Contacts of the strand formed by residues 48 - 55 (chain A) in PDB entry 2QLR


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 PHE 48 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  PHE      3.5     2.1    -      -       -      +
     47A  PRO*     1.3    81.4    -      -       +      +
     49A  LYS*     1.3    63.7    +      -       -      +
     68A  MET*     3.2    13.0    -      -       -      +
     69A  LYS*     6.1     0.9    -      -       -      +
     72A  LEU*     3.1    43.3    -      -       +      +
     53B  ILE*     3.9    25.1    -      -       +      -
     54B  THR      3.1     9.0    -      -       -      +
     55B  VAL*     4.3     6.3    -      -       +      -
     61B  ILE*     3.8    14.6    -      -       +      -
    265B  ILE*     3.9    22.9    -      -       +      -
    269B  LEU*     4.1    14.4    -      -       +      -
    302B  MET*     3.6    38.1    -      -       +      -
    303B  ILE*     4.1    12.6    -      -       +      -
    306B  LEU*     3.9    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  PRO      4.9     0.6    +      -       -      -
     44A  ASN*     3.4    25.9    +      -       -      +
     46A  PHE      2.9    25.4    +      -       -      -
     47A  PRO*     3.6     9.9    -      -       -      +
     48A  PHE*     1.3    75.3    -      -       -      +
     50A  THR*     1.3    66.9    +      -       +      +
     65A  GLU*     3.8    20.7    -      -       -      +
     68A  MET*     3.0    23.7    -      -       -      +
     69A  LYS*     6.1     5.0    -      -       +      +
     54B  THR*     2.8    20.5    +      -       -      +
     56B  GLU*     3.1    51.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  LYS*     1.3    81.2    -      -       +      +
     51A  ALA*     1.3    63.3    +      -       -      +
     52A  VAL*     5.1     5.7    -      -       -      +
     63A  PHE      3.4    14.1    -      -       -      +
     64A  GLY*     5.1     1.3    -      -       -      -
     65A  GLU*     3.8    26.9    -      -       -      +
     68A  MET*     3.3     7.2    -      -       -      -
     52B  VAL      4.9     1.2    +      -       -      -
     53B  ILE*     3.2     9.2    -      -       -      +
     54B  THR*     2.8    53.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  THR*     1.3    74.7    -      -       -      +
     52A  VAL*     1.3    67.0    +      -       -      +
     53A  ILE*     4.8     9.9    -      -       +      -
     61A  ILE      3.8     0.8    -      -       -      +
     62A  GLN*     3.5     3.1    -      -       -      +
     63A  PHE*     2.8    42.6    +      -       +      +
     68A  MET*     3.1    24.6    -      -       +      +
    298A  PHE*     4.2     8.7    -      -       +      -
     52B  VAL      3.2     5.6    -      -       -      -
     53B  ILE*     4.1    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  THR*     5.1     6.7    -      -       -      +
     51A  ALA*     1.3    79.2    -      -       -      +
     53A  ILE*     1.3    66.8    +      -       -      +
     54A  THR*     5.0     8.3    -      -       +      -
     60A  THR*     4.1     8.5    -      -       -      +
     61A  ILE      3.5     2.9    -      -       -      -
     62A  GLN*     3.9    31.9    -      -       +      +
     50B  THR      4.4     0.2    -      -       -      -
     51B  ALA*     3.1     4.5    -      -       -      -
     52B  VAL*     2.7    58.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  ALA*     4.8     9.0    -      -       +      -
     52A  VAL*     1.3    85.6    -      -       -      +
     54A  THR*     1.3    71.6    +      -       -      +
     55A  VAL*     3.8     1.4    +      -       +      +
     60A  THR*     3.5     2.2    -      -       -      -
     61A  ILE*     2.9    46.7    +      -       +      +
     63A  PHE*     5.6     2.2    -      -       +      -
    298A  PHE*     4.8     6.3    -      -       +      -
    302A  MET*     3.6    41.1    -      -       +      -
     48B  PHE*     4.1    27.1    -      -       +      -
     50B  THR      3.3    11.4    -      -       -      +
     51B  ALA*     4.3     8.1    -      -       +      -
     53B  ILE*     6.1     0.2    -      -       +      -
     68B  MET*     4.3     3.8    -      -       +      -
    298B  PHE*     4.6     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  VAL*     5.0     9.4    -      -       +      -
     53A  ILE*     1.3    78.4    -      -       -      +
     55A  VAL*     1.3    59.2    +      -       -      +
     60A  THR*     4.0    19.7    -      -       +      +
     48B  PHE*     3.4     4.5    -      -       -      -
     49B  LYS*     2.7    37.4    +      -       -      +
     50B  THR*     2.9    40.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  ILE      3.8     2.4    +      -       -      +
     54A  THR*     1.3    81.6    -      -       -      +
     56A  GLU*     1.3    73.5    +      -       -      +
     57A  ASN      3.7     1.0    +      -       -      -
     58A  GLY      3.3    31.9    -      -       -      +
     59A  LYS      3.7    16.6    -      -       -      +
     60A  THR*     4.6     5.3    +      -       -      +
     61A  ILE*     4.0    25.6    -      -       +      -
    306A  LEU*     3.6    25.6    -      -       +      -
    310A  TRP*     5.1     0.9    -      -       +      -
     47B  PRO*     3.6    11.7    -      -       +      +
     48B  PHE*     4.1    11.9    -      -       +      -
     49B  LYS*     4.7     2.0    -      -       -      -
----------------------------------------------------------
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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