Contacts of the strand formed by residues 211 - 219 (chain Q) in PDB entry 5A0Q


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 VAL 211 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46Q  ALA*     5.5     0.2    -      -       +      -
     47Q  ALA      3.4     7.4    -      -       -      +
     48Q  GLU*     5.4     1.1    -      -       +      -
     49Q  ARG*     3.9     3.9    +      -       -      -
    194Q  ILE*     5.1     7.2    -      -       +      -
    197Q  LEU*     3.6    39.0    -      -       +      -
    206Q  LEU*     3.7    18.4    -      -       +      -
    207Q  SER      3.8     2.5    -      -       -      +
    208Q  ALA      3.2    19.8    -      -       -      +
    210Q  LYS*     1.3    77.1    -      -       -      +
    212Q  GLU*     1.3    62.9    +      -       -      +
    213Q  ILE*     4.7    10.3    -      -       +      -
    233Q  VAL*     3.6    26.9    -      -       +      +
    237Q  ILE*     3.7    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 212 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45Q  LEU      3.8     1.4    -      -       -      +
     46Q  ALA*     3.6     0.3    -      -       -      -
     47Q  ALA*     3.1    36.7    +      -       +      +
     49Q  ARG*     3.2    41.6    +      -       +      +
     64Q  LYS*     3.3    38.1    +      -       -      +
     65Q  ILE*     5.1    13.4    -      -       +      +
    211Q  VAL*     1.3    75.7    -      -       -      +
    213Q  ILE*     1.3    64.1    +      -       -      +
    214Q  ALA      4.2     0.4    -      -       -      -
    227Q  VAL*     4.3    15.0    -      -       +      +
    233Q  VAL*     5.0     7.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 213 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44Q  LEU*     3.5    36.3    -      -       +      -
     45Q  LEU      3.5     6.3    -      -       -      +
     46Q  ALA*     4.2    13.2    -      -       +      -
    190Q  LEU*     4.4     6.3    -      -       +      -
    193Q  ALA*     5.3     0.4    -      -       +      -
    194Q  ILE*     4.0    27.1    -      -       +      -
    197Q  LEU*     5.1     0.2    -      -       +      -
    211Q  VAL*     4.7     8.5    -      -       +      -
    212Q  GLU*     1.3    85.1    -      -       -      +
    214Q  ALA*     1.3    60.2    +      -       -      +
    215Q  THR*     3.5    15.2    +      -       +      -
    227Q  VAL*     4.4     4.8    -      -       -      +
    228Q  LEU*     2.9    41.6    +      -       +      +
    233Q  VAL*     5.1     3.8    -      -       +      +
    236Q  LEU*     4.0    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 214 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44Q  LEU      3.8     1.0    -      -       -      -
     45Q  LEU*     3.0    34.1    +      -       +      +
     65Q  ILE*     3.7    39.0    -      -       +      +
    137Q  ILE*     3.8     8.2    -      -       +      +
    212Q  GLU      4.2     1.0    -      -       -      -
    213Q  ILE*     1.3    68.2    -      -       -      +
    215Q  THR*     1.4    62.7    +      -       -      +
    225Q  ILE*     4.3    15.7    -      -       +      -
    226Q  ARG      3.4     9.2    -      -       -      +
    227Q  VAL*     4.1     8.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 215 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43Q  VAL      3.9     4.7    -      -       -      -
     44Q  LEU*     4.4    14.1    -      -       +      +
    186Q  LEU*     4.8    13.7    -      -       +      -
    190Q  LEU*     4.6     8.7    -      -       +      -
    213Q  ILE*     3.5    24.1    +      -       +      -
    214Q  ALA*     1.4    70.7    -      -       -      +
    216Q  LEU*     1.3    59.8    +      -       -      +
    217Q  THR*     3.9    16.7    +      -       -      +
    225Q  ILE*     3.7     1.6    -      -       -      -
    226Q  ARG*     3.0    49.5    +      -       -      +
    228Q  LEU*     4.0    17.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 216 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42Q  GLY*     3.2     7.1    -      -       -      -
     43Q  VAL*     2.9    47.6    +      -       +      +
     70Q  GLU      4.5     1.6    -      -       -      +
     71Q  ASP      3.9     7.0    -      -       -      +
     72Q  MET*     4.8     0.7    -      -       -      +
    137Q  ILE*     3.9    15.3    -      -       +      +
    138Q  GLY*     3.2    47.6    -      -       -      +
    139Q  TRP*     3.9     2.0    -      -       +      +
    145Q  PHE*     3.6    10.8    -      -       +      -
    186Q  LEU*     4.9     0.9    -      -       -      +
    214Q  ALA      3.8     0.4    +      -       -      -
    215Q  THR*     1.3    70.3    -      -       -      +
    217Q  THR*     1.3    60.9    +      -       -      +
    223Q  THR*     3.7    17.0    -      -       +      -
    224Q  VAL      3.6    12.6    -      -       -      +
    225Q  ILE*     3.4    30.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 217 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41Q  ASP      4.7     3.8    -      -       -      +
    145Q  PHE*     4.0     2.7    -      -       -      -
    186Q  LEU*     4.1    21.5    -      -       +      -
    215Q  THR*     4.0    18.6    +      -       -      +
    216Q  LEU*     1.3    78.9    -      -       -      +
    218Q  ARG*     1.3    61.2    +      -       -      +
    219Q  GLU*     3.1     1.8    +      -       -      -
    223Q  THR*     3.3     5.7    -      -       -      +
    224Q  VAL      2.7    36.3    +      -       -      +
    226Q  ARG*     3.0    39.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 218 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41Q  ASP      4.3     4.8    +      -       -      +
    139Q  TRP*     2.9    57.3    -      -       -      +
    145Q  PHE*     3.6    17.4    -      -       +      -
    217Q  THR*     1.3    71.2    -      -       -      +
    219Q  GLU*     1.4    59.3    +      -       -      +
    220Q  ASN      3.1     7.3    +      -       -      -
    221Q  GLY*     4.6    20.1    +      -       -      +
    223Q  THR*     3.7    18.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 219 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217Q  THR*     3.1     5.2    +      -       -      -
    218Q  ARG*     1.4    67.5    -      -       -      +
    220Q  ASN*     1.3    85.4    +      -       +      +
    222Q  LYS*     2.6    36.3    +      -       -      +
    224Q  VAL*     3.6    30.0    -      -       +      +
    226Q  ARG*     3.1    33.0    +      -       -      +
----------------------------------------------------------
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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