Contacts of the strand formed by residues 199 - 208 (chain A) in PDB entry 1QYO


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 HIS 199 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  TYR*     2.7    40.9    +      +       -      -
     78A  MET*     3.9    11.0    -      -       +      -
     81A  HIS*     3.7     8.3    -      -       +      +
    151A  TYR*     3.7     4.0    -      -       -      +
    152A  ILE*     2.8    52.5    +      -       +      +
    196A  PRO*     3.6    23.9    -      -       +      +
    197A  ASP      3.0    18.6    +      -       -      -
    198A  ASN*     1.3    74.5    -      -       -      +
    200A  TYR*     1.3    77.9    +      -       -      +
    201A  LEU*     4.6     0.2    -      -       +      -
    226A  ALA*     4.3     1.6    -      -       +      -
    227A  ALA      3.3    11.9    -      -       -      +
    228A  GLY*     4.7     5.2    -      -       -      -
    229A  ILE*     3.8    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  ASN*     3.5    35.2    -      -       +      -
    150A  VAL      3.1    14.6    -      -       -      +
    151A  TYR*     3.8    30.5    -      +       +      -
    199A  HIS*     1.3    80.8    -      -       -      +
    201A  LEU*     1.3    64.6    +      -       -      +
    202A  SER*     4.0    12.1    -      -       -      -
    226A  ALA*     3.3     4.0    -      -       -      -
    227A  ALA*     2.9    57.9    +      -       +      +
    228A  GLY*     3.6    21.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  GLN*     3.7    32.3    -      -       +      +
     72A  SER*     3.6    22.7    -      -       -      +
     74A  TYR*     3.5    37.2    -      -       +      +
     84A  PHE*     4.0    13.2    -      -       +      -
    149A  ASN*     3.4     2.1    -      -       -      -
    150A  VAL*     2.9    37.9    +      -       +      +
    152A  ILE*     3.8    13.7    -      -       +      -
    199A  HIS*     4.5     0.7    -      -       -      +
    200A  TYR*     1.3    74.4    -      -       -      +
    202A  SER*     1.3    62.1    +      -       -      +
    203A  THR*     3.2     7.8    +      -       -      +
    224A  VAL*     3.7    13.0    -      -       +      -
    225A  THR      3.5     2.2    -      -       -      -
    226A  ALA*     4.0    13.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  HIS      4.8     0.5    +      -       -      -
    149A  ASN*     3.5    20.4    +      -       -      -
    200A  TYR*     4.0    12.9    -      -       -      -
    201A  LEU*     1.3    67.7    -      -       -      +
    203A  THR*     1.3    59.5    +      -       -      +
    204A  GLN*     4.9    15.2    +      -       -      +
    223A  PHE      3.5     2.8    -      -       -      +
    224A  VAL*     3.3     3.5    -      -       -      -
    225A  THR*     2.7    43.7    +      -       -      -
    227A  ALA*     5.5     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  GLY*     6.3     0.4    -      -       -      -
     69A  GLN*     5.5     0.5    +      -       -      -
    147A  SER*     3.4     5.9    -      -       -      -
    148A  HIS*     2.8    65.4    +      -       +      +
    150A  VAL*     3.8    12.0    -      -       +      +
    201A  LEU*     3.2    12.5    +      -       -      +
    202A  SER*     1.3    73.5    +      -       -      +
    204A  GLN*     1.3    63.9    +      -       -      +
    205A  SER*     4.2     2.6    +      -       -      +
    222A  GLU*     3.7    33.2    -      -       +      +
    223A  PHE      3.4     1.8    -      -       -      -
    224A  VAL*     3.5    19.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  SER*     4.0    19.2    -      -       -      -
    202A  SER*     4.9    14.2    +      -       -      +
    203A  THR*     1.3    78.0    -      -       -      +
    205A  SER*     1.3    61.6    +      -       -      +
    221A  LEU      3.9     0.9    -      -       -      +
    222A  GLU*     3.3     4.5    -      -       -      -
    223A  PHE*     2.9    63.3    +      -       +      +
    225A  THR*     5.5     4.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  VAL*     3.9     6.3    -      -       -      +
    145A  TYR*     3.7    54.4    +      -       -      +
    146A  ASN      5.7     0.2    -      -       -      -
    147A  SER*     5.3     2.6    -      -       -      +
    148A  HIS*     4.8     1.0    -      -       -      -
    203A  THR*     4.2     6.1    +      -       -      +
    204A  GLN*     1.3    73.6    -      -       -      +
    206A  ALA*     1.3    59.5    +      -       -      +
    207A  LEU*     4.6     1.1    -      -       -      -
    220A  LEU*     3.9    10.1    -      -       -      -
    221A  LEU      3.6     3.6    -      -       -      -
    222A  GLU*     2.9    30.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  SER*     1.3    74.6    -      -       -      +
    207A  LEU*     1.3    62.4    +      -       -      +
    208A  SER*     5.1     0.9    +      -       -      -
    219A  VAL      3.6     1.2    -      -       -      +
    220A  LEU*     3.5     5.2    -      -       -      +
    221A  LEU*     2.8    56.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  PRO*     3.8    33.7    -      -       +      -
     61A  VAL*     3.8    16.6    -      -       +      -
    143A  TYR*     3.8    33.8    -      -       +      +
    144A  ASN*     3.8    21.6    -      -       -      +
    145A  TYR*     4.5     7.5    -      -       +      +
    205A  SER*     4.6     5.4    -      -       -      -
    206A  ALA*     1.3    77.1    -      -       -      +
    208A  SER*     1.3    63.3    +      -       -      +
    218A  MET*     4.0    18.6    -      -       +      -
    219A  VAL      3.5     2.9    -      -       -      +
    220A  LEU*     3.7    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  TYR*     2.7    27.1    +      -       -      -
    206A  ALA      5.1     1.0    +      -       -      -
    207A  LEU*     1.3    75.7    -      -       -      +
    209A  LYS*     1.3    66.9    +      -       -      +
    219A  VAL*     3.0    43.4    +      -       -      +
----------------------------------------------------------
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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