Contacts of the strand formed by residues 13 - 24 (chain B) 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 ILE 13 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  PHE*     4.1     5.4    -      -       +      -
     12B  GLN*     1.3    76.3    -      -       +      +
     14B  GLN*     1.3    68.6    +      -       -      +
     15B  ARG      4.3     5.2    -      -       -      +
     16B  ILE*     3.7    30.1    -      -       +      -
     84B  PHE*     3.8    22.2    -      -       +      -
    105B  ILE*     4.6     8.7    -      -       +      -
    111D  ARG*     5.4     0.2    -      -       -      -
    127D  ASN*     3.8    18.4    -      -       +      -
    128D  LEU      4.3    12.8    -      -       -      +
    129D  ALA*     3.7    33.2    -      -       +      +
    130D  PRO*     4.0    10.3    -      -       +      +
    306E  VAL*     3.4    26.8    +      -       +      +
    307E  THR*     4.7     2.0    +      -       -      +
    308E  CYS      5.8     1.1    +      -       -      +
    309E  THR*     5.4     1.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  GLN*     3.2    28.2    -      -       -      +
     13B  ILE*     1.3    76.0    -      -       -      +
     15B  ARG*     1.3    62.8    +      -       -      +
     55B  VAL*     4.9     7.5    -      -       +      +
     83B  ILE*     3.0    25.9    +      -       +      +
     84B  PHE      4.1     1.6    -      -       -      -
     85B  SER*     3.2    41.7    +      -       -      +
    303E  LYS      4.0     1.7    -      -       -      +
    304E  PRO      3.2    26.4    +      -       -      +
    305E  ALA*     3.0    37.4    +      -       -      +
    306E  VAL*     3.2    18.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  PHE*     3.2    44.0    -      -       -      +
    122A  THR*     2.9    36.9    +      -       +      +
     13B  ILE*     3.9     1.7    -      -       -      +
     14B  GLN*     1.3    79.7    -      -       -      +
     16B  ILE*     1.3    73.2    +      -       -      +
     17B  TYR*     3.6    21.4    -      -       +      -
     82B  GLY*     3.1     4.8    -      -       -      -
     83B  ILE*     2.9    50.5    +      -       +      +
     84B  PHE*     4.6     2.3    -      -       -      -
    127D  ASN*     3.7     7.0    -      -       -      +
    301E  ILE*     4.7     0.2    -      -       -      +
    302E  ASP*     2.8    30.5    +      -       -      +
    303E  LYS*     3.0    30.8    +      -       -      +
    304E  PRO*     3.8     8.5    -      -       +      -
    306E  VAL*     4.2     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  THR*     3.1     3.3    +      -       -      -
     13B  ILE*     3.7    20.0    -      -       +      -
     15B  ARG*     1.3    80.2    -      -       -      +
     17B  TYR*     1.3    62.1    +      -       -      +
     80B  GLN*     3.5    17.3    -      -       +      +
     81B  GLY      3.6     5.4    -      -       -      -
     84B  PHE*     4.9     0.9    -      -       +      -
    105B  ILE*     3.5    30.5    -      -       +      -
    106B  LEU*     3.8    23.3    -      -       +      -
    109B  TYR*     3.6    46.0    -      -       +      +
    111D  ARG*     4.9     0.4    -      -       -      +
    125D  GLN*     2.7    28.7    +      -       -      +
    127D  ASN*     2.9    18.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  ALA*     3.5    31.4    -      -       +      -
     29A  PRO*     3.2    26.0    -      -       +      +
     32A  PHE*     3.9     7.9    -      +       -      -
    120A  ARG      3.9     1.8    -      -       -      -
    121A  GLY      3.5    10.5    -      -       -      +
    122A  THR*     3.3    19.5    -      -       -      +
     15B  ARG*     3.6    19.1    -      -       +      +
     16B  ILE*     1.3    81.8    -      -       -      +
     18B  THR*     1.3    65.4    +      -       -      +
     19B  LYS*     3.5    17.2    +      -       +      -
     57B  GLU*     3.1    25.4    +      -       -      +
     80B  GLN*     3.2     8.6    -      -       -      +
     81B  GLY      2.9    45.9    +      -       -      +
     83B  ILE*     3.5    26.1    -      -       +      +
    125D  GLN*     4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     3.3    17.8    -      -       +      -
     25A  ALA*     4.3     3.1    -      -       -      +
    117A  MET*     6.2     0.2    -      -       -      -
    120A  ARG*     3.0    37.0    +      -       +      +
    121A  GLY*     3.3    16.4    -      -       -      -
     17B  TYR*     1.3    73.7    -      -       -      +
     19B  LYS*     1.3    61.0    +      -       -      +
     20B  ASP      3.9     5.2    -      -       -      +
     21B  ILE*     3.4    40.8    -      -       +      -
     78B  VAL*     4.6     0.4    -      -       +      -
     79B  GLN      3.9     5.4    -      -       -      +
     80B  GLN*     3.0    22.1    +      -       -      +
    113B  CYS*     4.1     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     4.4     2.9    -      -       -      -
     25A  ALA*     2.8    46.4    +      -       -      +
     26A  PRO      5.4     3.0    +      -       -      -
     28A  ALA*     4.3     3.4    -      -       +      -
     29A  PRO*     3.5    30.1    -      -       -      +
     17B  TYR*     3.5    20.2    -      -       +      -
     18B  THR*     1.3    73.9    -      -       -      +
     20B  ASP*     1.3    61.8    +      -       +      +
     49B  SER*     5.2     1.0    +      -       -      -
     57B  GLU*     2.8    40.2    +      -       -      +
     59B  VAL*     3.7    15.0    -      -       +      +
     79B  GLN*     3.0    17.2    +      -       +      +
     81B  GLY*     3.7    19.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     3.1    13.9    -      -       -      +
     24A  GLU*     3.7    18.8    -      -       -      +
     18B  THR*     3.6     2.8    -      -       -      +
     19B  LYS*     1.3    81.7    -      -       -      +
     21B  ILE*     1.3    81.8    +      -       -      +
     22B  SER*     4.6     4.2    +      -       -      -
     77B  GLU*     3.9    19.8    -      -       -      +
     78B  VAL*     3.5     0.2    -      -       -      -
     79B  GLN*     2.9    56.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  ILE*     3.8    22.7    -      -       +      -
     22A  SER*     3.5     5.9    +      -       -      -
     23A  PHE*     2.8    45.9    +      -       +      +
     24A  GLU*     5.6     0.3    -      -       -      +
    117A  MET*     4.6     2.9    -      -       +      -
     18B  THR*     3.4    19.7    -      -       +      -
     20B  ASP*     1.3    87.0    -      -       -      +
     22B  SER*     1.3    69.2    +      -       -      +
     77B  GLU      3.4     4.9    -      -       -      +
     78B  VAL*     3.5    17.9    -      -       +      -
    113B  CYS*     3.1    33.4    -      -       -      -
    117B  MET*     3.8    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ASP*     5.5     0.2    +      -       -      -
     21A  ILE      3.5     8.3    +      -       -      -
     22A  SER*     5.6     0.8    -      -       -      -
     20B  ASP*     4.9     4.9    -      -       -      -
     21B  ILE*     1.3    78.7    -      -       -      +
     23B  PHE*     1.3    61.4    +      -       -      +
     24B  GLU*     3.0    29.2    +      -       -      +
     76B  CYS*     3.3     4.9    -      -       -      -
     77B  GLU*     2.9    47.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  THR*     4.0    21.3    -      -       -      -
     20A  ASP*     3.2     5.4    -      -       -      +
     21A  ILE*     2.8    45.3    +      -       +      +
     22B  SER*     1.3    74.4    +      -       -      +
     24B  GLU*     1.3    60.9    +      -       -      +
     25B  ALA*     4.5    10.5    -      -       +      -
     74B  PHE*     3.8    33.4    -      +       +      -
     75B  LEU      3.1    21.8    -      -       -      -
     76B  CYS*     3.8    11.4    -      -       +      -
    117B  MET*     3.4    45.5    -      -       +      -
    118B  VAL*     3.8    15.5    -      -       +      -
    121B  GLY*     3.6    25.6    -      -       -      -
    123B  PHE*     4.6     3.1    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLU 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  LYS      3.8     4.0    -      -       -      +
     20A  ASP*     3.8    16.6    -      -       +      +
     22B  SER*     3.0    28.1    +      -       -      +
     23B  PHE*     1.3    81.6    +      -       -      +
     25B  ALA*     1.3    60.4    +      -       -      +
     26B  PRO*     3.6     8.8    -      -       +      +
     74B  PHE*     3.9     0.7    -      -       -      +
     75B  LEU*     2.9    65.6    +      -       +      +
     76B  CYS*     4.3     1.4    +      -       -      -
     77B  GLU*     5.9     0.2    -      -       -      +
----------------------------------------------------------
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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