Contacts of the strand formed by residues 16 - 22 (chain C) in PDB entry 2I6A


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 LEU 16 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14C  ASN*     3.0    13.0    +      -       +      +
     15C  PRO*     1.3    86.4    -      -       -      +
     17C  LEU*     1.3    56.5    +      -       -      +
     18C  ASP      4.0     0.2    -      -       -      -
     63C  GLY*     2.6    37.8    +      -       -      +
     64C  GLY*     4.0     9.0    -      -       -      +
     99C  LEU*     3.5     9.5    -      -       -      +
    121C  GLY*     3.6    23.1    -      -       -      +
    122C  THR      4.0     6.5    -      -       -      +
    123C  CYS*     4.4     5.2    -      -       +      +
    136C  ALA*     3.9    16.2    -      -       +      -
    138C  LEU*     3.8    25.8    -      -       +      +
    141C  ALA*     3.6    21.8    -      -       +      -
    500C  5I5      3.9    31.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 17 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  LEU*     1.3    71.9    -      -       -      +
     18C  ASP*     1.3    68.7    -      -       -      +
     19C  ILE*     3.5     1.8    +      -       +      +
     60C  TYR*     4.6    13.9    -      -       +      -
     61C  HIS*     3.5    29.2    -      -       -      +
     62C  ALA*     3.8     7.4    -      -       -      +
     95C  PHE*     3.0    59.7    -      -       +      -
     98C  ILE*     4.3    19.3    -      -       +      -
     99C  LEU*     4.0    11.8    -      -       +      +
    120C  THR*     5.0     0.7    -      -       +      -
    121C  GLY      3.1    14.4    +      -       -      +
    122C  THR*     3.3    12.4    -      -       +      +
    123C  CYS      3.0    20.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 18 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  LEU*     4.8     0.2    -      -       -      +
     17C  LEU*     1.3    72.5    -      -       -      +
     19C  ILE*     1.3    61.5    +      -       -      +
     20C  SER*     3.9     2.9    +      -       -      +
     59C  GLU      3.4     0.3    -      -       -      +
     60C  TYR*     3.2    10.0    -      -       -      +
     61C  HIS*     2.6    40.0    +      -       -      +
     63C  GLY*     3.6     5.7    -      -       -      -
    123C  CYS*     3.5    16.3    -      -       -      +
    125C  ALA*     5.7     2.5    -      -       +      -
    332C  ARG*     2.5    46.3    +      -       -      +
    500C  5I5      2.9    39.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 19 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17C  LEU*     3.9     4.9    -      -       +      +
     18C  ASP*     1.3    75.4    -      -       -      +
     20C  SER*     1.3    58.8    +      -       -      +
     49C  PHE*     4.7    12.6    -      -       +      +
     52C  LEU*     3.7    21.0    -      -       +      +
     53C  VAL*     4.3    13.2    -      -       +      -
     58C  VAL*     3.1    24.2    -      -       +      -
     59C  GLU      3.3     4.5    -      -       -      -
     60C  TYR*     3.8    23.3    -      -       +      -
     95C  PHE*     4.8     4.9    -      -       +      -
    122C  THR*     3.4    37.7    -      -       +      +
    123C  CYS      2.9     8.6    +      -       -      +
    124C  ALA*     3.2     4.7    -      -       -      +
    125C  ALA*     2.8    24.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 20 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18C  ASP      5.1     0.5    -      -       -      -
     19C  ILE*     1.3    74.1    -      -       -      +
     21C  ALA*     1.3    61.5    +      -       -      +
     52C  LEU*     5.3     0.9    -      -       -      -
     57C  LYS      4.0     0.3    -      -       -      +
     58C  VAL*     3.1     4.1    -      -       -      +
     59C  GLU*     2.7    48.4    +      -       -      +
     61C  HIS*     4.3     5.7    -      -       -      -
    125C  ALA*     3.4    29.4    -      -       -      -
    127C  ILE*     3.8     9.9    -      -       -      -
    132C  ARG*     4.7     4.8    +      -       -      -
    332C  ARG*     4.3    14.6    +      -       -      -
    334C  THR*     5.4     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 21 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20C  SER*     1.3    78.6    -      -       -      +
     22C  VAL*     1.3    62.7    +      -       -      +
     23C  VAL*     3.6     4.5    +      -       -      +
     52C  LEU*     3.9    23.2    -      -       +      +
     56C  PHE*     4.0    12.6    -      -       +      -
     57C  LYS      3.4    22.2    -      -       -      +
     58C  VAL*     3.8     8.3    -      -       +      -
    125C  ALA      3.3     4.5    +      -       -      +
    126C  CYS*     4.0     0.3    -      -       -      -
    127C  ILE*     3.1    27.9    +      -       -      +
    334C  THR*     6.0     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 22 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21C  ALA*     1.3    75.1    -      -       -      +
     23C  VAL*     1.3    74.8    +      -       -      +
     56C  PHE*     3.4    17.7    -      -       -      +
     57C  LYS      4.7     1.8    +      -       -      -
    127C  ILE*     3.3    28.5    -      -       +      +
    128C  THR*     5.0     2.9    -      -       -      -
    129C  GLY      5.4     2.7    -      -       -      +
    334C  THR*     4.5    22.9    -      -       +      +
----------------------------------------------------------
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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