9    +      -       -      +
    219B  THR*     1.3    62.3    -      -       -      +
    220B  PHE*     3.7    24.2    +      +       +      -
    232B  CYS      3.9     1.7    -      -       -      +
    233B  LYS*     3.7    16.8    -      -       -      +
    299B  LEU*     3.6    20.4    -      -       +      +
    348B  ASP*     2.6    27.2    +      -       -      +
    350B  MET*     3.7    24.7    -      -       +      -
    351B  LEU*     3.9    27.7    -      -       +      +
    354B  ARG*     3.1    41.2    +      -       -      -
    600B  HEM      3.8    10.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218B  HIS*     1.3    74.3    -      -       -      +
    220B  PHE*     1.3    69.9    +      -       -      +
    231B  TYR*     3.8    27.1    -      -       +      -
    232B  CYS      3.5     5.6    -      -       -      +
    233B  LYS*     2.8    27.6    +      -       -      +
    296B  PRO      2.9    17.7    +      -       -      +
    297B  PHE*     3.9    19.7    -      -       +      -
    303B  TRP*     3.7    10.3    -      -       +      -
    346B  SER*     2.7    33.2    +      -       -      -
    348B  ASP*     4.4     3.8    +      -       -      -
    351B  LEU*     4.0     5.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 220 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143B  TRP*     6.2     1.8    -      -       -      -
    145B  LEU*     4.3    14.8    -      -       +      -
    146B  VAL      5.8     1.8    -      -       -      -
    216B  GLY*     4.1    14.4    -      -       -      -
    218B  HIS*     3.7    32.5    -      +       +      -
    219B  THR*     1.3    76.4    -      -       -      +
    221B  LYS*     1.3    62.9    +      -       -      +
    231B  TYR*     3.3    10.2    -      -       -      -
    232B  CYS*     2.9    36.5    +      -       -      -
    234B  PHE*     3.7    40.8    -      +       +      -
    336B  PRO*     5.3     6.3    -      -       +      -
    339B  MET*     4.2    16.6    -      -       +      -
    343B  ILE*     4.8     4.7    -      -       +      -
    344B  GLU      3.7    15.9    -      -       -      +
    345B  ALA      4.5     1.3    -      -       -      -
    346B  SER*     4.5     1.3    -      -       -      -
    351B  LEU*     4.0    28.9    -      -       +      -
    354B  ARG*     5.4     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 221 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  PHE*     1.3    77.1    -      -       -      +
    222B  LEU*     1.3    75.7    +      -       -      +
    223B  VAL*     4.2     2.7    -      -       +      -
    229B  ALA*     4.2    10.5    -      -       +      -
    230B  VAL      3.5     9.2    -      -       -      +
    231B  TYR*     4.3    16.4    -      -       +      +
    286B  PHE*     4.8     1.3    -      -       +      -
    343B  ILE*     3.6     5.0    -      -       -      +
    344B  GLU*     2.9    64.9    +      -       +      +
    345B  ALA      3.2    21.2    +      -       -      +
    421B  HIS*     3.2    42.2    +      -       -      +
    423B  ILE*     3.7    23.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 222 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  ILE*     5.8     2.5    -      -       +      -
     94B  TYR*     3.7    25.8    -      -       +      +
     95B  SER*     3.8    13.5    -      -       -      -
    100B  PHE*     5.0     3.4    -      -       +      -
    220B  PHE*     5.9     0.2    -      -       +      -
    221B  LYS*     1.3    77.2    -      -       -      +
    223B  VAL*     1.3    64.2    +      -       -      +
    228B  GLU      3.6     0.3    -      -       -      +
    229B  ALA*     3.0     6.9    -      -       -      +
    230B  VAL*     2.7    44.8    +      -       +      +
    231B  TYR      5.2     0.2    -      -       -      +
    232B  CYS*     3.8    31.9    -      -       +      -
    234B  PHE*     4.4    17.0    -      -       +      -
    281B  ILE*     4.4    18.4    -      -       +      -
    283B  VAL*     5.3     1.3    -      -       +      -
    342B  GLY      3.3    13.2    -      -       -      +
    343B  ILE*     3.9    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 223 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  TYR      3.4     4.9    -      -       -      -
     95B  SER*     3.2     0.3    -      -       -      -
     96B  LYS*     2.9    30.7    +      -       +      +
    221B  LYS*     4.2     6.3    -      -       +      -
    222B  LEU*     1.3    79.6    -      -       -      +
    224B  ASN*     1.3    72.8    +      -       -      +
    227B  GLY*     3.8    18.6    -      -       -      +
    228B  GLU      3.2     8.5    -      -       -      +
    229B  ALA*     4.0     9.0    -      -       +      -
    342B  GLY*     2.9    24.1    +      -       -      +
    344B  GLU*     3.9    13.9    -      -       +      +
    421B  HIS*     3.8    29.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 224 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  THR      3.9    10.1    -      -       -      +
     93B  LYS*     3.7    23.1    +      -       -      +
     94B  TYR      3.3    12.9    +      -       -      +
     95B  SER      4.1     0.2    -      -       -      -
     96B  LYS*     3.9    10.6    +      -       -      +
    223B  VAL*     1.3    78.6    -      -       -      +
    225B  ALA*     1.3    52.5    +      -       -      +
    226B  ASN*     2.5    31.4    +      -       -      +
    227B  GLY*     2.7    13.0    +      -       -      -
    228B  GLU*     2.7    69.3    +      -       -      +
----------------------------------------------------------
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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