Contacts of the strand formed by residues 245 - 252 (chain A) in PDB entry 1QCY


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 LYS 245 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  THR*     4.2    11.3    +      -       -      +
    142A  GLN      3.2     5.0    +      -       -      +
    143A  LEU*     3.2    31.0    -      -       +      +
    144A  ASP      3.0    24.8    +      -       -      +
    244A  VAL*     1.3    75.5    -      -       -      +
    246A  LYS*     1.3    77.2    +      -       -      +
    247A  VAL*     4.2     4.3    -      -       +      -
    273A  ASN*     2.9    30.3    +      -       +      +
    275A  GLN*     3.5    32.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  ASP*     3.6    10.1    -      -       +      +
    234A  PHE*     3.7    48.5    +      -       +      +
    240A  ALA*     5.3     8.3    -      -       -      -
    241A  ARG      5.3     7.2    -      -       -      +
    244A  VAL      3.6     9.2    +      -       -      +
    245A  LYS*     1.3    83.9    -      -       -      +
    247A  VAL*     1.3    63.7    +      -       -      +
    272A  GLU*     4.5    21.6    +      -       -      +
    273A  ASN      4.5     3.2    +      -       -      +
    274A  ILE*     3.6    28.5    -      -       +      +
    275A  GLN      3.0    23.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  LEU*     4.2    26.9    -      -       +      -
    144A  ASP      2.9    10.1    +      -       -      +
    145A  ILE*     3.3    10.7    -      -       +      +
    146A  VAL      2.8    25.6    +      -       -      -
    234A  PHE*     3.4     6.4    -      -       -      -
    245A  LYS*     4.2     2.9    -      -       +      +
    246A  LYS*     1.3    81.2    -      -       -      +
    248A  MET*     1.3    65.8    +      -       -      +
    249A  VAL*     4.6     5.6    -      -       +      -
    275A  GLN*     3.4    24.9    -      -       -      +
    277A  PHE*     3.8    30.1    -      -       +      -
    331A  ILE*     4.2    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  VAL      3.2    11.0    -      -       -      +
    148A  VAL*     3.7    19.7    -      -       +      -
    226A  THR*     3.6    38.4    -      -       -      +
    229A  ALA*     4.1     5.8    -      -       +      -
    230A  ARG      4.2     3.8    -      -       -      +
    234A  PHE*     4.0    15.9    -      -       +      -
    247A  VAL*     1.3    76.0    -      -       -      +
    249A  VAL*     1.3    65.3    +      -       -      +
    250A  ILE*     3.8    18.2    -      -       +      -
    269A  CYS*     3.9    21.5    -      -       -      -
    274A  ILE*     4.0    22.2    -      -       +      +
    275A  GLN      2.8     8.6    +      -       -      +
    276A  ARG*     3.5     8.3    -      -       +      +
    277A  PHE*     2.9    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  ILE*     4.2    17.3    -      -       +      -
    146A  VAL      2.9     7.5    +      -       -      -
    147A  ILE*     3.4    19.4    -      -       +      +
    148A  VAL      2.7    33.3    +      -       -      +
    164A  PHE*     4.8     3.6    -      -       +      -
    168A  LEU*     5.3     3.4    -      -       +      -
    247A  VAL*     4.6     3.6    -      -       +      -
    248A  MET*     1.3    77.9    -      -       -      +
    250A  ILE*     1.3    59.8    +      -       -      +
    251A  VAL*     4.0     7.6    +      -       +      -
    277A  PHE*     3.2    14.1    -      -       +      +
    279A  ILE*     4.0    25.1    -      -       +      -
    327A  LEU*     4.3    11.7    -      -       +      -
    331A  ILE*     4.2    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  VAL*     3.5    17.7    -      -       +      +
    186A  TYR*     4.6     7.2    -      -       -      +
    222A  THR*     4.5    15.3    -      -       +      -
    226A  THR*     3.7    26.9    -      -       +      +
    248A  MET*     3.8    28.3    -      -       +      +
    249A  VAL*     1.3    75.6    -      -       -      +
    251A  VAL*     1.3    62.3    +      -       -      +
    252A  THR*     4.2     4.2    -      -       +      +
    276A  ARG*     4.9     6.7    -      -       +      -
    277A  PHE      2.7    12.5    +      -       -      +
    278A  SER*     3.5     6.4    -      -       -      -
    279A  ILE*     2.7    35.9    +      -       -      +
    299A  ILE*     5.4     0.6    -      -       +      +
    302A  ILE*     3.2    35.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  ILE*     4.9     0.4    -      -       +      -
    148A  VAL      2.9     8.9    +      -       -      +
    149A  LEU*     3.8    28.9    -      -       +      -
    150A  ASP*     2.9    31.3    +      -       -      +
    155A  ILE*     5.3     2.9    -      -       +      +
    161A  VAL*     5.6     4.3    -      -       +      -
    164A  PHE*     4.1    13.5    -      -       +      -
    186A  TYR*     4.2     2.1    +      -       -      -
    249A  VAL*     4.4     8.1    -      -       +      +
    250A  ILE*     1.3    76.9    -      -       -      +
    252A  THR*     1.3    63.6    +      -       -      +
    279A  ILE*     3.6    28.9    -      -       +      +
    281A  ILE*     3.9    27.4    -      -       +      -
    320A  LEU*     4.6    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  ASP*     2.7    23.5    +      -       -      -
    155A  ILE*     4.9     1.8    -      -       -      -
    186A  TYR*     3.4    20.5    +      -       -      +
    220A  THR*     3.7     2.4    -      -       -      +
    222A  THR*     4.1     3.3    +      -       +      +
    250A  ILE*     5.2     7.0    -      -       +      -
    251A  VAL*     1.3    77.4    -      -       -      +
    253A  ASP*     1.3    63.4    +      -       -      +
    254A  GLY      3.4    13.6    +      -       -      +
    279A  ILE      3.1    12.3    +      -       -      +
    280A  ALA*     3.4     1.6    -      -       -      -
    281A  ILE*     2.9    26.5    +      -       -      +
    295A  PHE*     3.7     2.4    -      -       +      -
    299A  ILE*     3.4    36.6    -      -       +      -
    302A  ILE*     5.8     0.2    -      -       +      -
----------------------------------------------------------
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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