Contacts of the strand formed by residues 16 - 21 (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 SER 16 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  GLU*     3.7    17.3    +      -       -      +
     15A  GLU*     1.3    85.1    +      -       -      +
     17A  PHE*     1.3    59.1    +      -       -      +
     18A  LEU*     5.7     0.9    -      -       -      +
     85A  LYS*     3.9    30.5    -      -       -      +
     86A  MSE      2.9    19.6    +      -       -      -
     87A  ASN*     3.8    12.0    +      -       -      +
     88A  LYS*     3.8     8.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 17 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  SER*     1.3    75.1    -      -       -      +
     18A  LEU*     1.3    75.0    +      -       -      +
     19A  TYR*     3.9    11.7    -      -       +      -
     84A  TRP      3.7     0.2    -      -       -      +
     85A  LYS*     3.6     1.9    -      -       -      -
     86A  MSE      2.6    67.2    +      -       +      +
     87A  ASN      3.0    26.7    -      -       -      -
     88A  LYS*     3.6    15.9    -      -       +      -
     90A  ASN*     4.0     1.1    -      -       +      -
     91A  LEU*     3.5    40.8    -      -       +      -
     94A  LEU*     3.7    25.1    -      -       +      -
    123A  ARG*     4.1    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  SER      5.7     0.7    -      -       -      +
     17A  PHE*     1.3    77.9    -      -       -      +
     19A  TYR*     1.3    58.8    +      -       -      +
     41A  PHE*     4.0    32.1    -      -       +      -
     83A  VAL*     3.9    11.0    -      -       +      -
     84A  TRP      3.6     1.1    -      -       -      -
     85A  LYS*     4.0    34.1    -      -       +      -
    120A  ILE*     3.8    26.5    -      -       +      -
    121A  THR      4.0    15.0    -      -       -      +
    122A  CYS*     3.6     3.0    -      -       -      -
    123A  ARG*     3.0    27.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  PHE*     3.9    10.0    +      -       +      -
     18A  LEU*     1.3    72.7    -      -       -      +
     20A  PHE*     1.3    74.1    +      -       -      +
     21A  ALA*     3.2    25.4    -      -       +      +
     25A  ASN*     2.8    33.2    +      -       -      +
     31A  ILE*     4.0    16.6    -      -       +      -
     82A  VAL      3.5     1.9    -      -       -      +
     83A  VAL*     3.4     2.7    -      -       -      -
     84A  TRP*     2.7    46.6    +      -       +      +
     86A  MSE      3.8    27.4    -      -       -      -
     94A  LEU*     3.8    18.6    -      -       +      -
     98A  GLU*     3.7    10.0    +      -       -      -
    122A  CYS*     4.5     0.7    -      -       -      -
    123A  ARG*     3.4    11.4    -      -       +      -
    124A  SER*     4.9     0.2    -      -       -      -
    125A  TYR*     3.8    25.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with PHE 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  TYR*     1.3    76.1    -      -       -      +
     21A  ALA*     1.3    57.2    +      -       -      +
     22A  TYR*     4.4    13.7    -      +       +      -
     44A  ALA*     3.8    15.3    -      -       +      -
     46A  LEU*     4.0    26.2    -      -       +      -
     79A  VAL*     4.2     5.6    -      -       +      -
     80A  TRP      4.4     0.9    -      -       -      -
     81A  GLY*     3.6    36.6    -      -       -      -
     82A  VAL      3.6    13.2    -      -       -      -
     83A  VAL*     4.1    10.8    -      -       +      +
    110A  VAL*     3.9    17.3    -      -       +      -
    112A  VAL*     3.8    25.6    -      -       +      -
    122A  CYS*     3.4    26.3    -      -       +      +
    123A  ARG      2.9    10.0    +      -       -      +
    124A  SER*     2.6    36.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  TYR*     3.2    38.3    +      -       +      +
     20A  PHE*     1.3    75.0    -      -       -      +
     22A  TYR*     1.3    63.5    +      -       -      +
     23A  GLY      3.7     1.3    -      -       -      +
     25A  ASN*     3.7    24.2    -      -       +      +
     26A  LEU*     4.0     4.2    -      -       -      +
     81A  GLY*     3.2     4.0    -      -       -      -
     82A  VAL*     3.1    33.4    +      -       +      +
     84A  TRP*     4.8     0.9    -      -       +      -
    124A  SER*     4.7     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