Contacts of the strand formed by residues 72 - 85 (chain C) in PDB entry 5JTM


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 THR 72 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  PRO*     5.9     7.3    -      -       +      +
     27C  ASN*     3.9    22.3    -      -       -      +
     31C  VAL*     4.2     0.7    -      -       -      +
     65C  THR*     4.9     5.8    -      -       +      -
     66C  ALA      3.7    12.1    -      -       -      +
     67C  SER*     4.1    12.4    +      -       -      +
     70C  GLU      3.3     7.8    +      -       -      -
     71C  GLU*     1.3    84.8    +      -       -      +
     73C  ALA*     1.3    64.7    -      -       -      +
     74C  PHE*     3.8    19.5    -      -       -      +
     75C  LEU*     4.8     3.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 73 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25C  ALA*     3.9     8.8    -      -       -      +
     26C  PRO*     6.4     0.2    -      -       -      -
     27C  ASN*     5.5     1.0    -      -       -      +
     31C  VAL*     3.7    15.9    -      -       +      +
     36C  TRP*     3.8    28.5    -      -       +      -
     66C  ALA*     2.8    27.2    +      -       +      +
     68C  LEU*     4.0    16.4    -      -       +      -
     71C  GLU*     3.6     4.2    +      -       -      +
     72C  THR*     1.3    75.1    -      -       -      +
     74C  PHE*     1.3    61.6    +      -       +      +
    123C  PHE*     3.2    21.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 74 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  PHE*     3.7    24.9    -      +       +      -
     24C  GLU      3.3    14.1    -      -       -      +
     25C  ALA*     4.5     0.4    -      -       +      +
     26C  PRO*     6.0     0.2    -      -       -      -
     36C  TRP*     3.5    24.0    -      +       -      -
     64C  VAL*     4.2    21.3    -      -       +      -
     65C  THR*     3.8     1.9    -      -       -      +
     66C  ALA*     3.0    39.9    +      -       +      +
     72C  THR*     3.6    12.8    -      -       -      +
     73C  ALA*     1.3    81.0    -      -       -      +
     75C  LEU*     1.3    69.8    +      -       -      +
     76C  CYS*     4.4     2.0    -      -       +      -
    118C  VAL*     3.7    24.7    -      -       +      -
    123C  PHE*     3.6    35.2    -      +       +      -
    126C  LEU*     3.7    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 75 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  SER*     5.7     2.2    -      -       -      +
     23C  PHE*     3.4     6.8    -      -       -      -
     24C  GLU*     2.9    60.1    +      -       +      +
     63C  THR*     4.0    19.7    -      -       +      -
     64C  VAL      3.6     9.9    -      -       -      +
     65C  THR*     3.3    33.4    -      -       +      +
     72C  THR*     5.5     3.6    -      -       +      -
     74C  PHE*     1.3    75.1    -      -       -      +
     76C  CYS*     1.3    83.5    -      -       -      +
     77C  GLU*     4.3     7.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 76 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  SER      3.3    17.9    -      -       -      -
     23C  PHE*     3.8    11.0    -      -       +      +
     62C  VAL      4.0     0.6    -      -       -      +
     63C  THR*     3.3     4.7    -      -       -      +
     64C  VAL*     2.8    38.7    +      -       +      +
     74C  PHE*     4.5     5.2    -      -       +      -
     75C  LEU*     1.3    79.3    -      -       -      +
     77C  GLU*     1.3    59.7    +      -       -      +
     78C  VAL*     4.4     3.4    -      -       -      -
    114C  ILE*     3.6    49.1    -      -       +      -
    117C  MET*     3.9    16.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 77 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20C  ASP*     3.7    10.8    -      -       -      +
     21C  ILE*     3.4     2.9    -      -       -      -
     22C  SER*     2.8    44.5    +      -       -      -
     61C  ARG*     3.0    45.2    +      -       +      -
     62C  VAL      3.5     3.8    -      -       -      +
     63C  THR*     3.1    32.2    +      -       +      +
     75C  LEU*     4.3     7.6    -      -       +      +
     76C  CYS*     1.3    74.3    -      -       -      +
     78C  VAL*     1.3    61.2    +      -       -      +
     79C  GLN*     3.1    17.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 78 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18C  THR*     4.5     1.6    -      -       +      -
     20C  ASP      3.4    11.2    -      -       -      +
     21C  ILE*     4.3    10.3    -      -       +      -
     60C  LEU      3.7     1.0    -      -       -      +
     62C  VAL*     3.0    34.3    +      -       -      +
     76C  CYS*     4.4     4.5    -      -       -      -
     77C  GLU*     1.3    76.6    -      -       -      +
     79C  GLN*     1.3    63.7    +      -       -      +
     80C  GLN*     3.7    17.5    +      -       -      +
    110C  ALA*     4.2    14.3    -      -       -      +
    113C  CYS*     3.6    43.3    -      -       +      +
    114C  ILE*     3.6    30.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 79 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  LYS*     3.2    28.0    +      -       +      +
     20C  ASP*     2.9    50.2    +      -       +      +
     47C  ALA*     5.3     5.4    -      -       -      +
     59C  VAL*     4.0    17.8    -      -       +      +
     60C  LEU      3.7     5.6    -      -       -      -
     61C  ARG*     3.1    54.1    +      -       +      +
     77C  GLU*     3.1    14.5    +      -       -      +
     78C  VAL*     1.3    70.2    -      -       -      +
     80C  GLN*     1.3    62.1    +      -       -      +
     81C  GLY      3.4     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 80 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  ILE*     3.2    19.1    -      -       -      +
     17C  TYR*     3.0    25.5    +      -       -      +
     18C  THR*     3.3    28.3    -      -       -      +
     59C  VAL*     3.4     3.2    -      -       -      -
     60C  LEU*     3.1    33.1    +      -       +      +
     78C  VAL*     3.7     3.8    +      -       +      +
     79C  GLN*     1.3    68.9    -      -       -      +
     81C  GLY*     1.3    57.8    +      -       -      +
    106C  LEU*     3.5    42.6    -      -       +      +
    109C  TYR*     3.4    22.8    +      -       +      +
    110C  ALA*     3.7    26.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 81 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  ILE*     3.8     0.9    -      -       -      -
     17C  TYR*     2.8    47.4    +      -       -      +
     19C  LYS*     3.7    20.5    -      -       -      +
     57C  GLU*     5.0     0.2    -      -       -      -
     58C  VAL      3.6     4.3    -      -       -      -
     59C  VAL*     4.1     8.1    -      -       -      -
     79C  GLN      3.4     5.3    +      -       -      -
     80C  GLN*     1.3    78.4    -      -       -      +
     82C  GLY*     1.3    57.5    +      -       -      -
    106C  LEU*     4.0     3.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 82 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15C  ARG      3.5     8.7    -      -       -      -
     16C  ILE*     4.3     1.1    -      -       -      -
     17C  TYR*     4.6     0.2    -      -       -      -
     57C  GLU*     4.6     2.6    -      -       -      +
     58C  VAL      2.9    35.7    +      -       -      +
     81C  GLY*     1.3    74.8    -      -       -      -
     83C  ILE*     1.3    65.5    +      -       -      -
     84C  PHE*     3.2    16.1    -      -       -      -
    106C  LEU*     3.7    17.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 83 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13C  ILE*     3.9     0.5    -      -       -      +
     14C  GLN*     3.0    42.4    +      -       +      -
     15C  ARG*     2.9    22.9    +      -       +      +
     17C  TYR*     3.4    32.1    -      -       +      +
     51C  LEU*     3.6    36.1    -      -       +      -
     55C  VAL*     3.7    20.0    -      -       +      -
     56C  TYR      3.9     5.4    -      -       -      +
     57C  GLU*     3.7    17.3    -      -       +      -
     82C  GLY*     1.3    71.2    -      -       -      -
     84C  PHE*     1.3    66.9    +      -       -      +
     29D  PRO*     3.7     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 84 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11C  PHE*     3.5    32.5    -      +       +      -
     12C  GLN      3.8     3.8    -      -       -      -
     13C  ILE*     3.6    30.5    -      -       +      -
     14C  GLN*     4.2     4.6    -      -       -      +
     16C  ILE*     4.6     0.7    -      -       +      -
     55C  VAL*     3.9     2.6    -      -       -      +
     56C  TYR      3.1    27.8    +      -       -      +
     58C  VAL*     3.7    26.2    -      -       +      -
     82C  GLY*     3.2    27.4    -      -       -      -
     83C  ILE*     1.3    77.2    -      -       -      +
     85C  SER*     1.3    60.5    +      -       -      +
     86C  ILE*     3.3    20.2    -      -       +      +
    102C  CYS*     3.4    32.3    -      -       +      -
    105C  ILE*     4.0    12.3    -      -       +      -
    106C  LEU*     3.6    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 85 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9C  MET*     3.6     1.7    -      -       -      +
     10C  THR*     3.1    20.9    -      -       -      +
     11C  PHE*     3.2    20.0    -      -       -      -
     12C  GLN*     3.0    25.1    +      -       -      +
     14C  GLN*     2.8    34.1    +      -       -      -
     54C  ASP*     3.4     9.2    -      -       -      -
     55C  VAL*     5.0     4.0    -      -       -      +
     84C  PHE*     1.3    71.0    -      -       -      +
     86C  ILE*     1.3    60.0    +      -       -      +
----------------------------------------------------------
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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