Contacts of the strand formed by residues 116 - 128 (chain C) in PDB entry 5IPN


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 ASP 116 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102C  LEU      3.4     4.7    -      -       -      +
    104C  ILE*     2.9    54.5    +      -       +      +
    115C  LYS*     1.3   104.9    -      -       -      +
    117C  ILE*     1.3    62.4    +      -       -      +
    118C  LYS*     4.2     5.2    -      -       +      -
    484C  LEU*     4.4    13.0    -      -       -      +
    485C  ASP*     5.3     8.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 117 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101C  ARG*     3.5    36.6    -      -       +      -
    102C  LEU      3.3     2.0    -      -       -      -
    103C  VAL*     4.0    20.6    -      -       +      -
    113C  THR*     3.7    22.4    -      -       +      +
    114C  VAL*     5.0     8.1    -      -       +      -
    115C  LYS      4.3     0.6    -      -       -      +
    116C  ASP*     1.3    78.4    -      -       -      +
    118C  LYS*     1.3    61.8    +      -       -      +
    119C  GLU*     4.1     3.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 118 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100C  LEU      3.9     1.0    -      -       -      +
    101C  ARG*     3.5     1.2    -      -       -      -
    102C  LEU*     2.7    54.8    +      -       +      +
    116C  ASP*     4.2     4.7    -      -       +      -
    117C  ILE*     1.3    75.5    -      -       -      +
    119C  GLU*     1.3    58.8    +      -       -      +
    120C  GLN*     4.3     0.4    +      -       +      -
    484C  LEU      5.2     3.1    -      -       -      +
    485C  ASP*     2.7    35.1    +      -       -      +
    486C  THR*     4.3     0.8    +      -       -      +
    487C  LEU      4.1    12.7    +      -       -      +
    488C  MET*     3.1    43.3    -      -       +      -
    489C  PRO*     4.7    10.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 119 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71C  VAL*     3.7    10.7    -      -       +      +
     99C  LYS*     3.5    25.5    +      -       -      +
    100C  LEU      3.1    31.2    +      -       -      +
    101C  ARG*     3.7    27.8    -      -       +      +
    117C  ILE*     4.1     4.3    +      -       +      +
    118C  LYS*     1.3    74.1    -      -       -      +
    120C  GLN*     1.3    67.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 120 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98C  VAL      3.7     1.0    -      -       -      +
     99C  LYS*     4.3     2.9    -      -       -      -
    100C  LEU*     2.9    34.0    +      -       -      +
    118C  LYS      5.8     0.4    -      -       -      -
    119C  GLU*     1.3    81.4    -      -       -      +
    121C  GLU*     1.3    63.1    +      -       -      +
    122C  VAL*     3.9     6.1    +      -       +      +
    488C  MET*     3.7    22.1    -      -       -      +
    489C  PRO*     3.6    27.4    -      -       +      +
    490C  GLN*     3.1    43.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 121 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73C  TYR      5.5     0.2    -      -       -      -
     74C  ARG*     2.7    37.0    +      -       -      +
     97C  ARG*     3.2    36.4    -      -       +      +
     98C  VAL      3.4    12.8    -      -       -      +
     99C  LYS*     4.1    28.9    -      -       +      +
    120C  GLN*     1.3    77.0    -      -       -      +
    122C  VAL*     1.3    64.1    +      -       -      +
    123C  TYR      4.3     0.3    +      -       -      -
    490C  GLN*     4.5     6.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 122 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  LEU      3.8     0.9    -      -       -      +
     97C  ARG*     3.5     3.0    -      -       -      -
     98C  VAL*     2.8    39.4    +      -       +      +
    100C  LEU*     5.2     4.5    -      -       +      -
    120C  GLN*     4.1    16.4    -      -       +      +
    121C  GLU*     1.3    76.8    -      -       -      +
    123C  TYR*     1.3    75.3    +      -       -      +
    124C  MET*     3.8     4.4    +      -       +      +
    489C  PRO*     4.8     3.6    -      -       +      -
    490C  GLN*     3.4    44.0    -      -       +      +
    493C  ILE*     4.2    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 123 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95C  PRO*     4.0    11.2    -      -       +      -
     96C  LEU      3.7    17.5    -      -       -      -
     97C  ARG*     4.4    16.9    -      -       +      +
    121C  GLU      4.3     0.6    +      -       -      -
    122C  VAL*     1.3    82.7    -      -       -      +
    124C  MET*     1.3    68.0    +      -       -      +
    125C  GLY*     3.3    33.6    -      -       -      -
    126C  GLU*     3.3    35.9    +      -       +      +
    490C  GLN*     5.4     0.8    +      -       -      -
    493C  ILE*     4.8     1.6    -      -       -      +
    495C  ALA*     4.1    15.9    -      -       +      +
    499C  SER*     5.7     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 124 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53C  PHE*     3.6    21.5    -      -       +      -
     57C  PHE*     5.8     4.9    -      -       +      -
     96C  LEU*     3.1    27.0    +      -       +      +
     98C  VAL*     3.3    37.7    -      -       +      -
    122C  VAL*     4.4     4.9    -      -       +      +
    123C  TYR*     1.3    78.0    -      -       -      +
    125C  GLY*     1.3    65.1    +      -       -      +
    464C  PHE*     4.9     1.3    -      -       +      -
    468C  LEU*     4.7     7.2    -      -       +      -
    471C  VAL*     6.3     0.4    -      -       -      -
    493C  ILE*     4.4    23.8    -      -       +      -
    495C  ALA*     3.6    19.3    -      -       -      -
    498C  ILE*     3.4    41.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 125 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  LEU*     2.9    33.0    +      -       -      +
    123C  TYR*     3.3    22.7    -      -       -      -
    124C  MET*     1.3    72.4    -      -       -      +
    126C  GLU*     1.3    61.7    +      -       -      -
    127C  ILE*     5.0     1.8    -      -       -      -
    495C  ALA*     3.8     4.5    -      -       -      +
    498C  ILE*     5.3     1.6    -      -       -      -
    499C  SER*     4.3    25.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 126 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79C  VAL*     5.2     9.1    +      -       -      +
     93C  SER*     2.5    43.0    +      -       -      +
     94C  ALA      3.2     7.4    -      -       -      +
     95C  PRO*     3.5    33.4    -      -       +      +
    123C  TYR*     3.3    20.5    +      -       +      +
    125C  GLY*     1.3    72.9    -      -       -      -
    127C  ILE*     1.3    62.2    +      -       -      +
    128C  PRO*     3.6     8.1    -      -       -      +
    499C  SER*     5.1     8.1    +      -       -      -
    502C  VAL*     5.1     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 127 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  PHE*     5.1     0.2    -      -       +      -
     38C  PHE*     4.2    18.6    -      -       +      -
     39C  ILE*     4.1    19.7    -      -       +      -
     49C  LEU*     4.5    11.0    -      -       +      -
     75C  LEU*     3.6    32.5    -      -       +      -
     93C  SER*     3.6     1.6    -      -       -      -
     94C  ALA      2.9    30.0    +      -       -      +
     96C  LEU*     4.4    28.5    -      -       +      -
    125C  GLY      4.7     1.6    -      -       -      +
    126C  GLU*     1.3    75.4    -      -       -      +
    128C  PRO*     1.3    72.7    -      -       +      +
    129C  LEU*     3.9     5.4    -      -       +      +
    464C  PHE*     5.6     6.5    -      -       +      -
    502C  VAL*     5.1     9.6    -      -       +      -
    506C  PHE*     6.3     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 128 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  PHE*     3.4    20.1    -      -       -      -
     91C  THR*     4.3     8.3    -      -       +      -
     92C  TYR      3.3    12.8    -      -       -      +
     93C  SER*     3.8     3.1    -      -       -      -
    126C  GLU      3.6     8.1    -      -       -      +
    127C  ILE*     1.3    87.9    -      -       +      +
    129C  LEU*     1.3    60.6    +      -       -      +
    136C  PHE*     3.8    13.7    -      -       +      -
    138C  ILE*     3.9    24.0    -      -       +      -
    502C  VAL*     4.0    18.2    -      -       +      -
    503C  LYS*     6.1     2.2    -      -       -      -
    506C  PHE*     4.0    27.8    -      -       +      -
----------------------------------------------------------
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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