Contacts of the strand formed by residues 40 - 47 (chain A) in PDB entry 2QC8


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 LEU 40 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ILE*     3.8    21.8    -      -       +      -
     32A  TRP      3.3     8.1    -      -       -      +
     33A  ILE*     4.1    10.5    -      -       +      -
     38A  GLU      3.6     2.2    +      -       -      +
     39A  GLY*     1.3    77.1    -      -       -      -
     41A  ARG*     1.3    68.4    +      -       -      +
     98A  LEU*     4.9     4.0    -      -       +      -
    219A  TRP*     3.7    39.3    -      -       +      +
    222A  ARG*     4.2     6.5    -      -       +      -
    223A  PHE*     3.7    48.0    -      -       +      +
    226A  HIS*     4.2    13.9    -      -       +      +
    164B  GLY*     4.5     0.3    -      -       -      -
    165B  VAL*     3.7    25.1    +      -       +      +
    169B  ARG*     6.0     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ILE*     3.3     4.9    -      -       -      +
     32A  TRP*     2.8    60.6    +      -       +      +
     34A  ASP*     3.0    43.9    +      -       +      +
     36A  THR*     5.6     2.8    -      -       -      +
     40A  LEU*     1.3    81.6    +      -       -      +
     42A  CYS*     1.3    66.9    +      -       -      +
     66A  SER      3.8     8.3    +      -       -      -
     67A  THR*     4.1    23.5    +      -       +      +
     68A  LEU*     5.9     0.8    -      -       -      +
    223A  PHE*     5.0     1.6    -      -       -      -
    159B  GLY      3.0    29.5    +      -       -      -
    160B  PRO*     3.5    19.8    +      -       -      +
    162B  TYR      2.8    36.1    +      -       -      -
    163B  CYS*     3.0    10.8    -      -       +      +
    164B  GLY*     4.5     2.5    -      -       -      -
    165B  VAL*     5.5     0.2    -      -       -      -
    169B  ARG*     6.1     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  MET*     3.6    33.2    -      -       +      -
     30A  TYR      3.0    14.6    -      -       -      +
     31A  ILE*     4.2     1.1    -      -       -      -
     32A  TRP*     3.6     6.3    -      -       -      -
     41A  ARG*     1.3    78.4    -      -       -      +
     43A  LYS*     1.3    62.3    +      -       -      +
    223A  PHE*     3.7    26.5    -      -       +      -
    163B  CYS*     2.7    35.9    +      -       -      +
    164B  GLY      4.7     7.0    -      -       -      -
    165B  VAL*     5.0     1.3    -      -       -      -
    173B  ARG*     4.6    12.6    -      -       -      -
    194B  ASN*     5.0     2.1    -      -       -      +
    195B  ALA      5.2     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  ALA      3.7     0.3    -      -       -      +
     29A  MET*     4.3     1.6    -      -       -      -
     30A  TYR*     2.8    35.2    +      -       +      +
     32A  TRP*     4.0    11.7    -      -       +      -
     42A  CYS*     1.3    78.0    -      -       -      +
     44A  THR*     1.3    60.6    +      -       -      +
     60A  TRP*     3.5    41.1    -      -       +      +
     61A  ASN*     2.7    33.1    +      -       -      +
     62A  PHE*     4.1    14.8    -      -       -      +
     79A  LEU*     4.6     2.7    -      -       -      -
    162B  TYR*     4.9     3.9    +      -       -      +
    163B  CYS*     3.9     8.3    -      -       -      -
    193B  THR      3.6     9.4    -      -       -      +
    194B  ASN*     3.7    21.1    -      -       +      +
    205B  GLN*     6.3     0.4    -      -       -      +
    501B  ADP      4.9    13.9    +      -       -      -
    705B   CL      3.9     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  GLN*     3.8     8.1    -      -       +      -
     28A  ALA      3.2     9.9    -      -       -      +
     29A  MET*     3.4     8.5    -      -       -      +
     43A  LYS*     1.3    76.2    -      -       -      +
     45A  ARG*     1.3    68.0    +      -       -      +
     60A  TRP*     3.6     9.5    -      -       -      -
     90A  ARG*     3.1    40.2    +      -       -      +
    180B  TYR*     3.6    22.2    -      -       +      +
    192B  GLY*     3.1     3.2    -      -       -      -
    193B  THR*     3.1    35.6    +      -       -      +
    205B  GLN*     4.6     0.2    -      -       -      +
    705B   CL      3.1    13.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  GLN*     3.6     2.3    -      -       -      -
     28A  ALA*     2.9    42.6    +      -       +      +
     30A  TYR*     3.8    18.2    +      -       +      -
     44A  THR*     1.3    74.3    -      -       -      +
     46A  THR*     1.3    61.6    +      -       -      +
     47A  LEU*     3.8    17.4    +      -       +      +
     58A  PRO*     3.7    24.6    -      -       -      +
     59A  GLU      3.6    10.9    +      -       -      -
     60A  TRP*     3.3    65.4    -      -       +      +
    180B  TYR*     3.4     5.4    -      -       -      -
    191B  ALA      3.4     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LYS*     3.6    35.7    -      -       +      -
     26A  VAL      3.2     8.5    -      -       -      +
     27A  GLN*     4.8     0.2    -      -       -      +
     45A  ARG*     1.3    76.0    +      -       -      +
     47A  LEU*     1.3    69.6    +      -       -      +
     48A  ASP*     5.5     0.8    -      -       -      +
    180B  TYR*     2.4    26.5    +      -       +      -
    184B  LEU*     4.3     7.6    -      -       +      -
    190B  ILE      2.7    28.4    +      -       -      +
    191B  ALA*     2.8    16.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LYS*     3.4     6.9    -      -       -      +
     26A  VAL*     2.6    42.8    +      -       +      +
     28A  ALA*     3.7    18.4    -      -       +      -
     45A  ARG*     4.2    15.5    -      -       +      +
     46A  THR*     1.3    81.2    -      -       -      +
     48A  ASP*     1.3    64.5    +      -       -      +
     49A  SER      3.3    11.4    -      -       -      +
     51A  PRO*     3.9    22.2    -      -       +      -
     57A  LEU*     3.6    28.5    -      -       +      -
     58A  PRO*     3.9    28.9    -      -       +      -
----------------------------------------------------------
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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