Contacts of the strand formed by residues 39 - 52 (chain C) in PDB entry 5JTO


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 39 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37C  GLN      4.2     0.2    +      -       -      -
     38C  PRO*     1.3    68.0    -      -       -      +
     40C  VAL*     1.3    70.3    +      -       -      +
     41C  LYS*     3.5    31.8    +      -       +      +
     65C  THR      3.9     0.2    -      -       -      +
     67C  SER*     3.0    33.3    +      -       -      +
     68C  LEU*     3.8     6.0    -      -       -      +
     69C  GLY      4.8     3.1    -      -       -      +
    290F  TRP*     6.1     0.5    -      -       -      +
    293F  PRO*     4.2    14.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 40 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  PRO*     3.2    16.8    +      -       +      -
     39C  GLU*     1.3    79.2    +      -       -      +
     41C  LYS*     1.3    59.8    +      -       -      +
     64C  VAL*     3.6    19.1    -      -       +      -
     65C  THR      3.2    15.5    -      -       -      +
     66C  ALA*     3.9    19.5    -      -       +      +
     74C  PHE*     5.7     0.7    -      -       +      -
    126C  LEU*     4.0    11.2    -      -       +      -
    290F  TRP*     3.0    48.6    -      -       +      +
    293F  PRO*     3.7    28.8    -      -       +      +
    296F  THR*     5.9     3.1    -      -       +      -
    297F  TYR*     5.8     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 41 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39C  GLU*     3.8    29.8    -      -       +      +
     40C  VAL*     1.3    77.3    -      -       -      +
     42C  LEU*     1.3    62.7    +      -       -      +
     43C  ASP*     3.8     3.5    +      -       +      +
     63C  THR      3.8     1.0    -      -       -      +
     64C  VAL*     3.9     1.2    -      -       -      -
     65C  THR*     2.8    45.2    +      -       +      +
     67C  SER*     5.6     3.8    -      -       -      -
     69C  GLY      5.7     3.1    +      -       -      -
    290F  TRP*     3.6     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 42 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  LYS*     1.3    72.6    -      -       -      +
     43C  ASP*     1.3    58.4    +      -       -      +
     44C  LEU*     3.7    12.6    +      -       +      +
     62C  VAL*     4.1    14.6    -      -       +      -
     63C  THR      3.7     4.5    -      -       -      +
     64C  VAL*     3.8    22.0    -      -       +      -
    128C  LEU*     3.8    38.6    -      -       +      -
    288F  VAL*     3.7    42.8    +      -       +      +
    289F  ARG      5.1     2.2    -      -       -      +
    290F  TRP*     3.2    41.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 43 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  LYS*     3.8     5.3    +      -       +      +
     42C  LEU*     1.3    72.1    -      -       -      +
     44C  LEU*     1.3    63.1    +      -       -      +
     61C  ARG*     2.8    34.2    +      -       -      -
     62C  VAL      3.9     0.2    -      -       -      -
     63C  THR*     2.9    49.1    +      -       +      +
     65C  THR*     5.0     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 44 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42C  LEU*     3.7    37.0    -      -       +      +
     43C  ASP*     1.3    82.2    +      -       -      +
     45C  ASP*     1.3    62.4    +      -       -      +
     46C  THR*     5.5     3.4    -      -       +      -
     60C  LEU*     4.2    23.1    -      -       +      -
     61C  ARG*     3.3    12.7    +      -       -      +
     62C  VAL*     4.0    17.9    -      -       +      -
    107C  PHE*     6.2     4.5    -      -       +      -
    133C  PHE*     5.0     8.1    -      -       +      -
    285F  ASN*     4.6    10.7    +      -       -      +
    286F  MET      5.1     7.4    -      -       -      +
    287F  PRO*     6.3     0.7    -      -       +      -
    288F  VAL*     3.8    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 45 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  LEU*     1.3    76.6    -      -       -      +
     46C  THR*     1.3    71.7    +      -       -      +
     47C  ALA*     4.4     5.7    +      -       -      +
     59C  VAL*     4.3     0.5    -      -       -      +
     61C  ARG*     3.0    60.9    +      -       +      +
    285F  ASN*     3.0    23.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 46 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  LEU*     5.5     4.0    -      -       +      -
     45C  ASP*     1.3    81.4    -      -       -      +
     47C  ALA*     1.3    59.7    +      -       -      +
     59C  VAL      3.6     8.1    -      -       -      +
     60C  LEU*     3.7    28.7    -      -       +      -
    281F  PHE*     3.3    53.1    -      -       +      +
    282F  ALA*     4.6     1.4    +      -       -      -
    285F  ASN*     2.8    45.1    +      -       +      +
    286F  MET*     4.6     4.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 47 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45C  ASP*     4.4     7.7    +      -       -      +
     46C  THR*     1.3    74.6    -      -       -      +
     48C  SER*     1.3    68.8    +      -       -      +
     58C  VAL*     3.9     0.7    -      -       -      -
     59C  VAL*     3.0    47.6    +      -       +      +
    281F  PHE*     4.2     4.4    -      -       -      -
    282F  ALA      6.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 48 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47C  ALA*     1.3    81.0    +      -       -      +
     49C  SER*     1.3    62.5    +      -       -      +
     56C  TYR*     4.7     5.4    -      -       -      -
     57C  GLU      3.3    11.9    +      -       -      -
     58C  VAL*     4.5     6.5    -      -       -      +
     59C  VAL*     5.4     1.1    -      -       -      -
     98C  LEU*     4.8     0.3    -      -       -      +
    278F  LEU*     3.8    38.1    -      -       -      +
    281F  PHE*     3.4    23.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 49 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  SER*     1.3    76.9    -      -       -      +
     50C  GLN*     1.3    65.2    +      -       -      +
     51C  LEU*     3.5     7.8    +      -       -      +
     56C  TYR*     4.2     5.1    -      -       -      -
     57C  GLU*     2.9    58.1    +      -       -      +
     59C  VAL*     5.2     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 50 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  SER*     1.3    72.6    -      -       -      +
     51C  LEU*     1.3    63.0    +      -       -      +
     52C  ALA      3.1    34.4    +      -       -      +
     53C  ASP*     3.9    11.9    +      -       -      +
     54C  ASP      4.4     1.2    -      -       -      +
     55C  VAL      3.5     7.2    -      -       -      +
     56C  TYR*     3.7    39.6    +      -       +      +
    277F  LEU*     4.6     7.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 51 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  SER*     4.0    19.3    -      -       -      +
     50C  GLN*     1.3    79.3    -      -       -      +
     52C  ALA*     1.3    64.0    +      -       +      +
     55C  VAL*     3.1    15.2    +      -       +      -
     57C  GLU*     3.8     8.3    -      -       +      +
     83C  ILE*     3.5    47.1    -      -       +      -
     29D  PRO*     3.8    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 52 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50C  GLN*     3.1    20.1    +      -       -      +
     51C  LEU*     1.3    80.0    -      -       -      +
     53C  ASP*     1.3    67.5    +      -       -      +
     54C  ASP      3.3     0.2    +      -       -      -
     55C  VAL*     3.0    36.0    +      -       +      +
----------------------------------------------------------
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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