Contacts of the strand formed by residues 88 - 97 (chain C) in PDB entry 2N0A


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 88 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  SER      3.2     3.1    +      -       -      +
     88B  ILE*     3.4    33.7    -      -       +      -
     89B  ALA*     3.0    20.3    +      -       -      +
     90B  ALA      4.9     2.2    -      -       -      +
     91B  ALA*     4.0    19.3    -      -       +      -
     94B  PHE*     4.1     7.2    -      -       +      -
     82C  VAL*     5.4     1.7    -      -       -      +
     86C  GLY      3.9     9.6    -      -       -      +
     87C  SER*     1.3    84.5    +      -       -      +
     89C  ALA*     1.3    58.0    +      -       -      +
     91C  ALA*     4.2     9.2    -      -       +      -
     94C  PHE*     4.0    31.9    -      -       +      -
     86D  GLY      6.0     0.2    -      -       -      +
     87D  SER*     5.8     0.2    -      -       -      -
     88D  ILE*     3.4    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 89 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89B  ALA*     3.4    10.9    -      -       -      +
     90B  ALA*     2.8    32.6    +      -       -      +
     79C  GLN*     3.4     9.5    +      -       -      +
     82C  VAL*     4.2    23.2    -      -       +      +
     88C  ILE*     1.3    71.7    -      -       -      +
     90C  ALA*     1.3    61.0    +      -       -      +
     79D  GLN*     3.1    28.3    -      -       -      +
     82D  VAL*     5.7     0.2    -      -       +      -
     87D  SER*     5.3     0.4    +      -       -      -
     88D  ILE      3.0     7.7    +      -       -      +
     89D  ALA*     3.4    11.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 90 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  ALA*     3.3     5.4    -      -       -      -
     77C  VAL*     4.0    18.4    -      -       +      -
     89C  ALA*     1.3    76.7    -      -       +      +
     91C  ALA*     1.3    61.0    +      -       -      +
     92C  THR*     5.7     1.8    -      -       +      -
     77D  VAL*     3.8    30.3    -      -       +      -
     79D  GLN*     4.7     1.6    -      -       -      +
     88D  ILE*     4.9     1.3    -      -       -      +
     89D  ALA      2.8    25.3    +      -       -      +
     90D  ALA*     4.5     1.3    -      -       -      -
     91D  ALA*     3.1    18.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 91 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  ALA      3.1     7.9    +      -       -      +
     91B  ALA*     3.3     4.3    -      -       -      +
     92B  THR*     3.1    23.7    +      -       -      +
     88C  ILE*     4.2    18.8    -      -       +      -
     90C  ALA*     1.3    74.8    -      -       -      +
     92C  THR*     1.3    63.6    +      -       -      +
     93C  GLY      3.5     1.6    +      -       -      -
     94C  PHE*     4.3    13.1    +      -       +      -
     88D  ILE*     4.0    24.0    -      -       +      -
     91D  ALA*     3.3    10.5    -      -       +      +
     94D  PHE*     5.0     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 92 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  THR*     3.2    13.5    -      -       +      +
     69C  ALA      5.9     0.2    -      -       -      -
     71C  VAL*     3.5    15.7    -      -       +      +
     75C  THR*     4.7    17.0    -      -       +      +
     90C  ALA*     5.7     1.6    -      -       +      -
     91C  ALA*     1.3    71.5    -      -       -      +
     93C  GLY*     1.3    60.2    +      -       -      +
     71D  VAL*     3.0    25.7    -      -       +      +
     75D  THR*     4.1    31.9    -      -       +      +
     91D  ALA      3.1     9.4    +      -       -      +
     92D  THR*     3.2     6.1    -      -       +      -
     93D  GLY*     2.7    28.1    +      -       -      -
     94D  PHE      4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 93 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  ALA      5.2     0.4    -      -       -      -
     92B  THR*     2.7    24.6    +      -       -      -
     93B  GLY*     3.8     1.3    -      -       -      -
     69C  ALA*     3.6    25.8    -      -       -      +
     71C  VAL*     3.4     8.0    -      -       -      +
     91C  ALA      3.5     2.2    +      -       -      -
     92C  THR*     1.3    70.5    -      -       -      +
     94C  PHE*     1.3    58.4    +      -       -      +
     93D  GLY*     3.7     1.5    -      -       -      -
     94D  PHE*     2.8    34.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 94 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  ALA*     5.0     3.6    -      -       +      -
     92B  THR      4.0     0.2    +      -       -      -
     93B  GLY      2.8    23.1    +      -       -      +
     94B  PHE*     3.3    44.4    -      +       +      -
     95B  VAL*     3.1    18.9    +      -       -      +
     69C  ALA*     4.2     0.9    -      -       -      +
     88C  ILE*     4.0    25.1    -      -       +      -
     91C  ALA*     4.3     7.2    -      -       +      -
     93C  GLY*     1.3    73.1    -      -       -      +
     95C  VAL*     1.3    64.5    +      -       -      +
     96C  LYS*     4.2    27.1    -      -       +      -
     88D  ILE*     4.1    15.5    -      -       +      -
     94D  PHE*     3.3    49.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  GLY*     3.9    14.8    -      -       -      -
     95B  VAL*     3.3    27.8    -      -       +      +
     97B  LYS*     6.3     1.3    -      -       +      -
     68C  GLY*     3.6    23.6    -      -       -      +
     69C  ALA*     3.8     6.1    -      -       +      +
     94C  PHE*     1.3    79.1    -      -       -      +
     96C  LYS*     1.3    63.3    +      -       -      +
     97C  LYS*     4.6    22.7    -      -       +      -
     94D  PHE*     3.1     6.6    +      -       -      +
     95D  VAL*     3.3    29.6    -      -       +      +
     96D  LYS      3.1    22.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  VAL      3.1     7.5    +      -       -      +
     96B  LYS*     3.4    27.1    -      -       +      +
     97B  LYS*     3.0    24.1    +      -       -      +
     94C  PHE*     4.2    22.1    -      -       +      -
     95C  VAL*     1.3    74.5    -      -       -      +
     97C  LYS*     1.3    64.6    +      -       -      +
     98C  ASP      3.7    19.5    +      -       -      +
     99C  GLN*     2.8    38.8    +      -       -      +
     96D  LYS*     3.4    39.8    -      -       +      +
     98D  ASP*     5.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 97 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  GLY*     5.5     4.2    -      -       -      -
     68B  GLY*     5.5     3.4    -      -       -      +
     97B  LYS*     3.9    33.9    -      -       +      +
     67C  GLY*     4.6    16.2    +      -       -      -
     68C  GLY*     6.2     0.4    -      -       -      -
     95C  VAL*     4.6    18.8    -      -       +      -
     96C  LYS*     1.3    72.8    -      -       -      +
     98C  ASP*     1.3    79.0    +      -       -      +
     96D  LYS      3.0    10.4    +      -       -      +
     97D  LYS*     4.5    20.7    -      -       +      +
     98D  ASP      3.1    17.8    +      -       -      -
     99D  GLN*     3.2    25.6    +      -       -      +
----------------------------------------------------------
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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