Contacts of the strand formed by residues 192 - 199 (chain t) in PDB entry 5GJQ


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 192 (chain t).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26t  ASP*     3.2     5.5    -      -       -      -
     27t  THR*     3.1    42.0    +      -       +      +
     38t  ARG      4.8     2.0    -      -       -      +
    190t  GLY      2.8     8.5    +      -       -      +
    191t  ASP*     1.3    78.3    -      -       +      +
    193t  LEU*     1.3    62.6    +      -       -      +
    207t  THR*     4.6    10.1    -      -       +      -
    208t  VAL      3.5    11.9    -      -       -      +
    209t  SER*     5.0     1.1    -      -       -      -
    210t  LEU*     3.5     9.4    -      -       -      +
    212t  LYS*     4.9     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 193 (chain t). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24t  ALA*     4.0     6.5    -      -       +      -
     25t  SER      3.4    18.8    -      -       -      +
     26t  ASP*     4.3     0.2    -      -       -      +
     27t  THR*     4.6     0.7    -      -       -      -
    175t  VAL      4.7     0.2    -      -       -      +
    176t  LYS*     4.4    16.4    -      -       -      +
    179t  PHE*     3.6    51.8    -      -       +      -
    192t  ALA*     1.3    78.3    -      -       -      +
    194t  ARG*     1.3    68.8    +      -       -      +
    195t  ILE*     4.1    10.8    -      -       +      -
    206t  GLU      3.8     0.7    -      -       -      +
    207t  THR*     3.3     6.3    -      -       -      +
    208t  VAL*     2.9    49.9    +      -       +      +
    210t  LEU*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 194 (chain t). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23t  VAL      4.1     0.7    -      -       -      +
     24t  ALA*     3.1     3.1    -      -       -      +
     25t  SER*     2.8    43.8    +      -       -      +
     27t  THR*     4.4    12.6    -      -       +      +
     39t  ASP*     4.8     9.6    +      -       -      -
     41t  PRO*     3.9    32.7    -      -       +      +
     43t  CYS*     4.4     5.9    -      -       -      -
    193t  LEU*     1.3    75.4    -      -       -      +
    195t  ILE*     1.3    65.0    +      -       -      +
    196t  CYS*     4.7     5.6    -      -       -      -
    205t  GLU*     4.0    40.1    +      -       +      -
    206t  GLU      3.4     4.0    -      -       -      +
    207t  THR*     3.4    30.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 195 (chain t). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22t  ILE*     3.7    27.4    -      -       +      -
     23t  VAL      3.9     2.0    -      -       -      -
     24t  ALA*     4.0    12.8    -      -       +      +
    172t  MET*     3.8    38.1    -      -       +      +
    175t  VAL*     3.9    11.9    -      -       +      -
    176t  LYS*     3.9    30.3    -      -       +      -
    193t  LEU*     4.1    11.0    -      -       +      -
    194t  ARG*     1.3    78.1    -      -       -      +
    196t  CYS*     1.3    68.3    +      -       -      +
    197t  ILE*     4.1     1.6    +      -       +      +
    204t  ARG      3.7     0.2    -      -       -      +
    205t  GLU*     3.3     6.8    -      -       -      +
    206t  GLU*     2.8    38.5    +      -       +      +
    208t  VAL*     4.3     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 196 (chain t). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21t  ALA      3.5     1.4    -      -       -      +
     22t  ILE*     3.3     6.8    -      -       -      +
     23t  VAL*     2.9    46.1    +      -       +      +
     43t  CYS*     3.8    27.6    -      -       -      -
     51t  VAL*     4.2    18.6    -      -       +      -
    194t  ARG*     4.7     2.9    -      -       -      -
    195t  ILE*     1.3    76.3    -      -       -      +
    197t  ILE*     1.3    62.5    +      -       -      +
    198t  VAL*     4.9     0.6    -      -       -      +
    203t  ILE*     4.3    13.2    -      -       +      -
    204t  ARG      3.3     6.3    -      -       -      +
    205t  GLU*     4.0    24.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 197 (chain t). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20t  PHE*     4.6     2.2    -      -       +      -
     21t  ALA      3.6     5.2    -      -       -      +
     22t  ILE*     4.7     3.4    -      -       +      -
    168t  LEU*     3.9    34.3    -      -       +      -
    172t  MET*     3.7    38.1    -      -       +      -
    195t  ILE*     4.3     8.1    -      -       +      +
    196t  CYS*     1.3    77.0    -      -       -      +
    198t  VAL*     1.3    63.8    +      -       -      +
    199t  THR*     4.1    15.6    +      -       +      +
    202t  GLY      3.5     1.2    -      -       -      +
    203t  ILE*     3.2     7.6    -      -       -      +
    204t  ARG*     2.9    70.1    +      -       +      +
    206t  GLU*     4.5     8.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 198 (chain t). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20t  PHE*     3.1     9.2    -      -       -      -
     21t  ALA*     2.8    42.4    +      -       +      +
     23t  VAL*     5.5     1.8    -      -       +      -
     48t  ASP      5.3     0.4    -      -       -      +
     49t  LYS*     3.8    21.8    -      -       -      +
     51t  VAL*     3.6    32.8    -      -       +      +
    111t  GLY      4.7     4.5    -      -       -      +
    112t  GLY*     4.1     6.3    -      -       -      -
    113t  LEU*     3.7    27.1    -      -       +      +
    196t  CYS      4.9     2.7    -      -       -      +
    197t  ILE*     1.3    77.5    -      -       -      +
    199t  THR*     1.3    63.3    +      -       -      +
    202t  GLY      3.6     3.8    -      -       -      +
    203t  ILE*     4.2     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 199 (chain t). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19t  ASP*     3.6    23.3    -      -       -      +
     20t  PHE*     3.6    13.5    -      -       +      -
     48t  ASP      4.9     2.3    -      -       -      +
     49t  LYS*     5.6     1.2    -      -       -      +
    113t  LEU*     3.6    13.7    -      -       -      +
    168t  LEU*     5.1     7.2    -      -       +      -
    197t  ILE*     4.4    11.4    +      -       +      +
    198t  VAL*     1.3    80.7    -      -       -      +
    200t  LYS*     1.3    69.8    +      -       -      +
    201t  GLU*     3.1    23.7    +      -       -      +
    202t  GLY*     3.0    24.4    +      -       -      +
----------------------------------------------------------
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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