Contacts of the strand formed by residues 39 - 56 (chain A) in PDB entry 2Q53


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 ALA 39 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  SER      3.5     4.7    +      -       -      +
     38A  ALA*     1.3    72.9    -      -       -      +
     40A  PHE*     1.3    68.0    +      -       -      +
     41A  PHE      3.2     0.2    +      -       -      -
     84A  TRP*     3.3     5.7    -      -       -      -
     85A  LYS*     2.7    50.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ALA*     1.3    75.6    -      -       -      +
     41A  PHE*     1.3    64.3    +      -       -      +
     42A  CYS*     3.6    29.4    -      -       -      -
     43A  VAL*     3.9    18.2    -      -       +      -
     82A  VAL*     3.5    29.8    -      -       +      -
     84A  TRP*     3.2    24.3    -      +       +      -
     85A  LYS*     5.5     0.2    -      -       -      +
    150A  ASN*     3.8    28.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  LEU*     4.0    23.3    -      -       +      -
     40A  PHE*     1.3    84.5    -      -       -      +
     42A  CYS*     1.3    71.3    +      -       +      +
     83A  VAL*     2.7    43.5    +      -       +      +
     85A  LYS*     4.0    40.8    -      -       +      +
    118A  LYS*     5.7     8.5    -      -       -      -
    120A  ILE*     4.3    16.4    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     40A  PHE*     3.6    17.9    -      -       -      -
     41A  PHE*     1.3    90.2    -      -       +      +
     43A  VAL*     1.3    63.3    +      -       -      +
     44A  ALA*     4.7     0.4    -      -       -      -
     82A  VAL*     3.3     2.6    -      -       -      +
     83A  VAL*     2.5    51.4    +      -       -      +
    114A  THR*     3.8    15.3    -      -       +      -
    120A  ILE*     3.3    34.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  PHE*     3.9    17.4    -      -       +      -
     42A  CYS*     1.3    74.8    -      -       -      +
     44A  ALA*     1.3    64.6    +      -       -      +
     80A  TRP*     3.9    22.7    -      -       +      -
     81A  GLY      3.5    12.3    -      -       -      +
     82A  VAL*     4.1     1.8    -      -       +      -
    114A  THR*     3.3    25.3    -      -       -      +
    115A  GLN*     4.4    12.5    +      -       +      +
    150A  ASN      3.2    26.9    -      -       -      +
    151A  GLY      4.4     3.6    -      -       -      +
    152A  LEU*     4.0    26.2    -      -       +      -
    153A  PRO*     4.4     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PHE*     3.8     5.3    -      -       +      -
     42A  CYS*     4.0     2.6    +      -       -      -
     43A  VAL*     1.3    79.1    -      -       -      +
     45A  ARG*     1.3    60.7    +      -       -      +
     80A  TRP*     3.2    12.7    -      -       -      -
     81A  GLY      3.0    30.5    +      -       -      -
     82A  VAL*     4.8     0.2    -      -       -      +
     83A  VAL*     4.1    12.8    -      -       +      -
    112A  VAL*     3.5    29.8    -      -       +      -
    113A  ALA*     3.5    16.8    -      -       -      +
    114A  THR      4.0     0.9    -      -       -      +
    120A  ILE*     5.3     0.4    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     44A  ALA*     1.3    74.7    -      -       -      +
     46A  LEU*     1.3    63.3    +      -       -      +
     47A  GLN*     3.5    31.5    +      -       -      +
     78A  GLU*     3.4    36.6    +      -       +      -
     79A  VAL      3.5     5.6    -      -       -      +
     80A  TRP*     3.4    43.1    -      -       +      +
    112A  VAL*     3.3    19.3    -      -       -      +
    113A  ALA*     3.0    19.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PHE*     4.0    18.4    -      -       +      -
     45A  ARG*     1.3    73.8    -      -       -      +
     47A  GLN*     1.3    66.3    +      -       -      +
     49A  PHE*     3.3    50.2    -      -       +      +
     71A  ILE*     3.6    22.7    -      -       +      -
     78A  GLU*     3.3     1.6    -      -       -      -
     79A  VAL*     2.6    43.1    +      -       +      +
    110A  VAL*     4.4    15.5    -      -       +      -
    111A  LYS      4.2    11.9    -      -       -      +
    112A  VAL*     3.9    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ARG*     3.5    42.0    +      -       -      +
     46A  LEU*     1.3    75.5    -      -       -      +
     48A  ASP*     1.3    93.3    +      -       -      +
     49A  PHE*     3.1    17.8    +      -       -      -
     76A  GLY*     3.3    21.2    +      -       -      -
     77A  ASP      2.9    21.7    +      -       -      -
     78A  GLU*     3.7    11.3    -      -       -      +
    111A  LYS      5.7     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  GLN*     1.3    96.9    +      -       -      +
     49A  PHE*     1.3    54.7    +      -       +      +
     73A  GLN*     3.1    11.5    -      -       +      +
     74A  SER      2.6    40.7    +      -       -      +
     75A  PRO*     3.8    21.3    -      -       -      +
     76A  GLY      4.0     2.6    +      -       -      -
     77A  ASP      2.9    10.8    +      -       -      -
    101B  LYS      4.4    12.4    -      -       -      +
    102B  SER*     4.3    14.2    -      -       -      +
    103B  GLY*     5.9     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  LEU*     3.3    50.0    -      -       +      +
     47A  GLN      3.1     9.3    -      -       -      -
     48A  ASP*     1.3    81.6    -      -       +      +
     50A  LYS*     1.3    58.9    +      -       -      +
     71A  ILE*     3.9    11.0    -      -       +      -
     72A  PHE*     3.2    24.5    -      -       -      -
     73A  GLN*     3.4    28.5    -      -       +      -
     77A  ASP*     3.7     3.3    +      -       -      -
     78A  GLU*     3.2    21.5    +      -       -      -
     79A  VAL*     3.2    15.9    -      -       +      +
    110A  VAL*     5.3     5.6    -      -       +      -
    126A  LEU*     4.0    21.1    -      -       +      -
    106B  VAL*     3.4    30.3    -      -       +      -
    128B  THR*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  PHE*     1.3    73.8    -      -       -      +
     51A  LEU*     1.3    75.3    +      -       -      +
     52A  ASP*     5.9     0.4    -      -       -      -
     71A  ILE*     3.3     6.2    -      -       -      +
     72A  PHE*     2.8    57.5    +      -       +      -
     74A  SER*     3.7    12.1    -      -       -      +
     77A  ASP*     3.1    35.9    +      -       -      +
     78A  GLU      5.0     1.1    -      -       -      +
     79A  VAL*     3.8     2.9    -      -       -      -
    159A  LYS*     5.4     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  TYR*     3.7    38.1    -      -       +      +
     50A  LYS*     1.3    96.2    +      -       -      +
     52A  ASP*     1.3    80.5    +      -       -      +
     53A  PHE*     3.9    22.9    -      -       +      -
     69A  ALA*     4.4     8.3    -      -       +      -
     70A  THR      3.8     8.1    -      -       -      +
     71A  ILE*     4.0     3.6    -      -       +      -
     78A  GLU      5.1     1.9    +      -       -      +
     79A  VAL*     3.7     7.4    -      -       +      +
    143A  ILE*     5.9     0.7    -      -       +      -
    156A  TYR*     3.9    19.3    -      -       +      +
    160A  LEU*     3.8    28.9    -      -       +      -
    163A  ILE*     4.5     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  LYS*     5.9     0.7    -      -       -      -
     51A  LEU*     1.3    83.0    -      -       -      +
     53A  PHE*     1.3    96.5    +      -       -      +
     69A  ALA*     3.5     1.7    -      -       -      -
     70A  THR*     3.0    31.1    +      -       +      +
     72A  PHE*     4.1    14.5    -      -       +      -
    130A  TYR*     2.6    33.3    +      -       -      +
    132A  SER*     3.1    22.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  LEU*     3.9    24.9    -      -       +      -
     52A  ASP*     1.3    90.4    +      -       -      +
     54A  GLY*     1.3    59.2    +      -       -      +
     67A  GLY      4.0     4.7    -      -       -      -
     68A  ILE      3.3     6.5    -      -       -      +
     69A  ALA*     3.7    13.5    -      -       +      -
     70A  THR*     4.7     0.7    -      -       -      +
    130A  TYR*     4.0     2.9    -      -       -      -
    132A  SER*     3.3     8.5    -      -       -      -
    133A  ALA      2.9    31.8    +      -       -      +
    134A  PRO*     4.8     0.2    -      -       +      -
    135A  PRO*     3.8    26.2    -      -       +      -
    139A  TYR*     3.5    35.2    -      +       -      -
    140A  LYS*     6.2     1.1    -      -       -      -
    143A  ILE*     3.8    17.9    -      -       +      -
    163A  ILE*     3.7    37.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  PHE*     1.3    77.5    -      -       -      +
     55A  ASN*     1.3    61.0    +      -       -      +
     56A  SER      3.9     0.2    -      -       -      -
     67A  GLY*     3.4     7.3    -      -       -      -
     68A  ILE*     2.9    41.1    +      -       -      +
    127A  MSE      4.1     5.3    -      -       -      +
    130A  TYR*     3.8     8.5    -      -       -      -
    131A  GLU      3.3    12.3    -      -       -      -
    133A  ALA      3.5     8.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  GLY*     1.3    75.3    -      -       -      +
     56A  SER*     1.3    66.2    +      -       -      +
     57A  GLN      3.3     1.0    +      -       -      -
     58A  GLY*     3.0    20.2    +      -       -      -
     59A  LYS      2.9    22.6    -      -       -      +
     60A  THR*     3.3    31.3    +      -       -      +
     61A  SER      4.4     0.7    +      -       -      -
     66A  GLY      4.3     2.3    -      -       -      +
     67A  GLY*     4.2     7.4    +      -       -      -
     68A  ILE*     5.4     0.2    -      -       -      -
    130A  TYR*     3.6     2.8    -      -       -      +
    131A  GLU*     3.0    30.1    +      -       +      +
    133A  ALA*     3.2    25.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  GLY      3.8     3.6    +      -       -      -
     55A  ASN*     1.3    64.1    -      -       -      +
     57A  GLN*     1.3    66.2    +      -       -      +
     58A  GLY      2.9     1.6    -      -       -      -
     59A  LYS*     2.6    37.8    +      -       -      +
     68A  ILE*     4.6     6.6    -      -       -      +
    103A  GLY      4.2     0.9    +      -       -      -
    104A  MSE      3.2    48.9    +      -       -      +
    127A  MSE      3.5    28.0    -      -       -      -
    129A  ASN      3.9     5.9    +      -       -      -
    130A  TYR*     4.2     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