Contacts of the strand formed by residues 193 - 199 (chain a) 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 LEU 193 (chain a).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24a  ALA*     4.1     7.2    -      -       +      -
     25a  SER      3.6    22.7    -      -       -      +
     26a  ASP*     4.3     1.1    -      -       +      +
     27a  THR*     5.6     0.4    -      -       -      -
    175a  VAL      4.7     1.1    -      -       -      +
    176a  LYS*     4.4    19.1    -      -       +      +
    179a  PHE*     3.3    50.5    -      -       +      -
    190a  GLY      5.4     0.2    -      -       -      -
    191a  ASP      4.0     1.5    +      -       -      +
    192a  ALA*     1.3    76.1    -      -       -      +
    194a  ARG*     1.4    62.7    -      -       -      +
    195a  ILE*     4.1    27.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 194 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23a  VAL      4.1     0.5    -      -       -      +
     24a  ALA*     3.1     4.3    -      -       -      +
     25a  SER*     3.0    38.6    +      -       -      +
     27a  THR*     4.9    15.4    -      -       +      +
     39a  ASP*     4.3    16.0    +      -       -      -
     40a  SER      5.6     0.2    -      -       -      -
     41a  PRO*     3.5    35.4    -      -       +      +
     43a  CYS*     3.7    29.1    +      -       -      -
    192a  ALA      4.1     0.4    -      -       -      -
    193a  LEU*     1.4    74.2    -      -       -      +
    195a  ILE*     1.4    60.9    +      -       -      +
    196a  CYS*     4.9     0.7    -      -       -      -
    205a  GLU*     3.2    36.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 195 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22a  ILE*     3.3    30.5    -      -       +      -
     23a  VAL      3.8     2.7    -      -       -      -
     24a  ALA*     3.9    11.9    -      -       +      -
    172a  MET*     4.7     6.5    -      -       +      -
    175a  VAL*     4.6     8.3    -      -       +      -
    176a  LYS*     3.8    39.9    -      -       +      -
    193a  LEU*     4.1    16.4    -      -       +      +
    194a  ARG*     1.4    78.2    -      -       -      +
    196a  CYS*     1.4    64.8    +      -       -      +
    197a  ILE*     3.9    18.3    -      -       +      +
    204a  ARG      4.1     0.6    -      -       -      +
    205a  GLU*     3.5    28.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 196 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21a  ALA      2.9    15.2    -      -       -      +
     23a  VAL*     3.0    25.7    +      -       -      +
     43a  CYS*     3.6    32.3    -      -       -      -
     45a  LYS*     5.8     4.0    -      -       -      -
     51a  VAL*     3.9    24.2    -      -       +      -
    194a  ARG*     4.8     0.7    -      -       -      -
    195a  ILE*     1.4    78.5    -      -       -      +
    197a  ILE*     1.4    61.9    +      -       -      +
    198a  VAL*     4.2     2.9    -      -       -      +
    203a  ILE*     4.4     9.2    -      -       +      -
    204a  ARG      3.6     5.2    -      -       -      -
    205a  GLU*     3.9    24.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 197 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20a  PHE*     3.1    37.2    -      -       +      -
     21a  ALA      3.6     3.6    -      -       -      -
     22a  ILE*     4.1    10.8    -      -       +      +
    168a  LEU*     5.0     0.4    -      -       +      -
    172a  MET*     3.8    30.7    -      -       +      -
    195a  ILE*     3.9    20.0    -      -       +      +
    196a  CYS*     1.4    73.2    -      -       -      +
    198a  VAL*     1.3    61.3    +      -       -      +
    199a  THR*     3.9     6.7    -      -       +      -
    203a  ILE*     3.6     3.8    -      -       -      +
    204a  ARG*     2.8    80.1    +      -       +      +
    205a  GLU      5.3     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 198 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19a  ASP      2.8    24.4    -      -       -      +
     20a  PHE*     3.0     6.4    -      -       -      -
     21a  ALA*     3.3    25.3    +      -       +      +
     23a  VAL*     5.9     0.4    -      -       +      -
     48a  ASP      4.9     0.4    -      -       -      +
     49a  LYS*     3.5    27.8    -      -       -      +
     51a  VAL*     3.8    17.9    -      -       +      -
    111a  GLY*     3.6    11.2    -      -       -      +
    112a  GLY      4.5     0.7    -      -       -      -
    113a  LEU*     3.4    36.6    -      -       +      +
    118a  LYS      6.0     0.2    -      -       -      +
    196a  CYS      4.2     0.7    -      -       -      +
    197a  ILE*     1.3    81.4    -      -       -      +
    199a  THR*     1.3    63.0    +      -       -      +
    202a  GLY      3.9     3.8    -      -       -      +
    203a  ILE*     4.3     3.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 199 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19a  ASP*     3.0    13.5    -      -       +      -
     20a  PHE*     4.2    11.4    -      -       +      +
     49a  LYS*     5.8     0.9    -      -       -      +
    113a  LEU*     3.1    12.2    -      -       -      +
    168a  LEU*     4.7     6.5    -      -       +      -
    197a  ILE*     3.9    18.2    -      -       +      -
    198a  VAL*     1.3    79.2    -      -       -      +
    200a  LYS*     1.4    62.0    +      -       -      +
    201a  GLU*     3.1    32.5    +      -       -      +
    202a  GLY*     3.0    26.2    +      -       -      +
    204a  ARG*     4.2    19.0    +      -       -      +
----------------------------------------------------------
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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