Contacts of the strand formed by residues 119 - 126 (chain b) 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 GLU 119 (chain b).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15b  LYS*     4.7     3.5    +      -       -      -
     86b  ARG*     3.2    37.4    +      -       -      +
    115b  TYR*     3.3     4.4    -      -       -      -
    116b  ALA*     2.7    45.1    +      -       -      +
    117b  ASP      4.4     3.1    -      -       -      +
    118b  GLY*     1.3    80.7    -      -       -      +
    120b  SER*     1.3    76.3    +      -       -      +
    121b  PHE*     3.2    22.1    +      -       -      +
    133b  GLU*     5.0     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 120 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15b  LYS*     3.0    44.6    +      -       -      +
     16b  PHE      3.9     5.0    +      -       -      -
     17b  GLU*     5.5     0.2    -      -       -      -
     18b  GLY      4.5     1.6    +      -       -      -
     19b  GLY      3.3    18.0    +      -       -      -
     20b  VAL*     3.6    18.4    -      -       -      +
    114b  GLY      3.8     5.4    -      -       -      -
    115b  TYR*     3.6    16.3    -      -       -      -
    119b  GLU*     1.3    76.5    +      -       -      +
    121b  PHE*     1.4    60.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 121 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85b  PRO*     3.5    36.1    -      -       +      -
     86b  ARG*     3.1    52.5    -      -       +      +
     89b  HIS*     3.7    29.6    -      +       +      -
    112b  ILE      3.3     3.6    -      -       -      +
    114b  GLY      3.0    31.7    +      -       -      -
    119b  GLU*     3.2    15.7    +      -       -      +
    120b  SER*     1.4    72.3    -      -       -      +
    122b  LEU*     1.4    60.6    +      -       -      +
    123b  GLY*     3.5    33.0    -      -       -      -
    133b  GLU*     3.5    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 122 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13b  GLY*     3.7    12.3    -      -       -      +
     14b  VAL*     3.5    32.8    -      -       -      +
     15b  LYS*     3.8    13.5    -      -       +      -
     20b  VAL*     3.4    38.4    -      -       +      -
    111b  VAL*     4.2    10.3    -      -       +      -
    112b  ILE      3.5     3.1    -      -       -      -
    113b  GLY*     4.0     5.8    -      -       -      -
    120b  SER      3.6    10.6    +      -       -      +
    121b  PHE*     1.4    87.6    -      -       -      +
    123b  GLY*     1.3    65.5    +      -       -      +
    133b  GLU*     4.1     5.7    -      -       -      +
    134b  ALA      2.9    38.5    +      -       -      +
    135b  PRO*     3.9     5.2    -      -       +      +
    137b  LEU*     3.1     7.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 123 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89b  HIS*     3.5    18.2    -      -       -      -
    111b  VAL*     3.4     1.4    -      -       -      -
    112b  ILE*     3.0    35.0    +      -       -      -
    121b  PHE*     3.5    17.6    -      -       -      -
    122b  LEU*     1.3    78.0    -      -       -      +
    124b  TYR*     1.3    57.2    +      -       -      -
    132b  TYR      3.6     6.7    -      -       -      -
    133b  GLU*     4.1     0.2    -      -       -      -
    137b  LEU*     3.2     9.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 124 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31a  GLU*     5.2     4.3    -      -       -      +
     36a  HIS*     4.0    23.7    +      +       -      -
     89b  HIS*     3.0    12.8    -      -       -      -
    109b  THR*     3.3    34.3    -      -       +      +
    110b  MET      3.5     7.4    -      -       -      -
    111b  VAL*     4.5     1.6    -      -       +      +
    123b  GLY*     1.3    72.0    -      -       -      -
    125b  VAL*     1.3    60.9    +      -       -      +
    126b  ASP*     3.6    33.1    +      -       +      +
    130b  VAL*     4.3     5.2    -      -       +      -
    131b  ALA*     3.5     1.6    -      -       -      -
    132b  TYR*     2.9    54.8    +      +       +      +
    137b  LEU*     3.5    29.6    -      -       +      -
    138b  ALA      5.4     1.6    -      -       -      -
    139b  THR*     4.1    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 125 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89b  HIS*     3.0    37.5    -      -       +      +
     92b  LEU*     3.9    17.3    -      -       +      +
     93b  THR*     3.7    24.5    -      -       -      +
     96b  MET*     3.4    30.7    -      -       +      +
    108b  ASN      4.2     1.0    -      -       -      +
    109b  THR*     3.4     3.5    -      -       -      -
    110b  MET*     3.0    31.0    +      -       -      +
    112b  ILE*     3.7    13.7    -      -       +      -
    124b  TYR*     1.3    73.0    -      -       -      +
    126b  ASP*     1.3    64.2    +      -       -      +
    129b  GLY      4.7     2.0    -      -       -      +
    130b  VAL      3.7     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 126 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31a  GLU*     4.8    13.9    -      -       -      +
     96b  MET*     3.7     3.6    -      -       -      +
    108b  ASN      4.1     0.2    -      -       -      -
    109b  THR*     4.2     4.8    +      -       -      -
    124b  TYR*     3.6    30.9    +      -       +      +
    125b  VAL*     1.3    80.6    -      -       -      +
    127b  MET*     1.3    74.4    +      -       -      +
    128b  LEU*     3.1    33.7    +      -       -      +
    129b  GLY*     3.0    19.9    +      -       -      -
    130b  VAL*     3.0    39.4    +      -       +      +
----------------------------------------------------------
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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